MIPS: a database for protein sequences, homology data and yeast genome information

Abstract

The MIPS group (Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, collects, processes and distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence Database (,). MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. The database is distributed on CD-ROM together with PATCHX, an exhaustive supplement of unique, unverified protein sequences from external sources compiled by MIPS. Through its WWW server (http://www.mips.biochem.mpg.de/ ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the FASTA database for all proteins from PIR-International and PATCHX. The database is dynamically maintained and permits instant access to FASTA results. (ii) Starting with FASTA database queries, proteins have been classified into families and superfamilies (PROT-FAM). (iii) The HPT (hashed position tree) data structure () developed at MIPS is a new approach for rapid sequence and pattern searching. (iv) MIPS provides access to the sequence and annotation of the complete yeast genome (), the functional classification of yeast genes (FunCat) and its graphical display, the 'Genome Browser' (). A CD-ROM based on the JAVA programming language providing dynamic interactive access to the yeast genome and the related protein sequences has been compiled and is available on request.

Applicability of Tandem Affinity Purification MudPIT to Pathway Proteomics in Yeast

“…Annotation was added from SGD annotation tables (table release time (20,21), the General Repository for Interaction Datasets (GRID; release 1.0) (22), and the Yeast Protein Database (YPD; as of 06/09/03) (23). Based on known interaction annotation and the frequency of appearance in a reference dataset containing one representative experiment for every tagged open reading frame in this study (n ϭ 22), the data were then sorted into three tables: previously reported interactors retrieved in the experiment, potential new interacting proteins detected, and likely contaminants (see supplemental material).…”

Synthetic lethal interactions with conditional poly(A) polymerase alleles identify LCP5, a gene involved in 18S rRNA maturation

“…To identify further components of the pre-mRNA 39-end processing machinery, a screen for synthetic lethal mutations with the poly(A) polymerase temperaturesensitive allele pap1-7 was carried out (Fig+ 1A)+ Mutant strains that did not grow in the absence of the wild-type PAP1 gene were identified on plates containing 5-fluoroorotic acid [5-FOA; Figs+ 1B,C]+ We obtained 26 temperature-sensitive mutants+ For five of them, tetrad analysis demonstrated a genetic linkage between the temperature-and 5-FOA-sensitive phenotypes+ These mutations, termed lcp1 to lcp5, are not linked to the plasmid-borne pap1-7 allele and define five complementation groups (results not shown)+ lcp mutations were isolated by several outcrosses with the W303 wild-type strain (see Table 1)+ Extracts were prepared from each of the mutant strains and tested for pre-mRNA 39-end processing in vitro according to standard procedures (Minvielle-Sebastia et al+, 1994)+ We found that extracts from all five mutants processed a 32 P-labeled pre-mRNA substrate to an extent comparable to a wild-type extract, even at elevated temperature (Fig+ 2A; data not shown)+ These results suggested that the mutated genes were not coding for subunits of essential factors involved in mRNA 39-end formation+ Below, we describe the characterization of LCP5+ Wildtype LCP5 was cloned by complementation of the temperature-sensitive phenotype of its corresponding mutant+ Open reading frame YER127w (Mewes et al+, 1997) was sufficient to render the cells temperatureresistant+ The gene has been previously characterized by systematic Ty insertional analysis on chromosome V+ Ty insertion in YER127w resulted in severe growth defects on rich medium (Smith et al+, 1996)+ The protein has also been found to interact with Ngg1p in a two-hybrid screen (Martens et al+, 1996)+ Ngg1p acts as a transcriptional coactivator/repressor and is involved in acetylation of nucleosomal histones+ However, to the best of our knowledge no function has been assigned to YER127w so far+ LCP5 is a single copy gene+ It codes for a protein of 357 amino acids and has a calculated molecular mass of 40+8 kD+ The predicted polypeptide has a high content of charged residues (33% D ϩ E ϩ K ϩ R)+ Computational analysis detected a putative nuclear lo-FIGURE 1. Schematic representation of the synthetic lethal screen with pap1-7+ A: The starting strain, containing the PAP1 disruption, the wild-type PAP1 allele and the pap1-7 allele+ B: Genotype after UV mutagenesis in the presence of the wild-type PAP1 gene+ C: Resulting genotype after counterselection for the wild-type PAP1 gene on 5-FOA plates+ ϩ: interaction supporting cell viability+ Ϫ: aberrant interaction that fails to support cell viability+ LCP : wild-type allele before UV mutagenesis, lcp Ϫ : mutated allele after UV mutagenesis+ LEU2, ADE2, URA3: selectable marker genes+ calization signal (Dingwall & Laskey, 1991) and a potential coiled coil region (Fig+ 2B)+ The amino acid sequence of the protein shows similarities to a putative orthologue (accession No+ SWISS-PROT: Q09713) in Schizosaccharomyces pombe (26+3% identity), and to a CCAAT enhancer-binding-like protein of Caenorhabditis elegans (Wilson et al+, 1994)+…”

Comparison of Protein-Protein Interaction Confidence Assignment Schemes

“…Curated pair-wise interactions from the literature and membership in protein complexes from MIPS [23] were used as the gold standard positive set in each case. Randomly chosen protein pairs formed the gold standard negative data set.…”