Arabidopsis Thaliana Database Research Articles

Untargeted Metabolomics of Alternaria solani-Challenged Wild Tomato Species Solanum cheesmaniae Revealed Key Metabolite Biomarkers and Insight into Altered Metabolic Pathways.

Untargeted metabolomics of moderately resistant wild tomato species Solanum cheesmaniae revealed an altered metabolite profile in plant leaves in response to Alternaria solani pathogen. Leaf metabolites were significantly differentiated in non-stressed versus stressed plants. The samples were discriminated not only by the presence/absence of specific metabolites as distinguished markers of infection, but also on the basis of their relative abundance as important concluding factors. Annotation of metabolite features using the Arabidopsis thaliana (KEGG) database revealed 3371 compounds with KEGG identifiers belonging to biosynthetic pathways including secondary metabolites, cofactors, steroids, brassinosteroids, terpernoids, and fatty acids. Annotation using the Solanum lycopersicum database in PLANTCYC PMN revealed significantly upregulated (541) and downregulated (485) features distributed in metabolite classes that appeared to play a crucial role in defense, infection prevention, signaling, plant growth, and plant homeostasis to survive under stress conditions. The orthogonal partial least squares discriminant analysis (OPLS-DA), comprising a significant fold change (≥2.0) with VIP score (≥1.0), showed 34 upregulated biomarker metabolites including 5-phosphoribosylamine, kaur-16-en-18-oic acid, pantothenate, and O-acetyl-L-homoserine, along with 41 downregulated biomarkers. Downregulated metabolite biomarkers were mapped with pathways specifically known for plant defense, suggesting their prominent role in pathogen resistance. These results hold promise for identifying key biomarker metabolites that contribute to disease resistive metabolic traits/biosynthetic routes. This approach can assist in mQTL development for the stress breeding program in tomato against pathogen interactions.

Ovule Transcriptome Analysis Discloses Deregulation of Genes and Pathways in Sexual and Apomictic Limonium Species (Plumbaginaceae).

The genus Limonium Mill. (sea lavenders) includes species with sexual and apomixis reproductive strategies, although the genes involved in these processes are unknown. To explore the mechanisms beyond these reproduction modes, transcriptome profiling of sexual, male sterile, and facultative apomictic species was carried out using ovules from different developmental stages. In total, 15,166 unigenes were found to be differentially expressed with apomictic vs. sexual reproduction, of which 4275 were uniquely annotated using an Arabidopsis thaliana database, with different regulations according to each stage and/or species compared. Gene ontology (GO) enrichment analysis indicated that genes related to tubulin, actin, the ubiquitin degradation process, reactive oxygen species scavenging, hormone signaling such as the ethylene signaling pathway and gibberellic acid-dependent signal, and transcription factors were found among differentially expressed genes (DEGs) between apomictic and sexual plants. We found that 24% of uniquely annotated DEGs were likely to be implicated in flower development, male sterility, pollen formation, pollen-stigma interactions, and pollen tube formation. The present study identifies candidate genes that are highly associated with distinct reproductive modes and sheds light on the molecular mechanisms of apomixis expression in Limonium sp.

Arabidopsis-Based Dual-Layered Biological Network Analysis Elucidates Fully Modulated Pathways Related to Sugarcane Resistance on Biotrophic Pathogen Infection.

We assembled a dual-layered biological network to study the roles of resistance gene analogs (RGAs) in the resistance of sugarcane to infection by the biotrophic fungus causing smut disease. Based on sugarcane-Arabidopsis orthology, the modeling used metabolic and protein-protein interaction (PPI) data from Arabidopsis thaliana (from Kyoto Encyclopedia of Genes and Genomes (KEGG) and BioGRID databases) and plant resistance curated knowledge for Viridiplantae obtained through text mining of the UniProt/SwissProt database. With the network, we integrated functional annotations and transcriptome data from two sugarcane genotypes that differ significantly in resistance to smut and applied a series of analyses to compare the transcriptomes and understand both signal perception and transduction in plant resistance. We show that the smut-resistant sugarcane has a larger arsenal of RGAs encompassing transcriptionally modulated subnetworks with other resistance elements, reaching hub proteins of primary metabolism. This approach may benefit molecular breeders in search of markers associated with quantitative resistance to diseases in non-model systems.

Genetic Analysis of Resistance to Multiple Isolates of Phytophthora capsici and Linkage to Horticultural Traits in Bell Pepper

Phytophthora capsici is one of the major pathogens found in pepper production, especially in bell pepper. Due to the high level of genetic diversity of the pathogen, bell pepper varieties with broad genetic resistance are essential for disease management. Criollo de Morelos – 334 (CM334), a landrace that has a high level of genetic resistance to P. capsici, has been used as the resistant source for P. capsici to generate a recombinant inbred line (RIL) population with the susceptible bell pepper cultivar Maor. From the resulting population, quantitative trait locus (QTL) models explaining resistance to each of four isolates of P. capsici were derived from QTL regions on three chromosomes using stepwiseqtl in R/qtl. A single region of chromosome 5 contained major QTL for resistance to each of the four isolates. Two isolate-specific QTL conferring resistance to isolates PWB53 and PWB106 were located on chromosomes 10 and 11, respectively. Both isolate-specific QTL had epistatic interactions with a major QTL on chromosome 5. Using the pepper reference genome and gene annotation, candidate genes for P. capsici resistance within 1.5-logarithm of odds (LOD) interval were identified. Based on functional annotations derived from Arabidopsis thaliana and solanaceous crop databases, multiple candidate genes related to resistance (R) gene complexes or to plant immune system were found under the QTL on all three chromosomes. A comparison of the locations of resistance QTL and previously identified horticultural QTL using the same population revealed tight linkage between resistance to P. capsici and a stem pubescence QTL o chromosome 10. Both candidate genes for P. capsici resistance and the linkages between resistance and horticultural traits could be applied for selection to broad resistance to P. capsici in bell pepper–breeding programs.

On the roles of genes encoding methionine-rich proteins in Arabidopsis thaliana in response to abiotic stresses

Methionine (Met) is an essential amino acid, which plays an important role in the plant cells. Oxidation of Met residues in proteins caused by abiotic stresses can lead to damages in cellular components, which may further affect metabolism, signal transduction in the cell and consequently the viability of organisms. In this study, 121 genes encoding Met-rich proteins (MRP) were identified from Arabidopsis thaliana database. Gene ontology analysis showed that the cellular functions of half of these genes are yet be known. Based on their transcript levels under normal and stress conditions, we found that 23 and 16 AtMRP genes were induced and repressed more than 2-fold, respectively, under dehydration. On the other hand, 11 and 17 genes were induced and repressed more than 2-fold, respectively, under high salinity treatment. Of these, 10 AtMRP genes were transcriptionally responsive to both drought and high salinity. AT4G33467 was the most induced gene, its transcript level was up-regulated 337.5-fold by drought. Among stress-repressed genes, AT3G55240 was the most down-regulated gene, its transcript level was repressed by 60.3 and 26.9-fold under dehydration and high salinity treatments, respectively. The transgenic line RBC1, who overexpressed AT3G55240, was more sensitive to high salinity treatment than the wild type. Taken together, this is the first report on the involvement of genes encoding MRPs in the adaptation of plants to abiotic stresses.

RNA-Seq Analysis of Transcriptome and Glucosinolate Metabolism in Seeds and Sprouts of Broccoli (Brassica oleracea var. italic)

BackgroundBroccoli (Brassica oleracea var. italica), a member of Cruciferae, is an important vegetable containing high concentration of various nutritive and functional molecules especially the anticarcinogenic glucosinolates. The sprouts of broccoli contain 10–100 times higher level of glucoraphanin, the main contributor of the anticarcinogenesis, than the edible florets. Despite the broccoli sprouts’ functional importance, currently available genetic and genomic tools for their studies are very limited, which greatly restricts the development of this functionally important vegetable.ResultsA total of ∼85 million 251 bp reads were obtained. After de novo assembly and searching the assembled transcripts against the Arabidopsis thaliana and NCBI nr databases, 19,441 top-hit transcripts were clustered as unigenes with an average length of 2,133 bp. These unigenes were classified according to their putative functional categories. Cluster analysis of total unigenes with similar expression patterns and differentially expressed unigenes among different tissues, as well as transcription factor analysis were performed. We identified 25 putative glucosinolate metabolism genes sharing 62.04–89.72% nucleotide sequence identity with the Arabidopsis orthologs. This established a broccoli glucosinolate metabolic pathway with high colinearity to Arabidopsis. Many of the biosynthetic and degradation genes showed higher expression after germination than in seeds; especially the expression of the myrosinase TGG2 was 20–130 times higher. These results along with the previous reports about these genes’ studies in Arabidopsis and the glucosinolate concentration in broccoli sprouts indicate the breakdown products of glucosinolates may play important roles in the stage of broccoli seed germination and sprout development.ConclusionOur study provides the largest genetic resource of broccoli to date. These data will pave the way for further studies and genetic engineering of broccoli sprouts and will also provide new insight into the genomic research of this species and its relatives.

Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application).

BackgroundSmall peptides encoded as one- or two-exon genes in plants have recently been shown to affect multiple aspects of plant development, reproduction and defense responses. However, popular similarity search tools and gene prediction techniques generally fail to identify most members belonging to this class of genes. This is largely due to the high sequence divergence among family members and the limited availability of experimentally verified small peptides to use as training sets for homology search and ab initio prediction. Consequently, there is an urgent need for both experimental and computational studies in order to further advance the accurate prediction of small peptides.ResultsWe present here a homology-based gene prediction program to accurately predict small peptides at the genome level. Given a high-quality profile alignment, SPADA identifies and annotates nearly all family members in tested genomes with better performance than all general-purpose gene prediction programs surveyed. We find numerous mis-annotations in the current Arabidopsis thaliana and Medicago truncatula genome databases using SPADA, most of which have RNA-Seq expression support. We also show that SPADA works well on other classes of small secreted peptides in plants (e.g., self-incompatibility protein homologues) as well as non-secreted peptides outside the plant kingdom (e.g., the alpha-amanitin toxin gene family in the mushroom, Amanita bisporigera).ConclusionsSPADA is a free software tool that accurately identifies and predicts the gene structure for short peptides with one or two exons. SPADA is able to incorporate information from profile alignments into the model prediction process and makes use of it to score different candidate models. SPADA achieves high sensitivity and specificity in predicting small plant peptides such as the cysteine-rich peptide families. A systematic application of SPADA to other classes of small peptides by research communities will greatly improve the genome annotation of different protein families in public genome databases.

Construction and Analysis of Suppression Subtractive cDNA Library from Fertile Disk Floret Buds of Zinnia elegans

In order to isolate genes related to anther development and understand molecular basis of male sterility, cDNA library of Zinnia elegans was constructed using suppression subtractive hybridization (SSH) approach. 672 different expressed clones were selected from the fertile disk floret buds. PCR results showed that cDNA inserts were ranged from 100 to 750 bp. 303 positive clones screened by dot-blot hybridization were sequenced. 273 out of 303 sequenced clones produced readable sequences; these sequences represent 87 non-repetitive sequences. The homology alignment showed that 76 expressed sequence tags (ESTs) had functional annotations in GenBank, the other 11 ESTs without any homology to the known gene. In addition, 87 ESTs were divided into 17 groups according to MIPS of Arabidopsis thaliana database. Sequence data from the cDNA library have been deposited with the GenBank under the accession numbers GT067016-GT067085. As an important result in this study, 7 genes related to anther development were isolated. Results from semi-quantitative RT-PCR showed 6 genes were expressed only in disk florets of fertile plants compared with that of male sterile plants. These ESTs obtained provide important clues for further isolation and identification of fertility-related genes in Z. elegans.

Evidence for functional interaction between brassinosteroids and cadmium response in Arabidopsis thaliana

Plant hormones, in addition to regulating growth and development, are involved in biotic and abiotic stress responses. To investigate whether a hormone signalling pathway plays a role in the plant response to the heavy metal cadmium (Cd), gene expression data in response to eight hormone treatments were retrieved from the Genevestigator Arabidopsis thaliana database and compared with published microarray analysis performed on plants challenged with Cd. Across more than 3000 Cd-regulated genes, statistical approaches and cluster analyses highlighted that gene expression in response to Cd and brassinosteroids (BR) showed a significant similarity. Of note, over 75% of the genes showing consistent (e.g. opposite) regulation upon BR and Brz (BR biosynthesis inhibitor) exposure exhibited a BR-like response upon Cd exposure. This phenomenon was confirmed by qPCR analysis of the expression level of 10 BR-regulated genes in roots of Cd-treated wild-type (WT) plants. Although no change in BR content was observed in response to Cd in our experimental conditions, adding epibrassinolide (eBL, a synthetic brassinosteroid) to WT plants significantly enhanced Cd-induced root growth inhibition, highlighting a synergistic response between eBL and the metal. This effect was specific to this hormone treatment. On the other hand, dwarf1 seedlings, showing a reduced BR level, exhibited decreased root growth inhibition in response to Cd compared with WT, reversed by the addition of eBL. Similar results were obtained on Brz-treated WT plants. These results argue in favour of an interaction between Cd and BR signalling that modulates plant sensitivity, and opens new perspectives to understand the plant response to Cd.

Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies

With large-scale genomic data becoming the norm in biological studies, the storing, integrating, viewing and searching of such data have become a major challenge. In this article, we describe the development of an Arabidopsis thaliana database that hosts the geographic information and genetic polymorphism data for over 6000 accessions and genome-wide association study (GWAS) results for 107 phenotypes representing the largest collection of Arabidopsis polymorphism data and GWAS results to date. Taking advantage of a series of the latest web 2.0 technologies, such as Ajax (Asynchronous JavaScript and XML), GWT (Google-Web-Toolkit), MVC (Model-View-Controller) web framework and Object Relationship Mapper, we have created a web-based application (web app) for the database, that offers an integrated and dynamic view of geographic information, genetic polymorphism and GWAS results. Essential search functionalities are incorporated into the web app to aid reverse genetics research. The database and its web app have proven to be a valuable resource to the Arabidopsis community. The whole framework serves as an example of how biological data, especially GWAS, can be presented and accessed through the web. In the end, we illustrate the potential to gain new insights through the web app by two examples, showcasing how it can be used to facilitate forward and reverse genetics research. Database URL: http://arabidopsis.usc.edu/

Identification of genes in Arabidopsis thaliana with homology to a novel acyl-glucose dependent glucosyltransferase of carnations

Recently, we characterized an acyl-glucose : anthocyanin 5-O-glucosyltransferase (DcAA5GT) in Dianthus caryophyllus that has novel characteristics. We also showed that a homologous enzyme, acyl-glucose:anthocyanin 7-O-glucosyltransferase (DgAA7GT), is present in Delphinium grandiflorum. These enzymes are both classified as members of glycoside hydrolase family 1 (GH1). Here, we searched the Arabidopsis thaliana database for genes with homology to DcAA5GT and DgAA7GT and identified 11 β-glucosidases (BGLU1–11) of unknown function. In a co-expression analysis, using genes for enzymes involved in anthocyanin modification as baits, we found that expression of AtBGLU6 and AtBGLU9 appeared to be correlated to that of the baits. Real-time RT-PCR showed that AtBGLU1, 6, 7 and 9 were expressed at their highest levels in anthocyanin-inducing medium, although AtBGLU6 was a pseudogene in which there was a stop codon on the middle of its cDNA sequence. These results suggest that AtBGLU1, 7 and 9 might be candidate glucosyltransferases for anthocyanin/flavonoid modification or biosynthesis.

Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases

Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases

Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases

The development of a systems based approach to problems in plant sciences requires integration of existing information resources. However, the available information is currently often incomplete and dispersed across many sources and the syntactic and semantic heterogeneity of the data is a challenge for integration. In this article, we discuss strategies for data integration and we use a graph based integration method (Ondex) to illustrate some of these challenges with reference to two example problems concerning integration of (i) metabolic pathway and (ii) protein interaction data for Arabidopsis thaliana. We quantify the degree of overlap for three commonly used pathway and protein interaction information sources. For pathways, we find that the AraCyc database contains the widest coverage of enzyme reactions and for protein interactions we find that the IntAct database provides the largest unique contribution to the integrated dataset. For both examples, however, we observe a relatively small amount of data common to all three sources. Analysis and visual exploration of the integrated networks was used to identify a number of practical issues relating to the interpretation of these datasets. We demonstrate the utility of these approaches to the analysis of groups of coexpressed genes from an individual microarray experiment, in the context of pathway information and for the combination of coexpression data with an integrated protein interaction network.

Coexpression characteristics of trehalose‐6‐phosphate phosphatase subfamily genes reveal different functions in a network context

Arabidopsis thaliana databases are available that highlight the behavior of the transcriptome under literally hundreds of experimental manipulations, making attempts possible that integrate this information into gene networks. We present and discuss the functioning of a gene network model generated using deposited microarray experiments. Based on a graphical Gaussian model, the network describes conditional coregulation of genes under a variety of external factors and abiotic, biotic and chemical treatments. In this study, we show an aspect of this network that pertains to functions of genes in families where all members appear to carry out the same biochemical reaction. Chosen in this study were 10 genes in the Arabidopsis genome encoding trehalose-6-phosphate phosphatases (TPPs). Nine of these genes were highlighted by the network. Generally, each TPP formed a network associated with genes that identify different functional categories. Thus, network structures were obtained that identified connections to carbon distribution, drought, cold, pathogen responses, calcium and reactive oxygen species/redox signatures, including transcriptional control genes that separated network graphs seeded with different TPP genes. The structure of the transcript coexpression networks, by associating diverse members of gene families into separate clusters, facilitates hypothesis building and in-depth studies of functions of individual genes in families.

A workflow to increase the detection rate of proteins from unsequenced organisms in high‐throughput proteomics experiments

We present and evaluate a strategy for the mass spectrometric identification of proteins from organisms for which no genome sequence information is available that incorporates cross-species information from sequenced organisms. The presented method combines spectrum quality scoring, de novo sequencing and error tolerant BLAST searches and is designed to decrease input data complexity. Spectral quality scoring reduces the number of investigated mass spectra without a loss of information. Stringent quality-based selection and the combination of different de novo sequencing methods substantially increase the catalog of significant peptide alignments. The de novo sequences passing a reliability filter are subsequently submitted to error tolerant BLAST searches and MS-BLAST hits are validated by a sampling technique. With the described workflow, we identified up to 20% more groups of homologous proteins in proteome analyses with organisms whose genome is not sequenced than by state-of-the-art database searches in an Arabidopsis thaliana database. We consider the novel data analysis workflow an excellent screening method to identify those proteins that evade detection in proteomics experiments as a result of database constraints.

Novel Tonoplast Transporters Identified Using a Proteomic Approach with Vacuoles Isolated from Cauliflower Buds

Young meristematic plant cells contain a large number of small vacuoles, while the largest part of the vacuome in mature cells is composed by a large central vacuole, occupying 80% to 90% of the cell volume. Thus far, only a limited number of vacuolar membrane proteins have been identified and characterized. The proteomic approach is a powerful tool to identify new vacuolar membrane proteins. To analyze vacuoles from growing tissues we isolated vacuoles from cauliflower (Brassica oleracea) buds, which are constituted by a large amount of small cells but also contain cells in expansion as well as fully expanded cells. Here we show that using purified cauliflower vacuoles and different extraction procedures such as saline, NaOH, acetone, and chloroform/methanol and analyzing the data against the Arabidopsis (Arabidopsis thaliana) database 102 cauliflower integral proteins and 214 peripheral proteins could be identified. The vacuolar pyrophosphatase was the most prominent protein. From the 102 identified proteins 45 proteins were already described. Nine of these, corresponding to 46% of peptides detected, are known vacuolar proteins. We identified 57 proteins (55.9%) containing at least one membrane spanning domain with unknown subcellular localization. A comparison of the newly identified proteins with expression profiles from in silico data revealed that most of them are highly expressed in young, developing tissues. To verify whether the newly identified proteins were indeed localized in the vacuole we constructed and expressed green fluorescence protein fusion proteins for five putative vacuolar membrane proteins exhibiting three to 11 transmembrane domains. Four of them, a putative organic cation transporter, a nodulin N21 family protein, a membrane protein of unknown function, and a senescence related membrane protein were localized in the vacuolar membrane, while a white-brown ATP-binding cassette transporter homolog was shown to reside in the plasma membrane. These results demonstrate that proteomic analysis of highly purified vacuoles from specific tissues allows the identification of new vacuolar proteins and provides an additional view of tonoplastic proteins.

ACTIN BINDING PROTEIN29 fromLiliumPollen Plays an Important Role in Dynamic Actin Remodeling

Villin/gelsolin/fragmin superfamily proteins have been shown to function in tip-growing plant cells. However, genes encoding gelsolin/fragmin do not exist in the Arabidopsis thaliana and rice (Oryza sativa) databases, and it is possible that these proteins are encoded by villin mRNA splicing variants. We cloned a 1006-bp full-length cDNA from Lilium longiflorum that encodes a 263-amino acid predicted protein sharing 100% identity with the N terminus of 135-ABP (Lilium villin) except for six C-terminal amino acids. The deduced 29-kD protein, Lilium ACTIN BINDING PROTEIN29 (ABP29), contains only the G1 and G2 domains and is the smallest identified member of the villin/gelsolin/fragmin superfamily. The purified recombinant ABP29 accelerates actin nucleation, blocks barbed ends, and severs actin filaments in a Ca(2+)- and/or phosphatidylinositol 4,5-bisphosphate-regulated manner in vitro. Microinjection of the protein into stamen hair cells disrupted transvacuolar strands whose backbone is mainly actin filament bundles. Transient expression of ABP29 by microprojectile bombardment of lily pollen resulted in actin filament fragmentation and inhibited pollen germination and tube growth. Our results suggest that ABP29 is a splicing variant of Lilium villin and a member of the villin/gelsolin/fragmin superfamily, which plays important roles in rearrangement of the actin cytoskeleton during pollen germination and tube growth.

Biochemical and molecular characterization of flavonoid 7-sulfotransferase from Arabidopsis thaliana

Flavonoid compounds play important roles as flower pigments, stress metabolites formed in response to UV, during pollen germination and for polar auxin transport (Trends Plant Sci. 1 (1996) 377). Flavonoid sulfate esters are common in plants, especially the Asteraceae; however, due to the lack of information regarding the factors that regulate their accumulation, their exact role remains to be elucidated. The biosynthesis of flavonol sulfate esters is catalyzed by a number of position specific flavonol sulfotransferases (STs). An Arabidopsis thaliana database search has allowed us to identify and classify 18 putative ST coding sequences. We report here the cloning and characterization of the AtST3a member of this family that is expressed at early stages of seedling development and in the inflorescence stem and siliques of mature plants. The recombinant AtST3a protein exhibits strict specificity for position 7 of flavonoids. In contrast to previously characterized flavonol 7-ST from Flaveria bidentis that sulfonates only flavonol disulfates, AtST3a was found to accept as substrates a number of flavonols and flavone aglycones, as well as their monosulfate esters. The discovery of a flavonol ST from A. thaliana suggests that flavonol sulfates are more widely distributed than originally believed and this model plant could be used to study their biological significance.

CDNA array analysis of mercury- and ozone-induced genes in Arabidopsis thaliana

Selected cDNA clones of Arabidopsis thaliana, isolated previously by suppression subtractive hybridisation, were used to differentiate between abiotic stress factors. Changes in expression patterns of 79 genes were examined by array analysis in Arabidopsis thaliana after fumigation with ozone and after short- or long-term mercuric-ion exposure. Substantial changes in the abundance of 42 transcripts were recorded in response to the treatments, and 6 transcript clusters were observed. The abundance of 37 mRNAs was increased more then 1.5-fold, whereas that of 5 mRNAs was reduced. The abundances of 5, 6 and 9 mRNAs were specifically increased by short-term mercury application, ozone fumigation, and long-term mercuric-ion exposure, respectively. The transcription of the other 5 transcripts was induced by both ozone and short-term mercuric-ion treatment. The abundance of 10 different mRNAs was increased by the different mercuric-ion applications. Two transcripts were induced by ozone fumigation, as well as long-term, mercury treatment. Finally, 5 transcripts were repressed by ozone exposure, and 3 out of them by short-term mercuric-ion treatment. These results show that the array technique can be used to analyse the expression pattern in Arabidopsis thaliana under ozone and mercuric-ion stress. Searches against the Arabidopsis database furthermore provide a classification of most genes. In addition possible cis-acting regulatory elements were identified by an in silico approach using the MIPS Arabidopsis thaliana database.

MIPS: analysis and annotation of proteins from whole genomes.

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein-protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).