The PSI formal document process and its implementation on the PSI website

The Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI) has recently developed formal document processes for reviewing MIAPE documents, specifications, community practice and informational documents. These document workflows rely on community participation as well as more traditional expert review. We here present the web interface used to support these document processes, and explain briefly how interested parties can participate in the review process. The HUPO-PSI website can be found at http://www.psidev.info.     

Insights into function of PSI domains from structure of the Met receptor PSI domain

PSI domains are cysteine-rich modules found in extracellular fragments of hundreds of signaling proteins, including plexins, semaphorins, integrins, and attractins. Here, we report the solution structure of the PSI domain from the human Met receptor, a receptor tyrosine kinase critical for proliferation, motility, and differentiation. The structure represents a cysteine knot with short regions of secondary structure including a three-stranded antiparallel beta-sheet and two alpha-helices. All eight cysteines are involved in disulfide bonds with the pattern consistent with that for the PSI domain from Sema4D. Comparison with the Sema4D structure identifies a structurally conserved core comprising the N-terminal half of the PSI domain. Interestingly, this part links adjacent SEMA and immunoglobulin domains in the Sema4D structure, suggesting that the PSI domain serves as a wedge between propeller and immunoglobulin domains and is responsible for the correct positioning of the ligand-binding site of the receptor.     

Physiology of PSI cyclic electron transport in higher plants

Having long been debated, it is only in the last few years that a concensus has emerged that the cyclic flow of electrons around Photosystem I plays an important and general role in the photosynthesis of higher plants. Two major pathways of cyclic flow have been identified, involving either a complex termed NDH or mediated via a pathway involving a protein PGR5 and two functions have been described-to generate ATP and to provide a pH gradient inducing non-photochemical quenching. The best evidence for the occurrence of the two pathways comes from measurements under stress conditions-high light, drought and extreme temperatures. In this review, the possible relative functions and importance of the two pathways is discussed as well as evidence as to how the flow through these pathways is regulated. Our growing knowledge of the proteins involved in cyclic electron flow will, in the future, enable us to understand better the occurrence and diversity of cyclic electron transport pathways. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.     

[PSI+] turns 50

abstract

The year 2015 sees the fiftieth anniversary of the publication of a research paper that underpins much of our understanding of fungal prion biology, namely “ψ, a cytoplasmic suppressor of super-suppressor in yeast” by Brian Cox. Here we show how our understanding of the molecular nature of the [PSI⁺] determinant evolved from an ‘occult’ determinant to a transmissible amyloid form of a translation termination factor. We also consider the impact studies on [PSI] have had – and continue to have - on prion research. To demonstrate this, leading investigators in the yeast prion field who have made extensive use of the [PSI⁺] trait in their research, provide their own commentaries on the discovery and significance of [PSI].     

Responsibility of phosphatidylglycerol for biogenesis of the PSI complex

Phosphatidylglycerol (PG) ubiquitous in thylakoid membranes of photosynthetic organisms was previously shown to contribute to accumulation of chlorophyll through analysis of the cdsA⁻ mutant of a cyanobacterium Synechocystis sp. PCC6803 defective in PG synthesis (SNC1). Here, we characterized effects of manipulation of the PG content in thylakoid membranes of Synechocystis sp. PCC6803 on the photosystem complexes to specify roles of PG in biogenesis of thylakoid membranes. SNC1 cells with PG deprivation in vivo, together with the chlorophyll decrease, exhibited a decline not in PSII, but in PSI, at the complex level as well as the subunit levels. On the other hand, the decrease in the PSI complex was accounted for by a remarkable decrease in the PSI trimer with an increase in the monomer. These symptoms of SNC1 cells were complemented in vivo by supplementation of PG. Besides, a reduction in the PG content of thylakoid membranes isolated from the wild type in vitro on treatment with phospholipase A2 (PLA2), similar to the PG-deprivation in SNC1 in vivo, brought about a decrease in the trimer population of PSI with accumulation of the monomer. These results demonstrated that PG contributes to the synthesis and/or stability of the PSI complex for maintenance of the cellular content of chlorophyll, and also to construction of the PSI trimer from the monomer at least through stabilization of the trimerized conformation.     

Protein-protein and protein-function relationships in Arabidopsis photosystem I: cluster analysis of PSI polypeptide levels and photosynthetic parameters in PSI mutants

In flowering plants, photosystem I (PSI) mediates electron transport across the thylakoid membrane and contains at least 14 proteins. The availability of co-suppression and/or mutant lines deficient for individual PSI polypeptides in Arabidopsis thaliana allows one to assign functions to PSI subunits. We have performed cluster analysis on an extensive set of data on PSI polypeptide levels in ten different PSI mutants. This type of analysis serves to group proteins that exhibit similar changes in amount in different genotypes, and also identifies genotypes which show similar PSI compositions. The interdependence of levels of PSI-C, -D and -E, of -H and -L, and of Lhca2 and 3, which was previously proposed based on the study of single genotypes or on cross-linking experiments, was confirmed by our analyses. In addition, the levels of the lumenal subunits F and N are found to be interdependent. The incorporation of photosynthetic parameters into the cluster analysis revealed that the level of photosynthetic state transitions correlates with the abundance of PSI-H in all 8 genotypes tested, supporting the hypothesis that PSI-H serves as a docking site for LHCII during state transitions.     

PSI: indexing protein structures for fast similarity search

MOTIVATION: We consider the problem of finding similarities in protein structure databases. Current techniques sequentially compare the given query protein to all of the proteins in the database to find similarities. Therefore, the cost of similarity queries increases linearly as the volume of the protein databases increase. As the sizes of experimentally determined and theoretically estimated protein structure databases grow, there is a need for scalable searching techniques. RESULTS: Our techniques extract feature vectors on triplets of SSEs (Secondary Structure Elements). Later, these feature vectors are indexed using a multidimensional index structure. For a given query protein, this index structure is used to quickly prune away unpromising proteins in the database. The remaining proteins are then aligned using a popular alignment tool such as VAST. We also develop a novel statistical model to estimate the goodness of a match using the SSEs. Experimental results show that our techniques improve the pruning time of VAST 3 to 3.5 times while maintaining similar sensitivity.     

Structure-based view on [PSI+] prion properties

ABSTRACT

Yeast [PSI⁺] prion is one of the most suitable and well characterized system for the investigation of the prion phenomenon. However, until recently, the lack of data on the 3D arrangement of Sup35p prion fibrils hindered progress in this area. The recent arrival in this field of new experimental techniques led to the parallel and in-register superpleated β-structure as a consensus model for Sup35p fibrils. Here, we analyzed the effect of amino acid substitutions of the Sup35 protein through the prism of this structural model. Application of a newly developed computational approach, called ArchCandy, gives us a better understanding of the effect caused by mutations on the fibril forming potential of Sup35 protein. This bioinformatics tool can be used for the design of new mutations with desired modification of prion properties. Thus, we provide examples of how today, having progress toward elucidation of the structural arrangement of Sup35p fibrils, researchers can advance more efficiently to a better understanding of prion [PSI⁺] stability and propagation.     

Excitonic interactions in wild-type and mutant PSI reaction centers

Femtosecond excitation of the red edge of the chlorophyll a Q(Y) transition band in photosystem I (PSI), with light of wavelength > or = 700 nm, leads to wide transient (subpicosecond) absorbance changes: positive DeltaA between 635 and 665 nm, and four negative DeltaA bands at 667, 675, 683, and 695 nm. Here we compare the transient absorbance changes after excitation at 700, 705, and 710 nm at 20 K in several PSI preparations of Chlamydomonas reinhardtii where amino acid ligands of the primary donor, primary acceptor, or connecting chlorophylls have been mutated. Most of these mutations influence the spectrum of the absorbance changes. This supports the view that the chlorophylls of the electron transfer chain as well as the connecting chlorophylls are engaged in the observed absorbance changes. The wide absorption spectrum of the electron transfer chain revealed by the transient measurements may contribute to the high efficiency of energy trapping in photosystem 1. Exciton calculations, based on the recent PSI structure, allow an assignment of the DeltaA bands to particular chlorophylls: the bands at 675 and 695 nm to the dimers of primary acceptor and accessory chlorophyll and the band at 683 nm to the connecting chlorophylls. The subpicosecond transient absorption bands decay may reflect rapid charge separation in the PSI reaction center.     

Effects of proteasome inhibitor PSI on neoplastic and non-transformed cell lines

In this study we compared the sensitivity of different human and murine cell lines varying in the stage of transformation to dose- and time-dependent cytostatic and/or cytotoxic effects of PSI (a selective proteasome inhibitor), measured by a standard MTT assay. It was found that intensively proliferating cell lines were more sensitive to very small doses of PSI after 24 h incubation than the slow proliferating ones. Non-transformed cell lines showed no sensitivity to PSI, as there was no difference in cell viability in comparison with the control group even after 72 h incubation.     

Reprint of: physiology of PSI cyclic electron transport in higher plants

Having long been debated, it is only in the last few years that a concensus has emerged that the cyclic flow of electrons around Photosystem I plays an important and general role in the photosynthesis of higher plants. Two major pathways of cyclic flow have been identified, involving either a complex termed NDH or mediated via a pathway involving a protein PGR5 and two functions have been described-to generate ATP and to provide a pH gradient inducing non-photochemical quenching. The best evidence for the occurrence of the two pathways comes from measurements under stress conditions-high light, drought and extreme temperatures. In this review, the possible relative functions and importance of the two pathways is discussed as well as evidence as to how the flow through these pathways is regulated. Our growing knowledge of the proteins involved in cyclic electron flow will, in the future, enable us to understand better the occurrence and diversity of cyclic electron transport pathways. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.     

The Possible Mechanism of Photoinhibition of Purified PSI Complexes

The protecting effect of histidine on the photodamage of pigments and proteins of the isolated PSⅠ particles from the chloroplast of Spinacia oleracea L. during the strong illumination (2 300 μmol·m-2·s-1) was studied by spectroscopy and SDS-PAGE. The absorbance of PSⅠ particles decreased during the strong illumination treatment, but the decrease would be slowed down in the presence of externally added histidine after 30 min illumination. The decrease of CD （circular dichroism）signal intensities of PSⅠ particles also was slowed down by the added histidine after about 10 min illumination. The retarded protecting effect of the added histidine on the photobleaching of pigments of PSⅠ complexes implied that the mechanisms of photoinhibition of isolated PSⅠ complexes are different from early stage to later stage during the strong illumination treatment. In addition, the added histidine suppressed the decrease of 77 K fluorescence yield of PSⅠ particles during the illumination. SDS-PAGE showed that the added histidine not only protected the reaction center proteins of PSⅠ particles, but also protected other subunits of PSⅠ particles from degradation.     

Variant-specific [PSI+] infection is transmitted by Sup35 polymers within [PSI+] aggregates with heterogeneous protein composition

The [PSI(+)] prion is the aggregated self-propagating form of the Sup35 protein from the yeast Saccharomyces cerevisiae. Aggregates of Sup35 in [PSI(+)] cells exist in different heritable conformations, called "variants," and they are composed of detergent-resistant Sup35 polymers, which may be closely associated with themselves, other proteins, or both. Here, we report that disassembly of the aggregates into individual Sup35 polymers and non-Sup35 components increases their infectivity while retaining their variant specificity, showing that variant-specific [PSI(+)] infection can be transmitted by Sup35 polymers alone. Morphological analysis revealed that Sup35 isolated from [PSI(+)] yeast has the appearance of short barrels, and bundles, which seem to be composed of barrels. We show that the major components of two different variants of [PSI(+)] are interacting infectious Sup35 polymers and Ssa1/2. Using a candidate approach, we detected Hsp104, Ssb1/2, Sis1, Sse1, Ydj1, and Sla2 among minor components of the aggregates. We demonstrate that Ssa1/2 efficiently binds to the prion domain of Sup35 in [PSI(+)] cells, but that it interacts poorly with the nonaggregated Sup35 found in [psi(-)] cells. Hsp104, Sis1, and Sse1 interact preferentially with the prion versus nonprion form of Sup35, whereas Sla2 and Ssb1/2 interact with both forms of Sup35 with similar efficiency.     

The evolution of the evolvability properties of the yeast prion [PSI+

Abstract.— Saccharomyces cerevisiae's ability to form the prion [PSI⁺] may increase the rate of evolvability, defined as the rate of appearance of heritable and potentially adaptive phenotypic variants. The increase in evolvability occurs when the appearance of the prion causes read-through translation and reveals hidden variation in untranslated regions. Eventually the portion of the phenotypic variation that is adaptive loses its dependence on the revealing mechanism. The mechanism is reversible, so the restoration of normal translation termination conceals the revealed deleterious variation, leaving the yeast without a permanent handicap. Given that the ability to form [PSI⁺] is known to be fixed and conserved in yeast, we construct a mathematical model to calculate whether this ability is more likely to have become fixed due to chance alone or due to its evolvability characteristics. We find that evolvability is a more likely explanation, as long as environmental change makes partial read-through of stop codons adaptive at a frequency of at least once every million years.     

Differential expression inArabidopsis ofLhca2, a PSI cab gene

A cDNA clone of the geneLhca2 encoding a photosystem I (PSI) type II chlorophylla/b-binding protein was isolated fromArabidopsis thaliana. The isolation of this, the fourth PSI cab gene fromArabidopsis, confirms a previous report [1] that indicatedArabidopsis may contain all four PSI cab genes identified in other plant species.Lhca2 is a single-copy gene as are the other knownArabidopsis PSI cab genes. The patterns of developmental expression and tissue-specific regulation ofLhca2 are similar to those of other PSI and PSII cab genes, but the light induction pattern and the steady-state mRNA level ofLhca2 are distinct. This suggests that a different mechanism may be employed to regulate the expression ofLhca2.