The Sup35 domains required for maintenance of weak, strong or undifferentiated yeast [PSI+] prions

The Sup35 protein can exist in a non-infectious form or in various infectious forms called [PSI+] prion variants (or prion strains). Each of the different [PSI+] prion variants converts non-infectious Sup35 molecules into that prion variant's infectious form. One definition of a 'prion domain' is the minimal fragment of a prion protein that is necessary and sufficient to maintain the prion form. We now demonstrate that the Sup35 N region (residues 1-123), which is frequently referred to as the 'prion domain', is insufficient to maintain the weak or strong [PSI+] variants per se, but appears to maintain them in an 'undifferentiated' [PSI+] state that can differentiate into weak or strong [PSI+] variants when transferred to the full-length Sup35 protein. In contrast, Sup35 residues 1-137 are necessary and sufficient to faithfully maintain weak or strong [PSI+] variants. This implicates Sup35 residues 124-137 in the variant-specific maintenance of the weak or strong [PSI+] forms. Structure predictions indicate that the residues in the 124-137 region form an alpha-helix and that the 1-123 region may have beta structure. In view of these findings, we discuss a plausible molecular basis for the [PSI+] prion variants as well as the inherent difficulties in defining a 'prion domain'.     

URE3] and [PSI] are prions of yeast and evidence for new fungal prions

[URE3] and [PSI] are two non-Mendelian genetic elements discovered over 25 years ago and never assigned to a nucleic acid replicon. Their genetic properties led us to propose that they are prions, altered self-propagating forms of Ure2p and Sup35p, respectively, that cannot properly carry out the normal functions of these proteins. Ure2p is partially protease-resistant in [URE3] strains and Sup35p is aggregated specifically in [PSI] strains supporting this idea. Overexpression of Hsp104 cures [PSI], as does the absence of this protein, suggesting that the prion change of Sup35p in [PSI] strains is aggregation. Strains of [PSI], analogous to those described for scrapie, have now been described as well as an in vitro system for [PSI] propagation. Recently, two new potential prions have been described, one in yeast and the other in the filamentous fungus, Podospora.     

Sequestration of essential proteins causes prion associated toxicity in yeast

Prions are infectious, aggregated proteins that cause diseases in mammals but are not normally toxic in fungi. Excess Sup35p, an essential yeast protein that can exist as the [ PSI ⁺] prion, inhibits growth of [ PSI ⁺] but not [ psi ^-] cells. This toxicity is rescued by expressing the Sup35Cp domain of Sup35p, which is sufficient for cell viability but not prion propagation. We now show that rescue requires Sup35Cp levels to be proportional to Sup35p overexpression. Overexpression of Sup35p appeared to cause pre-existing [ PSI ⁺] aggregates to coalesce into larger aggregates, but these were not toxic per se because they formed even when Sup35Cp rescued growth. Overexpression of Sup45p, but not other tested essential Sup35p binding partners, caused rescue. Sup45–GFPp formed puncta that colocalized with large [ PSI ⁺] Sup35-RFPp aggregates in cells overexpressing Sup35p, and the frequency of the Sup45–GFPp puncta was reduced by rescuing levels of Sup35Cp. In contrast, [ PSI ⁺] toxicity caused by a high excess of the Sup35p prion domain (Sup35NMp) was rescued by a single copy of Sup35Cp, was not rescued by Sup45p overexpression and was not associated with the appearance of Sup45–GFPp puncta. This suggests [ PSI ⁺] toxicity caused by excess Sup35p verses Sup35NMp is, respectively, through sequestration/inactivation of Sup45p verses Sup35p.     

Molecular interactions between photosystem I and ferredoxin: an integrated energy frustration and experimental model

The stromal domain (PsaC, PsaD, and PsaE) of photosystem I (PSI) reduces transiently bound ferredoxin (Fd) or flavodoxin. Experimental structures exist for all of these protein partners individually, but no experimental structure of the PSI/Fd or PSI/flavodoxin complexes is presently available. Molecular models of Fd docked onto the stromal domain of the cyanobacterial PSI site are constructed here utilizing X‐ray and NMR structures of PSI and Fd, respectively. Predictions of potential protein‐protein interaction regions are based on experimental site‐directed mutagenesis and cross‐linking studies to guide rigid body docking calculations of Fd into PSI, complemented by energy landscape theory to bring together regions of high energetic frustration on each of the interacting proteins. The results identify two regions of high localized frustration on the surface of Fd that contain negatively charged Asp and Glu residues. This study predicts that these regions interact predominantly with regions of high localized frustration on the PsaC, PsaD, and PsaE chains of PSI, which include several residues predicted by previous experimental studies. Copyright © 2014 John Wiley & Sons, Ltd.     

Structural characterization of a plant photosystem I and NAD(P)H dehydrogenase supercomplex

Cyclic electron transport (CET) around photosystem I (PSI) plays an important role in balancing the ATP/NADPH ratio and the photoprotection of plants. The NAD(P)H dehydrogenase complex (NDH) has a key function in one of the CET pathways. Current knowledge indicates that, in order to fulfill its role in CET, the NDH complex needs to be associated with PSI; however, until now there has been no direct structural information about such a supercomplex. Here we present structural data obtained for a plant PSI–NDH supercomplex. Electron microscopy analysis revealed that in this supercomplex two copies of PSI are attached to one NDH complex. A constructed pseudo‐atomic model indicates asymmetric binding of two PSI complexes to NDH and suggests that the low‐abundant Lhca5 and Lhca6 subunits mediate the binding of one of the PSI complexes to NDH. On the basis of our structural data, we propose a model of electron transport in the PSI–NDH supercomplex in which the association of PSI to NDH seems to be important for efficient trapping of reduced ferredoxin by NDH.     

The yeast non-Mendelian factor [ETA+] is a variant of [PSI+], a prion-like form of release factor eRF3

The yeast non-Mendelian factor [ETA+] is lethal in the presence of certain mutations in the SUP35 and SUP45 genes, which code for the translational release factors eRF3 and eRF1, respectively. One such mutation, sup35-2, is now shown to contain a UAG stop codon prior to the essential region of the gene. The non-Mendelian inheritance of [ETA+] is reminiscent of the yeast [PSI+] element, which is due to a self-propagating conformation of Sup35p. Here we show that [ETA+] and [PSI+] share many characteristics. Indeed, like [PSI+], the maintenance of [ETA+] requires the N-terminal region of Sup35p and depends on an appropriate level of the chaperone protein Hsp104. Moreover, [ETA+] can be induced de novo by excess Sup35p, and [ETA+] cells have a weak nonsense suppressor phenotype characteristic of weak [PSI+]. We conclude that [ETA+] is actually a weak, unstable variant of [PSI+]. We find that although some Sup35p aggregates in [ETA+] cells, more Sup35p remains soluble in [ETA+] cells than in isogenic strong [PSI+] cells. Our data suggest that the amount of soluble Sup35p determines the strength of translational nonsense suppression associated with different [PSI+] variants.     

The stable assembly of newly synthesized PsaE into the photosystem I complex occurring via the exchange mechanism is facilitated by electrostatic interactions

Photosystem I (PSI) is a photochemically active membrane protein complex that functions at the reducing site of the photosynthetic electron-transfer chain as plastocyanin-ferredoxin oxidoreductase. PsaE, a peripheral subunit of the PSI complex, plays an important role in the function of PSI. PsaE is involved in the docking of ferredoxin/flavodoxin to the PSI complex and also participates in the cyclic electron transfer around PSI. The molecular characterization of the assembly of newly synthesized PsaE in the thylakoid membranes or in isolated PSI complexes is the subject of the present study. For this purpose the Mastigocladus laminosus psaE gene was cloned and overexpressed in Escherichia coli, and the resulting PsaE protein was purified to homogeneity by affinity chromatography. The purified PsaE was then introduced into thylakoids isolated from M. laminosus, and the newly introduced PsaE subunit saturates the membrane. The solubilization and separation of the different thylakoid protein complexes indicated that PsaE accumulates specifically in its functional location, the PSI complex. A similar stable assembly was detected when PsaE was introduced into purified PSI complexes, i.e., in the absence of other thylakoid components. This strongly indicates that the information for the stable assembly of PsaE into PSI lies within the polypeptide itself and within other subunits of the PSI complex that interact with it. To determine the nature of these interactions, the assembly reaction was performed in conditions affecting the ionic/osmotic strength. We found that altering the ionic strength significantly affects the capability of PsaE to assemble into isolated thylakoids or PSI complexes, strongly supporting the fact that electrostatic interactions are formed between PsaE and other PSI subunits. Moreover, the data suggest that the formation of electrostatic interactions occurs concomitantly with an exchange step in which newly introduced PsaE replaces the subunit present in situ.     

Multiple Gln/Asn-rich prion domains confer susceptibility to induction of the yeast [PSI(+)] prion

The yeast prion [PSI(+)] results from self-propagating aggregates of Sup35p. De novo formation of [PSI(+)] requires an additional non-Mendelian trait, thought to result from a prion form of one or more unknown proteins. We find that the Gln/Asn-rich prion domains of two proteins, New1p and Rnq1p, can control susceptibility to [PSI(+)] induction as well as enhance aggregation of a human glutamine expansion disease protein. [PSI(+)] inducibility results from gain-of-function properties of New1p and Rnq1p aggregates rather than from inactivation of the normal proteins. These studies suggest a molecular basis for the epigenetic control of [PSI(+)] inducibility and may reveal a broader role for this phenomenon in the physiology of protein aggregation.     

Oxidizing side of the cyanobacterial photosystem I. Evidence for interaction between the electron donor proteins and a luminal surface helix of the PsaB subunit.

Photosystem I (PSI) interacts with plastocyanin or cytochrome c6 on the luminal side. To identify sites of interaction between plastocyanin/cytochrome c6 and the PSI core, site-directed mutations were generated in the luminal J loop of the PsaB protein from Synechocystis sp. PCC 6803. The eight mutant strains differed in their photoautotrophic growth. Western blotting with subunit-specific antibodies indicated that the mutations affected the PSI level in the thylakoid membranes. PSI proteins could not be detected in the S600R/G601C/N602I, N609K/S610C/T611I, and M614I/G615C/W616A mutant membranes. The other mutant strains contained different levels of PSI proteins. Among the mutant strains that contained PSI proteins, the H595C/L596I, Q627H/L628C/I629S, and N638C/N639S mutants showed similar levels of PSI-mediated electron transfer activity when either cytochrome c6 or an artificial electron donor was used. In contrast, cytochrome c6 could not function as an electron donor to the W622C/A623R mutant, even though the PSI activity mediated by an artificial electron donor was detected in this mutant. Thus, the W622C/A623R mutation affected the interaction of the PSI complex with cytochrome c6. Biotin-maleimide modification of the mutant PSI complexes indicated that His-595, Trp-622, Leu-628, Tyr-632, and Asn-638 in wild-type PsaB may be exposed on the surface of the PSI complex. The results presented here demonstrate the role of an extramembrane loop of a PSI core protein in the interaction with soluble electron donor proteins.     

Yeast prion protein derivative defective in aggregate shearing and production of new 'seeds'.

According to the nucleated polymerization model, in vivo prion proliferation occurs via dissociation (shearing) of the huge prion polymers into smaller oligomeric 'seeds', initiating new rounds of prion replication. Here, we identify the deletion derivative of yeast prion protein Sup35 (Sup35-Delta22/69) that is specifically defective in aggregate shearing and 'seed' production. This derivative, [PSI+], previously thought to be unable to turn into a prion state, in fact retains the ability to form a prion ([PSI+](Delta22/69)) that can be maintained in selective conditions and transmitted by cytoplasmic infection (cytoduction), but which is mitotically unstable in non-selective conditions. MorePSI+](Delta22/69) retains its mitotic stability defect. The [PSI+](Delta22/69) cells contain more Sup35 protein in the insoluble fraction and form larger Sup35 aggregates compared with the conventional [PSI+] cells. Moderate excess of Hsp104 disaggregase increases transmission of the [PSI+](Delta22/69) prion, while excess Hsp70-Ssa chaperone antagonizes it, opposite to their effects on conventional [PSI+]. Our results shed light on the mechanisms determining the differences between transmissible prions and non-transmissible protein aggregates.     

Effect of glycerol and PVA on the conformation of photosystem I

Single-molecule spectroscopy at cryogenic temperatures was used to examine the impact of buffer solution, glycerol/buffer mixtures (25% and 66%), and poly(vinyl alcohol) (PVA) films on the conformation of photosystem I (PSI) from Thermosynechoccocus elongatus. PSI holds a number of chromophores embedded at different places within the protein complex that show distinguishable fluorescence at low temperatures. The fluorescence emission from individual complexes shows inter- and intracomplex heterogeneity depending on the solution wherein PSI was dissolved. Statistical evaluation of spectra of a large number of complexes shows that the fluorescence emission of some of these chromophores can be used as sensors for their local nanoenvironment and some as probe for the conformation of the whole protein complex. Preparation in glycerol/buffer mixtures yields a high homogeneity for all chromophores, indicating a more compact protein conformation with less structural variability. In buffer solution a distinct heterogeneity of the chromophores is observed. PSI complexes in PVA show highly heterogeneous spectra as well as a remarkable blue shift of the fluorescence emission, indicating a destabilization of the protein complex. Photosystem I prepared in PVA cannot be considered fully functional, and conclusions drawn from experiments with PSI in PVA films are of questionable value.     

Protein phosphorylation and Mg2+ influence light harvesting and electron transport in chloroplast thylakoid membrane material containing only the chlorophyll-a/b-binding light-harvesting complex of photosystem II and photosystem I.

A material containing only photosystem I (PSI) and the chlorophyll-a/b-binding light-harvesting complex of PSII (LHC-II) has been isolated from the chloroplast thylakoid membrane by solubilization with Triton X-100. Fluorescence spectroscopy shows that, within the material, LHC-II is coupled to PSI for excitation-energy transfer and that this coupling is decreased by the presence of Mg2+, which also decreased PSI electron transport specifically at limiting light intensity. Inclusion of phosphorylated LHC-II within the material did not alter its structure, but gave decreased energy transfer to PSI and inhibition of electron transport which was independent of light intensity, implying effects of phosphorylation on both light harvesting and directly on electron transport. Inclusion of Mg2+ within the phosphorylated material gave decreased energy transfer, but slightly increased PSI electron transport. A cation-induced direct promotion of PSI electron transport was also observed in isolated PSI particles. The PSI/LHC-II material represents a model system for examining protein interactions during light-state adaptations and the possibility that LHC-II can contribute to the antenna of PSI in light state 2 in vivo is discussed.     

A previously found thylakoid membrane protein of 14kDa (TMP14) is a novel subunit of plant photosystem I and is designated PSI-P

We show that the thylakoid membrane phosphoprotein TMP14 is a novel subunit of plant photosystem I (PSI). Blue native/SDS-PAGE and sucrose gradient fractionation demonstrated the association of the protein exclusively with PSI. We designate the protein PSI-P. The presence of PSI-P subunit in Arabidopsis mutants lacking other PSI subunits was analyzed and suggested a location in the proximity of PSI-L, -H and -O subunits. The PSI-P protein was not differentially phosphorylated in state 1 and state 2.     

Lhca5 interaction with plant photosystem I

In the outer antenna (LHCI) of higher plant photosystem I (PSI) four abundantly expressed light-harvesting protein of photosystem I (Lhca)-type proteins are organized in two heterodimeric domains (Lhca1/Lhca4 and Lhca2/Lhca3). Our cross-linking studies on PSI-LHCI preparations from wildtype Arabidopsis and pea plants indicate an exclusive interaction of the rarely expressed Lhca5 light-harvesting protein with LHCI in the Lhca2/Lhca3-site. In PSI particles with an altered LHCI composition Lhca5 assembles in the Lhca1/Lhca4 site, partly as a homodimer. This flexibility indicates a binding-competitive model for the LHCI assembly in plants regulated by molecular interactions of the Lhca proteins with the PSI core.     

Analysis of photosynthetic complexes from a cyanobacterial ycf37 mutant

The Ycf37 protein has been suggested to be involved in the biogenesis and/or stability of the cyanobacterial photosystem I (PSI). With Ycf37 specific antibodies, we analyzed the localization of Ycf37 within the thylakoid membranes of the cyanobacterium Synechocystis sp. PCC 6803. Inspection of a sucrose gradient profile indicated that small amounts of Ycf37 co-fractionated with monomeric photosynthetic complexes, but not with trimeric PSI. Isolating 3xFLAG epitope-tagged Ycf37 by affinity-tag purification rendered several PSI subunits that specifically co-precipitated with this protein. Blue-native PAGE newly revealed two monomeric PSI complexes (PSI and PSI*) in wild-type thylakoids. The lower amount of PsaK present in PSI* may explain its higher electrophoretic mobility. PSI* was more prominent in high-light grown cells and interestingly proved absent in the Deltaycf37 mutant. PSI* appeared again when the mutant was complemented in trans with the wild-type ycf37 gene. In the Deltaycf37 mutant the amount of trimeric PSI complexes was reduced to about 70% of the wild-type level with no significant changes in photochemical activity and subunit composition of the remaining photosystems. Our results indicate that Ycf37 plays a specific role in the preservation of PSI* and the biogenesis of PSI trimers.     

Effect of light quality on chloroplast-membrane organization and function in pea

The effect of light quality during plant growth of chloroplast membrane organization and function in peas (Pisum sativum L. cv. Alaska) was investigated. In plants grown under photosystem (PS) I-enriched (far-red enriched) illumination both the PSII/PSI stoichiometry and the electrontransport capacity ratios were high, about 1.9. In plants grown under PSII-enriched (far-red depleted) illumination both the PSII/PSI stoichiometry and the electron-transport capacity ratios were significantly lower, about 1.3. In agreement, steady-state electron-transport measurements under synchronous illumination of PSII and PSI demonstrated an excess of PSII in plants grown under far-red-enriched light. Sodium dodecylsulfate polyacrylamide gel electrophoretic analysis of chlorophyll-containing complexes showed greater relative amounts of the PSII reaction center chlorophyll-protein complex in plants grown under farred-enriched light. Additional changes were observed in the ratio of light-harvesting chlorophyll a/b protein to PSII reaction center chlorophyll-protein under the two different light-quality regimes. The results demonstrate the dynamic nature of chloroplast structure and support the notion that light quality is an important factor in the regulation of chloroplast membrane organization and-function.Abbreviations and symbols Chl chlorophyll - CPa PSII reaction center chlorophyll protein complex - CPI PSI chlorophyll protein complex - FR-D light depleted in far-red sensitizing primarily PSII - FR-E light enriched in far-red sensitizing primarily PSI - LHCP PSII light-harvesting chlorophyll a/b protein complex - P ₇₀₀ primary electron donor of PSI - PSI, PSII photosystems I and II, respectively - Q primary electron acceptor of PSII     

Proteomic analysis of the photosystem I light-harvesting antenna in tomato (Lycopersicon esculentum)

Until now, more genes of the light-harvesting antenna of higher-plant photosystem I (PSI) than proteins have been described. To improve our understanding of the composition of light-harvesting complex I (LHCI) of tomato (Lycopersicon esculentum), we combined one- and two-dimensional (1-D and 2-D, respectively) gel electrophoresis with immunoblotting and tandem mass spectrometry (MS/MS). Separation of PSI with high-resolution 1-D gels allowed separation of five bands attributed to proteins of LHCI. Immunoblotting with monospecific antibodies and MS/MS analysis enabled the correct assignment of the four prominent bands to light-harvesting proteins Lhca1-4. The fifth band was recognized by only the Lhca1 antibody. Immunodetection as well as mass spectrometric analysis revealed that these protein bands contain not only the eponymous protein but also other Lhca proteins, indicating a heterogeneous protein composition of Lhca bands. Additionally, highly sensitive MS/MS allowed detection of a second Lhca4 isoform and of Lhca5. These proteins had not been described before on the protein level in higher plants. Two-dimensional gel electrophoresis revealed an even more diverse composition of individual Lhca proteins than was apparent from 1-D gels. For each of the four prominent Lhca proteins, four to five isoforms with different isoelectric points could be identified. In the case of Lhca1, Lhca4, and Lhca3, additional isoforms with slightly differing molecular masses were identified. Thus, we were able to detect four to ten isoforms of each individual Lhca protein in PSI. Reasons for the origin of Lhca heterogeneity are discussed. The observed variety of Lhca proteins and their isoforms is of particular interest in the context of the recently published crystal structure of photosystem I from pea, which showed the presence of only four Lhca proteins per photosystem I. These findings indicate that several populations of photosystem I that differ in their Lhca composition may exist.     

Identification and characterization of a stable intermediate in photosystem I assembly in tobacco

Photosystem I (PSI) is the most efficient bioenergetic nanomachine in nature and one of the largest membrane protein complexes known. It is composed of 18 protein subunits that bind more than 200 co‐factors and prosthetic groups. While the structure and function of PSI have been studied in great detail, very little is known about the PSI assembly process. In this work, we have characterized a PSI assembly intermediate in tobacco plants, which we named PSI*. We found PSI* to contain only a specific subset of the core subunits of PSI. PSI* is particularly abundant in young leaves where active thylakoid biogenesis takes place. Moreover, PSI* was found to overaccumulate in PsaF‐deficient mutant plants, and we show that re‐initiation of PsaF synthesis promotes the maturation of PSI* into PSI. The attachment of antenna proteins to PSI also requires the transition from PSI* to mature PSI. Our data could provide a biochemical entry point into the challenging investigation of PSI biogenesis and allow us to improve the model for the assembly pathway of PSI in thylakoid membranes of vascular plants.