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.

Many microorganisms, including Escherichia coli, can survive extended periods of starvation. The properties of cells that survived prolonged incubation in stationary phase were studied by mixture of 10-day-old (aged) cultures with 1-day-old (young) cultures of the same strain of Escherichia coli. Mutants from the aged cultures that could grow eventually took over the population, which resulted in the death of the cells from the young cultures. This phenotype was conferred by mutations in rpoS, which encodes a putative stationary phase-specific sigma factor. These rapid population shifts have implications for the studies of microbial evolution and ecology.

In the natural environment bacteria seldom encounter conditions that permit periods of exponential growth. Rather, bacterial growth is characterized by long periods of nutritional deprivation punctuated by short periods that allow fast growth, a feature that is commonly referred to as the feast-or-famine lifestyle. In this chapter we review the recent advances made in our understanding of the molecular events that allow some gram-negative bacteria to survive prolonged periods of starvation. After an introductory description of the properties of starved gram-negative bacteria, the review presents three aspects of stationary phase: entry into stationary phase, responses during prolonged starvation, and reentry into the growth cycle.

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Gene expression from plasmids containing the araBAD promoter can be regulated by the concentration of arabinose in the growth medium. Guzman et al. The ability to express a cloned gene under controlled conditions is often very useful. In Escherichia coli, plasmid-based inducible promoter systems have been implemented using bacterial, phage, and chimeric promoters. These systems have been generally designed to respond to an external inducer by expressing high levels of the gene product(s) of interest, often for the purpose of obtaining material for purification. Plasmid systems also have been designed to have low basal levels of expression to minimize the effects of exposing cells to toxic gene products during growth.Plasmid systems based on the lac promoter are notoriously leaky; repression is often incomplete due to a combination of plasmid copy number effects and the absence of secondary operators required for the full range of gene control in the natural lac operon (1). Background expression levels should be lower in systems based on positive rather than negative control. Recently, expression plasmids based on the araBAD promoter (P araBAD ) have been constructed by Guzman et al. (2). Because the ara system can be induced by arabinose and is repressed by both catabolite repression in the presence of glucose or by competitive binding of the anti-inducer fucose, these plasmids have very low background levels of expression. In addition, gene expression can be turned on and off rapidly by changing the sugars in the medium.In addition to providing material for biochemical studies, the ability to conditionally control the expression of specific genes is useful for understanding how the presence or absence of the genes of interest affects the physiology of E. coli. Conditional expression also allows for selections and screens for mutations in other genes. For example, cells that express an essential gene under control of the araBAD promoter can be grown in the presence of arabinose, and then plated for growth on glucose to select for mutations that bypass the requirement for that function (2). Similarly, mutants that affect the toxicity of an expressed gene product could be isolated by selecting for growth in the presence of the inducer.For physiological and genetic studies, the very high levels of protein expressed by most inducible systems are often inappropriate. Ideally, one would like to be able to modulate gene expression over a range of levels. Guzman et al. (2) presented evidence that the pBAD vectors are also suitable for this purpose. Using alkaline phosphatase as a reporter, they showed that the levels of alkaline phosphatase in cultures grown in different concentrations of arabinose could be varied over an approximately 300-fold range. Moreover, expression could be set at intermediate levels by using inducer concentrations between 1.33 M and 133 M.

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new ‘phylogenetic annotation’ process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

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.

A remarkable feature of bacterial species is their capacity for rapid growth when nutrients are available and conditions are appropriate for growth. Perhaps even more remarkable is their ability to remain viable under conditions not propitious for growth. Many bacteria have evolved highly sophisticated mechanisms that allow them to maintain cell viability during starvation and resume growth rapidly when nutrients again become available. Some species form dormant spores, while others form multicellular aggregates and fruiting bodies in response to starvation conditions (26,34 Examination of starved cells using light microscopy reveals changes in cell morphology. Escherichia coli cells become much smaller and almost spherical when they enter stationary phase (22,31). This phenomenon is even more striking for a number of marine bacteria which greatly decrease in size during starvation and form ultramicrocells, as small as 0. 03 ,um3 (28). Ultramicrocells result from cells that undergo several cell divisions without an increase in biomass and then a further decrease in their size as a result of endogenous metabolism. One possible selective advantage of the reductive divisions seen in marine bacteria is to improve the survival of the clonal population by increasing the probability that some cells will encounter nutrients (38). In E. coli, these changes in cell size and shape are accompanied by changes in the subcellular compartments; the cytoplasm is condensed and the volume of the periplasm increases (48).The surface properties of starved cells are also different from those of growing cells. The surface of many marine bacteria becomes increasingly hydrophobic and the cells become more adhesive during starvation (28). Changes in the fatty acid composition of the cell membranes have been seen during starvation of several species (28). For example, in E. coli there is a conversion of all unsaturated membrane fatty acids to the cyclopropyl derivatives as cells enter stationary phase (14). Vibrio sp. strain S14 acquires new fimbraelike structures and forms cellular aggregates or clumps after prolonged starvation (1). In E. coli, such starvation-induced aggregates appear to form as the result of a self-generated and secreted attractant that is sensed by the chemotaxis machinery (7).The cell wall synthesized during amino acid starvation has a different structure from the cell wall synthesized during growth (46, 56). These changes in structure appear to protect cells against the autolysis induced by either penicillin or * Corresponding author. chaotropic agents. In E. coli, the increased resistance to autolysis is dependent on induction of the stringentresponse (29). It is likely that other starvation conditions such as carbon starvation, which increase the intracellular levels of the signal molecule ppGpp (9), may also induce resistance to autolysis.Changes in the topology of the chromosome occur in starved cells. After several hours in stationary phase, changes in the negative superhelical density of reporter plasmids can...