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.