The yeast Saccharomyces cerevisiae is, arguably, the best understood eukaryotic model organism, yet comparatively little is known about its membrane proteome. Here, we report the cloning and expression of 617 S. cerevisiae membrane proteins as fusions to a C-terminal topology reporter and present experimentally constrained topology models for 546 proteins. By homology, the experimental topology information can be extended to Ϸ15,000 membrane proteins from 38 fully sequenced eukaryotic genomes.membrane proteins ͉ membrane proteomics ͉ yeast S ubsequent to the determination of the Saccharomyces cerevisiae genome sequence (1), a wide variety of genomics and proteomics studies have been carried out, and there is now ample information available on, e.g., gene expression under different conditions (2, 3), gene dispensability (4, 5), protein expression profiles (6), organellar proteomes (7), global protein localization patterns (8, 9), and protein-protein interaction networks (10, 11).However, the yeast integral membrane proteins are generally underrepresented in the proteomics studies and are even less well represented in the Protein Data Bank (12). In the absence of high-resolution structural data, good topology models provide a necessary background to all structure-function studies of membrane proteins, but, also here, S. cerevisiae lags far behind (13).There is currently no experimental method that makes it possible to derive full-topology models in a high-throughput mode, and one generally has been forced to resort to sequencebased prediction methods to study membrane protein topology on a proteome-wide scale. We have shown that much improved topology models can be achieved by a combination of large-scale experimental mapping of the location of the C terminus of membrane proteins and topology prediction constrained by this information (14). In a first application of this approach, we recently presented experimentally constrained topology models for 601 Escherichia coli inner membrane proteins (15) and were able to extend this information to Ͼ50,000 bacterial proteins by sequence homology (16).As a first step toward the exploration of the S. cerevisiae membrane proteome, we now report the construction and experimental analysis of a clone collection of Ͼ600 predicted membrane proteins. Based on the experimental data, we assign the location of the C termini and produce constrained topology models for 546 polytopic membrane proteins and for Ϸ15,000 homologous membrane proteins from other eukaryotes. We find that topologies with both the N and C termini of the protein in the cytosol (N in -C in ) predominate and that the overall distribution of membrane protein topologies is surprisingly similar between S. cerevisiae and E. coli. ResultsThe most direct way to characterize the S. cerevisiae membrane proteome is by constructing strain collections in which each strain expresses a suitably tagged membrane protein. The choice of tag and expression strategy (expression from endogenous promoters on the chromosome or from a pl...

TIM23-mediated insertion of transmembrane α-helices into the mitochondrial inner membraneThis comprehensive analysis of the sequence determinants for TIM23-mediated insertion of mitochondrial inner membrane proteins reveals strikingly different requirements for protein insertion into the mitochondrial inner membrane and the endoplasmic reticulum.

The text mining function in Rayyan successfully helped reviewers identify relevant studies early in the screening process.

Background: There has been no in vivo assay to determine mitochondrial membrane protein sorting. Results: The Mgm1 fusion approach provides a versatile experimental tool for determining the mitochondrial sorting pathways in vivo. Conclusion: Sorting of mitochondrial inner membrane proteins carrying moderately hydrophobic transmembrane segments are modulated, depending on the cellular environment. Significance: Mitochondrial membrane protein sorting may be a dynamic process.

Large-scale protein overexpression phenotype screens provide an important complement to the more common gene knockout screens. Here, we have targeted the so far poorly understood Saccharomyces cerevisiae membrane proteome and report growth phenotypes for a strain collection overexpressing Ϸ600 C-terminally tagged integral membrane proteins grown both under normal and three different stress conditions. Although overexpression of most membrane proteins reduce the growth rate in synthetic defined medium, we identify a large number of proteins that, when overexpressed, confer specific resistance to various stress conditions. Our data suggest that regulation of glycosylphosphatidylinositol anchor biosynthesis and the Na ؉ ͞K ؉ homeostasis system constitute major downstream targets of the yeast PKA͞RAS pathway and point to a possible connection between the early secretory pathway and the cells' response to oxidative stress. We also have quantified the expression levels for >550 membrane proteins, facilitating the choice of well expressing proteins for future functional and structural studies.caffeine ͉ paraquat ͉ salt tolerance ͉ yeast

Anaerobic xylulose fermentation was compared in strains of Zygosaccharomyces and Saccharomyces cerevisiae, mutants and wild-type strains to identify host-strain background and genetic modifications beneficial to xylose fermentation. Overexpression of the gene (XKS1) for the pentose phosphate pathway (PPP) enzyme xylulokinase (XK) increased the ethanol yield by almost 85% and resulted in ethanol yields [0.61 C-mmol (C-mmol consumed xylulose)(-1)] that were close to the theoretical yield [0.67 C-mmol (C-mmol consumed xylulose)(-1)]. Likewise, deletion of gluconate 6-phosphate dehydrogenase (gnd1delta) in the PPP and deletion of trehalose 6-phosphate synthase (tps1delta) together with trehalose 6-phosphate phosphatase (tps2delta) increased the ethanol yield by 30% and 20%, respectively. Strains deleted in the promoter of the phosphoglucose isomerase gene (PGI1) - resulting in reduced enzyme activities - increased the ethanol yield by 15%. Deletion of ribulose 5-phosphate (rpe1delta) in the PPP abolished ethanol formation completely. Among non-transformed and parental strains S. cerevisiae ENY. WA-1A exhibited the highest ethanol yield, 0.47 C-mmol (C-mmol consumed xylulose)(-1). Other non-transformed strains produced mainly arabinitol or xylitol from xylulose under anaerobic conditions. Contrary to previous reports S. cerevisiae T23D and CBS 8066 were not isogenic with respect to pentose metabolism. Whereas, CBS 8066 has been reported to have a high ethanol yield on xylulose, 0.46 C-mmol (C-mmol consumed xylulose)(-1) (Yu et al. 1995), T23D only formed ethanol with a yield of 0.24 C-mmol (C-mmol consumed xylulose)(-1). Strains producing arabinitol did not produce xylitol and vice versa. However, overexpression of XKS1 shifted polyol formation from xylitol to arabinitol.

Background Systematic reviews often conclude low confidence in the results due to heterogeneity in the reported outcomes. A Core Outcome Set (COS) is an agreed standardised collection of outcomes for a specific area of health. The outcomes included in a COS are to be measured and summarized in clinical trials as well as systematic reviews to counteract this heterogeneity. Aim The aim is to identify, compile and assess final and ongoing studies that are prioritizing outcomes in the area of pregnancy and childbirth. Methods All studies which prioritized outcomes related to pregnancy and childbirth using consensus method, including Delphi surveys or consensus meetings were included. Searches were conducted in Ovid MEDLINE, EMBASE, PsycINFO, Academic Search Elite, CINAHL, SocINDEX and COMET databases up to June 2021. For all studies fulfilling the inclusion criteria, information regarding outcomes as well as population, method, and setting was extracted. In addition, reporting in the finalized studies was assessed using a modified version of the Core Outcome Set–STAndards for Reporting. Results In total, 27 finalized studies and 42 ongoing studies were assessed as relevant and were included. In the finalized studies, the number of outcomes included in the COS ranged from 6 to 51 with a median of 13 outcomes. The majority of the identified COS, both finalized as well as ongoing, were relating to physical complications during pregnancy. Conclusion There is a growing number of Core Outcome Set studies related to pregnancy and childbirth. Although several of the finalized studies follow the proposed reporting, there are still some items that are not always clearly reported. Additionally, several of the identified COS contained a large number (n > 20) outcomes, something that possibly could hinder implementation. Therefore, there is a need to consider the number of outcomes which may be included in a COS to render it optimal for future research.

In conclusion, there is a need for well-conducted clinical research in the fields of oral and maxillofacial surgery.