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.     

[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].     

Protein-only inheritance in yeast: something to get [PSI+]-ched about

Recent work suggests that two unrelated phenotypes, [PSI+] and [URE3], in the yeast Saccharomyces cerevisiae are transmitted by non-covalent changes in the physical states of their protein determinants, Sup35p and Ure2p, rather than by changes in the genes that encode these proteins. The mechanism by which alternative protein states are self-propagating is the key to understanding how proteins function as elements of epigenetic inheritance. Here, we focus on recent molecular-genetic analysis of the inheritance of the [PSI+] factor of S. cerevisiae. Insights into this process might be extendable to a group of mammalian diseases (the amyloidoses), which are also believed to be a manifestation of self-perpetuating changes in protein conformation.     

Low PSI content limits the photoprotection of PSI and PSII in early growth stages of chlorophyll b-deficient wheat mutant lines

Photosynthesis Research - In vivo analyses of electron and proton transport-related processes as well as photoprotective responses were carried out at different stages of growth in chlorophyll b...     

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 PSI semantic validator: A framework to check MIAPE compliance of proteomics data

The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio‐ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at http://psidev.info/validator .     

The NatA Acetyltransferase Couples Sup35 Prion Complexes to the [PSI+] Phenotype

Protein-only (prion) epigenetic elements confer unique phenotypes by adopting alternate conformations that specify new traits. Given the conformational flexibility of prion proteins, protein-only inheritance requires efficient self-replication of the underlying conformation. To explore the cellular regulation of conformational self-replication and its phenotypic effects, we analyzed genetic interactions between [PSI⁺], a prion form of the S. cerevisiae Sup35 protein (Sup35^[PSI+]), and the three N^α-acetyltransferases, NatA, NatB, and NatC, which collectively modify ~50% of yeast proteins. Although prion propagation proceeds normally in the absence of NatB or NatC, the [PSI⁺] phenotype is reversed in strains lacking NatA. Despite this change in phenotype, [PSI⁺] NatA mutants continue to propagate heritable Sup35^[PSI+]. This uncoupling of protein state and phenotype does not arise through a decrease in the number or activity of prion templates (propagons) or through an increase in soluble Sup35. Rather, NatA null strains are specifically impaired in establishing the translation termination defect that normally accompanies Sup35 incorporation into prion complexes. The NatA effect cannot be explained by the modification of known components of the [PSI⁺] prion cycle including Sup35; thus, novel acetylated cellular factors must act to establish and maintain the tight link between Sup35^[PSI+] complexes and their phenotypic effects.     

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.     

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.     

A role for cytosolic hsp70 in yeast [PSI(+)] prion propagation and [PSI(+)] as a cellular stress

[PSI(+)] is a prion (infectious protein) of Sup35p, a subunit of the Saccharomyces cerevisiae translation termination factor. We isolated a dominant allele, SSA1-21, of a gene encoding an Hsp70 chaperone that impairs [PSI(+)] mitotic stability and weakens allosuppression caused by [PSI(+)]. While [PSI(+)] stability is normal in strains lacking SSA1, SSA2, or both, SSA1-21 strains with a deletion of SSA2 cannot propagate [PSI(+)]. SSA1-21 [PSI(+)] strains are hypersensitive to curing of [PSI(+)] by guanidine-hydrochloride and partially cured of [PSI(+)] by rapid induction of the heat-shock response but not by growth at 37 degrees. The number of inheritable [PSI(+)] particles is significantly reduced in SSA1-21 cells. SSA1-21 effects on [PSI(+)] appear to be independent of Hsp104, another stress-inducible protein chaperone known to be involved in [PSI(+)] propagation. We propose that cytosolic Hsp70 is important for the formation of Sup35p polymers characteristic of [PSI(+)] from preexisting material and that Ssa1-21p both lacks and interferes with this activity. We further demonstrate that the negative effect of heat stress on [PSI(+)] phenotype directly correlates with solubility of Sup35p and find that in wild-type strains the presence of [PSI(+)] causes a stress that elevates basal expression of Hsp104 and SSA1.     

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.