The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and non-coding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains and updates the GO knowledgebase. The GO knowledgebase consists of three components: 1) the Gene Ontology – a computational knowledge structure describing functional characteristics of genes; 2) GO annotations – evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and 3) GO Causal Activity Models (GO-CAMs) – mechanistic models of molecular “pathways” (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised and updated in response to newly published discoveries, and receives extensive QA checks, reviews and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, as well as guidance on how users can best make use of the data we provide. We conclude with future directions for the project.

The Ti plasmids of Agrobacterium tumefaciens are conjugal elements whose transfer is strongly repressed. Transfer is induced by the conjugal opines, a group of unique carbon compounds synthesized in crown gail tumors.The opines also induce Ti plasmid-encoded genes required by the bacteria for' opine catabolism. We have cloned and sequenced a gene from the Ti plasmid pTiC58, whose product mediates the opine-dependent regulation of conjugal transfer and catabolism of the conjugal opines, agrocinopines A and B. The gene, accR, is closely linked to the agrocinopine catabolic locus. A spontaneous mutant Ti plasmid, pTiC58Trac, which constitutively expresses conjugal transfer and opine catabolism, was complemented in trans by a clone of wild-type accR.Comparative sequence analysis identified a 5-base-pair deletion close to the 5' end of the mutant accR allele from pTiC58Trac. Analysis During interactions between Agrobacterium tumefaciens and its plant hosts, the bacterium senses and responds to several plant-produced signals. For example, virulent agrobacteria use a two-component signal transduction system to sense small phenolic compounds released from wounded plant tissue. In response, the bacteria express Ti plasmid-encoded Vir functions, which, in turn, facilitate T-strand excision and transfer to susceptible plant cells (1). The resulting plant neoplasias synthesize unique low molecular weight carbon compounds, called opines, which are thought to provide a source of carbon for tumor-colonizing agrobacteria (2).The opines also act as signals. For example, the Ti plasmidencoded functions required for opine catabolism are specifically induced by their cognate substrates (3, 4). In addition, conjugal transfer of the Ti plasmid, which is normally repressed, is induced by a subclass of opines, the conjugal opines (5,6). A model proposing that conjugation and catabolism of the conjugal opines are coregulated emerged from the observation that mutants constitutive for conjugation are often derepressed for conjugal opine catabolism. Similarly, mutants selected for constitutive expression of these opine catabolic functions are generally transfer-constitutive (5, 7-9).For nopaline-type Ti plasmids such as pTiC58, conjugation is induced by the sugar phosphate opines, agrocinopines A and B (6). We report here that the coregulation of agrocinopine catabolism (Acc) and conjugal transfer (Tra) of pTiC58 is mediated by a repressor, AccR. This repressor is related to negative regulatory proteins that control sugar catabolic operons in several unrelated bacteria (10). Our findings provide a molecular framework for the coregulation model and illustrate the diversity of regulatory mechanisms that govern the interaction between Agrobacterium and its plant hosts. 11 MATERIALS AND METHODS Strains and Plasmids. A. tumefaciens strains used were C58 (11), NT1(pTiC58Trac) (12), C58ClCE (pWI1003) (8), NT1(pAgK84-A1) (13), and C58C1RS (rifampin resistant, streptomycin resistant) (8); Escherichia coli strains were DH5a, RR1, and S17-1...

Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat. Because the laboratory rat, Rattus norvegicus, has been used as a model for complex human diseases such as cardiovascular disease, diabetes, cancer, neurological disorders and arthritis, among others, for >150 years, RGD has always been disease-focused and committed to providing data and tools for researchers doing comparative genomics and translational studies. At its inception, before the sequencing of the rat genome, RGD started with only a few data types localized on genetic and radiation hybrid (RH) maps and offered only a few tools for querying and consolidating that data. Since that time, RGD has expanded to include a wealth of structured and standardized genetic, genomic, phenotypic, and disease-related data for eight species, and a suite of innovative tools for querying, analyzing and visualizing this data. This article provides an overview of recent substantial additions and improvements to RGD’s data and tools that can assist researchers in finding and utilizing the data they need, whether their goal is to develop new precision models of disease or to more fully explore emerging details within a system or across multiple systems.

Overlapping segments of pTiC58 inserted into cosmid vectors were used to characterize the agrocinopineagrocin 84 locus from the nopaline/agrocinopine A and B Agrobacterium tumefaciens strain C58. All of the clones conferring agrocin 84 sensitivity on agrobacteria also conferred uptake of agrocin 84 and agrocinopines A and B. Transposon Tn3-HoHol insertion mutations of one such clone were generated that simultaneously abolished agrocin 84 sensitivity and transport of agrocinopines A and B and agrocin 84. Such insertions were found to cluster within a 4.4-kilobase region. Analysis of ,B-galactosidase activity in these insertion mutants suggested a single transcriptional unit regulated at the transcriptional level by agrocinopines A and B. The smallest DNA fragment subcloned from theiregion to confer all three activities was 8.5 kilobases long. This subclone was still properly regulated, indicating that the regulatory gene is closely linked to the locus. The data are consistent with a single operon encoding catabolism of agrocinopines A and B and conferring sensitivity to agrocin 84. Based on these results, we support the locus name acc, for agrocinopine catabolism.Classical nopaline strains of Agrobacterium tumefaciens such as C58 induce crown gall tumors that produce nopaline and agrocinopines A and B. These opines can be catabolized by the inciting bacteria by using functions encoded by the Ti plasmid (2,14,29,38,39). The structures for agrocinopines A and B were recently determined. Agrocinopine A consists of sucrose and L-arabinose linked by a phosphodiester bond from the 2-OH of arabinose to the 4-OH of the fructose moiety. The glucose moiety of agrocinopine A can be removed either enzymatically or chemically to produce agrocinopine B (30).Agrocinopine A -has roles in two phenomena associated with nopaline strains. First, this opine is the specific inducer of Ti plasmid conjugal transfer in strain C58 (12). Second, nopaline/agrocinopine A strains take up and are killed by the toxic adenine analog agrocin 84, produced by the biotype 2 Agrobacterium radiobacter strain K84 (13,21,28). Transport of this highly specific antiagrobacterial agent is inducible by agrocinopine A (14), suggesting a link between opine catabolism and agrocin 84 sensitivity.Several lines of evidence indicate that agrocin 84 and agrocinopines A and B are transported by the same uptake system. First, spontaneous mutations causing constitutive transfer of pTiC58 result in increased transport rates for both agrocinopine A and agrocin 84 (15). Such mutants are supersensitive to agrocin 84. Second, agrocin 84-resistant mutants of A. tumefaciens A208 no longer transport agrocinopine A (14). Third, a molar excess of agrocinopine A blocks the transport of agrocin 84 into another nopaline strain, K57A (14). A periplasmic protein fraction thought to be involved in transport has been identified from this strain which binds reversibly to agrocin 84 with high affinity (27). Finally, determinants for agrocin 84 sensitivity, some conjugal transfer functio...