Biomedical subjects

James Barber

Publications and source records attributed to James Barber.

At least 19 recordsLinked to original sources

PubMed2006

Subsequent events to GTP binding by the plant PsbO protein: structural changes, GTP hydrolysis and dissociation from the photosystem II complex.

Besides an essential role in optimizing water oxidation in photosystem II (PSII), it has been reported that the spinach PsbO protein binds GTP [C. Spetea, T. Hundal, B. Lundin, M. Heddad, I. Adamska, B. Andersson, Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 1409-1414]. Here we predict four GTP-binding domains in the structure of spinach PsbO, all localized in the beta-barrel domain of the protein, as judged from comparison with the 3D-structure of the cyanobacterial counterpart. These domains are not conserved in the sequences of the cyanobacterial or green algae PsbO proteins. MgGTP induces specific changes in the structure of the PsbO protein in solution, as detected by circular dichroism and intrinsic fluorescence spectroscopy. Spinach PsbO has a low intrinsic GTPase activity, which is enhanced fifteen-fold when the protein is associated with the PSII complex in its dimeric form. GTP stimulates the dissociation of PsbO from PSII under light conditions known to also release Mn(2+) and Ca(2+) ions from the oxygen-evolving complex and to induce degradation of the PSII reaction centre D1 protein. We propose the occurrence in higher plants of a PsbO-mediated GTPase activity associated with PSII, which has consequences for the function of the oxygen-evolving complex and D1 protein turnover.

Amino Acid Sequence↗

PubMed2006

Biochemical and structural analyses of a higher plant photosystem II supercomplex of a photosystem I-less mutant of barley. Consequences of a chronic over-reduction of the plastoquinone pool.

Photosystem II of higher plants is a multisubunit transmembrane complex composed of a core moiety and an extensive peripheral antenna system. The number of antenna polypeptides per core complex is modulated following environmental conditions in order to optimize photosynthetic performance. In this study, we used a barley (Hordeum vulgare) mutant, viridis zb63, which lacks photosystem I, to mimic extreme and chronic overexcitation of photosystem II. The mutation was shown to reduce the photosystem II antenna to a minimal size of about 100 chlorophylls per photosystem II reaction centre, which was not further reducible. The minimal photosystem II unit was analysed by biochemical methods and by electron microscopy, and found to consist of a dimeric photosystem II reaction centre core surrounded by monomeric Lhcb4 (chlorophyll protein 29), Lhcb5 (chlorophyll protein 26) and trimeric light-harvesting complex II antenna proteins. This minimal photosystem II unit forms arrays in vivo, possibly to increase the efficiency of energy distribution and provide photoprotection. In wild-type plants, an additional antenna protein, chlorophyll protein 24 (Lhcb6), which is not expressed in viridis zb63, is proposed to associate to this minimal unit and stabilize larger antenna systems when needed. The analysis of the mutant also revealed the presence of two distinct signalling pathways activated by excess light absorbed by photosystem II: one, dependent on the redox state of the electron transport chain, is involved in the regulation of antenna size, and the second, more directly linked to the level of photoinhibitory stress perceived by the cell, participates in regulating carotenoid biosynthesis.

Cryoelectron Microscopy↗

PubMed2006

Environmentally modulated phosphoproteome of photosynthetic membranes in the green alga Chlamydomonas reinhardtii.

Mapping of in vivo protein phosphorylation sites in photosynthetic membranes of the green alga Chlamydomonas reinhardtii revealed that the major environmentally dependent changes in phosphorylation are clustered at the interface between the photosystem II (PSII) core and its light-harvesting antennae (LHCII). The photosynthetic membranes that were isolated form the algal cells exposed to four distinct environmental conditions affecting photosynthesis: (i) dark aerobic, corresponding to photosynthetic State 1; (ii) dark under nitrogen atmosphere, corresponding to photosynthetic State 2; (iii) moderate light; and (iv) high light. The surface-exposed phosphorylated peptides were cleaved from the membrane by trypsin, methyl-esterified, enriched by immobilized metal affinity chromatography, and sequenced by nanospray-quadrupole time-of-flight mass spectrometry. A total of 19 in vivo phosphorylation sites were mapped in the proteins corresponding to 15 genes in C. reinhardtii. Amino-terminal acetylation of seven proteins was concomitantly determined. Sequenced amino termini of six mature LHCII proteins differed from the predicted ones. The State 1-to-State 2 transition induced phosphorylation of the PSII core components D2 and PsbR and quadruple phosphorylation of a minor LHCII antennae subunit, CP29, as well as phosphorylation of constituents of a major LHCII complex, Lhcbm1 and Lhcbm10. Exposure of the algal cells to either moderate or high light caused additional phosphorylation of the D1 and CP43 proteins of the PSII core. The high light treatment led to specific hyperphosphorylation of CP29 at seven distinct residues, phosphorylation of another minor LHCII constituent, CP26, at a single threonine, and double phosphorylation of additional subunits of a major LHCII complex including Lhcbm4, Lhcbm6, Lhcbm9, and Lhcbm11. Environmentally induced protein phosphorylation at the interface of PSII core and the associated antenna proteins, particularly multiple differential phosphorylations of CP29 linker protein, suggests the mechanisms for control of photosynthetic state transitions and for LHCII uncoupling from PSII under high light stress to allow thermal energy dissipation.

Algal Proteins↗

PubMed2006

Refinement of the structural model for the Photosystem II supercomplex of higher plants.

Recent X-ray structures determined for the Photosystem II (PSII) core complex isolated from cyanobacteria have provided important information for understanding the functionality of this photosynthetic enzyme including its water splitting activity. As yet, no high-resolution structure is available for PSII of plants or eukaryotes in general. However, crystal structures have been determined for some components of plant PSII which together with the cyanobacterial structure can be used to interpret lower resolution structures of plant PSII derived from electron cryomicroscopy (cryo-EM). Here, we utilise the published X-ray structures of a cyanobacterial PSII core, Light Harvesting Complex II (LHCII), PsbP and PsbQ proteins to construct a model of the plant LHCII-PSII supercomplex using a 17 A resolution 3D electron density map of the spinach supercomplex determined by cryo-EM and single particle analysis. In so doing, we tentatively identify the relative positioning of the chlorophylls within the supercomplex and consider energy transfer pathways between the different subunits. The modelling has also allowed density to be assigned to the three extrinsic proteins of plant PSII, PsbO, PsbP and PsbQ associated with the water splitting centre and concluded that although the position of PsbO is the same as in cyanobacteria, PsbP and PsbQ are located in different positions to the cyanobacterial extrinsic PsbU and PsbV proteins.

Chlorophyll↗

PubMed2006

Identification of a calcium-binding site in the PsbO protein of photosystem II.

Analysis of the anomalous X-diffraction data reported by Ferreira et al. (PDB entry 1S5L) for crystals of photosystem II isolated from Thermosynechococcus elongatus indicates that a calcium ion is bound to the PsbO protein. The Ca2+-binding site is located close to the lumenal exit of a putative proton channel leading from the water splitting site.

Binding Sites↗

PubMed2006

CP43-like chlorophyll binding proteins: structural and evolutionary implications.

CP43, encoded by the psbC gene, is a chlorophyll (Chl)-binding protein of Photosystem II (PSII), the water-splitting and oxygen-evolving enzyme of photosynthesis. CP47, encoded by psbB, a Chl-binding protein of PSII, is closely related to CP43. The Chl-binding six transmembrane helical unit typified by CP43, is also structurally related to the N-terminal domains of the PsaA and PsaB proteins of Photosystem I (PSI) as well as to the family of light-harvesting proteins encoded by cyanobacterial isiA genes and prochlorophyte pcb genes. Here we use recent structural information derived for PSII and PSI to review similarities and differences between the various members of the CP43-like class of light-harvesting proteins, exploring both functional and evolutionary implications.

Bacterial Proteins↗

PubMed2006

Light harvesting in photosystem I supercomplexes.

In photosynthetic membranes of cyanobacteria, algae, and higher plants, photosystem I (PSI) mediates light-driven transmembrane electron transfer from plastocyanin or cytochrome c6 to the ferredoxin-NADP complex. The oxidoreductase function of PSI is sensitized by a reversible photooxidation of primary electron donor P700, which launches a multistep electron transfer via a series of redox cofactors of the reaction center (RC). The excitation energy for the functioning of the primary electron donor in the RC is delivered via the chlorophyll core antenna in the complex with peripheral light-harvesting antennas. Supermolecular complexes of the PSI acquire remarkably different structural forms of the peripheral light-harvesting antenna complexes, including distinct pigment types and organizational principles. The PSI core antenna, being the main functional unit of the supercomplexes, provides an increased functional connectivity in the chlorophyll antenna network due to dense pigment packing resulting in a fast spread of the excitation among the neighbors. Functional connectivity within the network as well as the spectral overlap of antenna pigments allows equilibration of the excitation energy in the depth of the whole membrane within picoseconds and loss-free delivery of the excitation to primary donor P700 within 20-40 ps. Low-light-adapted cyanobacteria under iron-deficiency conditions extend this capacity via assembly of efficiently energy coupled rings of CP43-like complexes around the PSI trimers. In green algae and higher plants, less efficient energy coupling in the eukaryotic PSI-LHCI supercomplexes is probably a result of the structural adaptation of the Chl a/b binding LHCI peripheral antenna that not only extends the absorption cross section of the PSI core but participates in regulation of excitation flows between the two photosystems as well as in photoprotection.

Light-Harvesting Protein Complexes↗

PubMed2006

Ductal access for prevention and therapy of mammary tumors.

In cancer patients and in those at high risk, systemic exposure to agents for therapy or prevention is accompanied by undesirable side effects. We hypothesized that it is possible to prevent and treat breast cancer by introducing anticancer agents into the mammary ductal network. Here, we show the efficacy of intraductally administered anticancer agents 4-hydroxytamoxifen and pegylated liposomal doxorubicin (PLD) in the prevention and treatment of breast cancer using the rat N-methyl-N'-nitrosourea-induced and spontaneous HER-2/neu transgenic mouse (neu-N) models of breast cancer. Intraductal administration of PLD to neu-N mice caused regression of established tumors and prevented tumor development more effectively than i.v. injection (P < 0.0001). Intraductal administration resulted in lower circulating levels of PLD compared with i.v. administration, with no evidence of systemic toxicity or long-term histopathologic changes in the mammary gland. Compared with systemic administration, intraductal injection provides direct access to breast lesions with higher local and lower systemic drug exposure. These studies suggest that this approach has potential for application to prevention and neoadjuvant therapy of early breast cancer.

Animals↗

PubMed2005

The nature of the photosystem II reaction centre in the chlorophyll d-containing prokaryote, Acaryochloris marina.

Pigment-protein complexes enriched in photosystem II (PS II) have been isolated from the chlorophyll (Chl) d containing cyanobacterium, Acaryochloris marina. A small PS II-enriched particle, we call 'crude reaction centre', contained 20 Chl d, 0.5 Chl a and 1 redox active cytochrome b-559 per 2 pheophytin a, plus the D1 and D2 proteins. A larger PS II-enriched particle, we call 'core', additionally bound the antenna complexes, CP47 and CP43, and had a higher chlorophyll per pheophytin ratio. Pheophytin a could be photoreduced in the presence of a strong reductant, indicating that it is the primary electron acceptor in photosystem II of A. marina. A substoichiometric amount of Chl a (less than one chlorophyll a per 2 pheophytin a) strongly suggests that Chl a does not have an essential role in the photochemistry of PS II in this organism. We conclude that PS II, in A. marina, utilizes Chl d and not Chl a as primary electron donor and that the primary electron acceptor is one of two molecules of pheophytin a.

Chlorophyll↗

PubMed2005

Iron deficiency induces a chlorophyll d-binding Pcb antenna system around Photosystem I in Acaryochloris marina.

The prochlorophyte-like cyanobacterium Acaryochloris marina contains two pcb genes, pcbA and pcbC, which encode chlorophyll (Chl) d-binding antenna proteins PcbA and PcbC, respectively. Using real-time reverse transcriptase polymerase chain reaction (RT-PCR), it is shown that when Acaryochloris cells are grown in an iron-deficient medium, the transcription of the pcbC gene is up-regulated compared to that of pcbA. Biochemical and immunological analyses indicated that under the same iron-deficient conditions, the level of Photosystem I (PSI) decreased compared with that of Photosystem II (PSII). Electron microscopy revealed that concomitant with these changes was the formation of Pcb-PSI supercomplexes which, in their largest form, were composed of 18 Pcb subunits forming a ring around the trimeric PSI reaction centre core. Mass spectrometry indicated that the PcbC protein is the main constituent of this outer PSI antenna system. It is therefore concluded that in Acaryochloris, the PcbC protein forms an antenna for PSI when iron levels become limiting and in this way compensates for the drop in the level of PSI relative to PSII which occurs under these conditions.

Bacterial Proteins↗

PubMed2005

Structure of a large photosystem II supercomplex from Acaryochloris marina.

Acaryochloris marina is a prochlorophyte-like cyanobacterium containing both phycobilins and chlorophyll d as light harvesting pigments. We show that the chlorophyll d light harvesting system, composed of Pcb proteins, functionally associates with the photosystem II (PSII) reaction center (RC) core to form a giant supercomplex. This supercomplex has a molecular mass of about 2300 kDa and dimensions of 385 A x 240 A. It is composed of two PSII-RC core dimers arranged end-to-end, flanked by eight symmetrically related Pcb proteins on each side. Thus each PSII-RC monomer has four Pcb subunits acting as a light harvesting system which increases the absorption cross section of the PSII-RC core by almost 200%.

Cyanobacteria↗

PubMed2005

Spectral and kinetic analysis of the energy coupling in the PS I-LHC I supercomplex from the green alga Chlamydomonas reinhardtii at 77 K.

Energy transfer processes in the chlorophyll antenna of the PS I-LHCI supercomplexes from the green alga Chlamydomonas reinhardtii have been studied at 77 K using transient absorption spectroscopy with multicolor excitation in the 640-670 nm region. Comparison of the kinetic data obtained at low and room temperatures indicates that the slow approximately approximately 100 ps excitation equilibration phase that is characteristic of energy coupling of the LHCI peripheral antenna to the PS I core at physiological temperatures (Melkozernov AN, Kargul J, Lin S, Barber J and Blankenship RE (2004) J Phys Chem B 108: 10547-10555) is not observed in the excitation dynamics of the PS I-LHCI supercomplex at 77 K. This suggests that at low temperatures the peripheral antenna is energetically uncoupled from the PS I core antenna. Under these conditions the observed kinetic phases on the time scales from subpicoseconds to tens of picoseconds represent the superposition of the processes occurring independently in the PS I core antenna and the Chl a/b containing LHCI antenna. In the PS I-LHCI supercomplex with two uncoupled antennas the excitation is channeled to the excitation sinks formed at low temperature by clusters of red pigments. A better spectral resolution of the transient absorption spectra at 77 K results in detection of two DeltaA bands originating from the rise of photobleaching on the picosecond time scale of two clearly distinguished pools of low energy absorbing Chls in the PS I-LHCI supercomplex. The first pool of low energy pigments absorbing at 687 nm is likely to originate from the red pigments in the LHCI where the Lhca1 protein is most abundant. The second pool at 697 nm is suggested to result either from the structural interaction of the LHCI and the PS I core or from other Lhca proteins in the antenna. The kinetic data are discussed based on recent structural models of the PS I-LHCI. It is proposed that the uncoupling of pigment pools may be a control mechanism that regulates energy flow in Photosystem I.

Animals↗

PubMed2005

Effects of imatinib and interferon on primitive chronic myeloid leukaemia progenitors.

Imatinib has impressive activity against chronic myeloid leukaemia (CML), but does not appear to completely eradicate the disease. Although responses to interferon-alpha (IFN) are slower and less dramatic than those to imatinib, they can be durable even after discontinuation of the drug. Unlike imatinib, the specific mechanisms responsible for IFN's clinical activity in CML are unknown. We found that IFN induced a G1 cell cycle arrest, as well as terminal differentiation, of the CML cell line KT-1 and CML CD34+ cells from clinical specimens. Myeloid growth factors augmented the antileukaemic activity of IFN, and neutralising antibodies directed against myeloid growth factors inhibited IFN's antileukaemic activity. We next directly compared the effects of imatinib and IFN against differentiated and primitive CML progenitors from newly-diagnosed patients. Although less active against CML granulocyte-macrophage colony forming units than imatinib, IFN was significantly more toxic to primitive CML progenitors responsible for the maintenance of long-term cultures. Imatinib and IFN appear to have divergent effects on CML progenitors at different stages of maturation, with imatinib more active against differentiated CML progenitors and IFN more active against primitive CML progenitors. The different target cells for these agents may explain the disparities in the kinetics and durability of their clinical responses. At least part of the clinical effect of IFN in CML appears to result from its ability to differentiate primitive CML progenitors.

Adult↗

PubMed2005

Light-harvesting complex II protein CP29 binds to photosystem I of Chlamydomonas reinhardtii under State 2 conditions.

The State 1 to State 2 transition in the photosynthetic membranes of plants and green algae involves the functional coupling of phosphorylated light-harvesting complexes of photosystem II (LHCII) to photosystem I (PSI). We present evidence suggesting that in Chlamydomonas reinhardtii this coupling may be aided by a hyper-phosphorylated form of the LHCII-like CP29 protein (Lhcbm4). MS analysis of CP29 showed that Thr6, Thr16 and Thr32, and Ser102 are phosphorylated in State 2, whereas in State 1-exposed cells only phosphorylation of Thr6 and Thr32 could be detected. The LHCI-PSI supercomplex isolated from the alga in State 2 was found to contain strongly associated CP29 in phosphorylated form. Electron microscopy suggests that the binding site for this highly phosphorylated CP29 is close to the PsaH protein. It is therefore postulated that redox-dependent multiple phosphorylation of CP29 in green algae is an integral part of the State transition process in which the structural changes of CP29, induced by reversible phosphorylation, determine the affinity of LHCII for either of the two photosystems.

Animals↗

PubMed2004

The trimeric organisation of photosystem I is not necessary for the iron-stress induced CP43' protein to functionally associate with this reaction centre.

A mutant of Synechocystis PCC 6803 lacking the PsaL subunit of photosystem I (PSI) has been grown in iron-deficient media to induce the expression of the isiA gene, which encodes the chlorophyll a-binding protein CP43'. The purpose of this was to establish whether or not the formation of an 18-mer CP43'-PSI supercomplex reported for wild type Synechocystis cells [Nature 412 (2001) 743-745] was dependent on the trimeric conformation of the cyanobacterial PSI reaction centre. Structural characterisation by electron microscopy and single particle image analysis has revealed that the PsaL-mutant does not form trimers of PSI. However, despite this, CP43' was found to associate with the PSI monomer. The PSI monomer bound six or seven copies of CP43' along one edge of the PSI monomer and can be compared with one segment of the trimeric 18-mer CP43'-PSI supercomplex. We therefore conclude that the trimeric nature of cyanobacterial PSI is not required for the assembly of the CP43' antenna system under iron-deficient conditions.

Biopolymers↗

PubMed2004

Architecture of the photosynthetic oxygen-evolving center.

Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). We report the structure of PSII of the cyanobacterium Thermosynechococcus elongatus at 3.5 angstrom resolution. We have assigned most of the amino acid residues of this 650-kilodalton dimeric multisubunit complex and refined the structure to reveal its molecular architecture. Consequently, we are able to describe details of the binding sites for cofactors and propose a structure of the oxygen-evolving center (OEC). The data strongly suggest that the OEC contains a cubane-like Mn3CaO4 cluster linked to a fourth Mn by a mono-micro-oxo bridge. The details of the surrounding coordination sphere of the metal cluster and the implications for a possible oxygen-evolving mechanism are discussed.

Binding Sites↗

PubMed2004

Structure of photosystem II and molecular architecture of the oxygen-evolving centre.

Photosynthesis utilizes light energy to oxidize water molecules to molecular oxygen at the oxygen-evolving centre of photosystem II. The structure of photosystem II from the cyanobacterium Thermosynechococcus elongatus has been reported at 3.5A resolution and, for the first time, the complete molecular structure of this 650 kDa complex, including the oxygen-evolving centre, has been revealed.

Cyanobacteria↗

PubMed2004

Evolution of oxygenic photosynthesis: genome-wide analysis of the OEC extrinsic proteins.

The appearance of oxygenic photosynthesis was a key event in the evolution of our green biosphere. Oxygen in the atmosphere is generally believed to come from the biomolecular water-splitting reaction that occurs in oxyphotosynthetic organisms catalysed by the oxygen evolving centre (OEC) of Photosystem II. Using knowledge from complete genomes and current databases, we have investigated the nature and composition of the extrinsic proteins forming the OECs of different organisms, with particular focus on the manganese stabilizing protein that is present in all known oxyphototrophs. This analysis traces the evolution of the extrinsic proteins from ancient cyanobacteria to higher plants and gives hints about the ancestral form of the OEC.

Bacteria↗