Bacterial cells must be able to efficiently induce transcription of a number of genes whose products are required to survive environmental stresses. Escherichia coli can survive environments characterized by nutrient scarcity, limited oxygen availability, toxic chemicals, and high osmolarity. Several of the genes induced by environmental stress rely on the rpoS gene for induction (2, 9, 22-25, 30, 36, 61, 64).rpoS encodes an alternate sigma factor (47) which acts as a principal regulator of E. coli's stress response by modifying the promoter recognition capacity of core RNA polymerase. Stationary-phase induction is characteristic of rpoS-dependent genes (9, 22-24, 30, 34-36, 45, 58, 60, 61, 64). Several rpoSdependent genes (bolA, otsBA, treA, osmB, osmY, and pexB) are also induced by hyperosmotic stress during exponential growth in a defined minimal medium (24,25,30,34,35,38,64). The cellular content of the S protein correlates with Sdependent gene induction, increasing during stationary phase and following hyperosmotic shock (37). Thus far, no DNAbinding protein that acts specifically as an activator of Sdependent genes has been identified. However, a mutation in hns, which encodes a nonspecific DNA-associated protein, leads to accumulation of the S protein during exponential growth (4, 63). An increase in the level of the alarmone ppGpp correlates with increased amounts of S protein (16). UDPglucose and homoserine lactone have also been proposed as signal molecules that influence production of S (5, 27 , which is encoded by the rpoD gene, is the chief determinant of promoter recognition by RNA polymerase during exponential growth. A large body of statistical and genetic evidence has identified the D consensus promoter as two hexamers centered at about Ϫ10 and Ϫ35 nucleotides upstream relative to the start site of transcription (19,20,66). The ability of certain rpoD mutants to specifically suppress mutations at the Ϫ10 and Ϫ35 sites of the E. coli lac and P22 ant promoters strongly suggests that promoter recognition is determined by direct interactions between certain amino acids of regions 2.4 and 4.2 of the D protein and nucleotides in the conserved Ϫ10 and Ϫ35 promoter hexamers (15,52,59).Studies of promoters used by secondary sigmas in a variety of bacteria, including E. coli, Bacillus subtilis, and Pseudomonas aeruginosa, have also identified two regions of conserved sequence believed to function as promoter recognition elements (10, 21, 67). The homology between S and D in the regions thought to determine promoter specificity is sufficient to predict that S holoenzyme will interact with promoter DNA in a manner resembling that of D holoenzyme. Specifically, one would suppose that S promoters would consist of two conserved sequence elements.It has been demonstrated through in vitro assays that transcription by S holoenzyme is determined by recognition of nucleotides downstream from position Ϫ17 of rpoS-dependent promoters (56). We have investigated the in vivo requirements for transcription by E S . We ...

No abstract

The yeast Saccharomyces cerevisiae has evolved to dominate grape juice fermentation. A suite of cellular properties, rapid nutrient depletion, production of inhibitory compounds and the metabolic narrowing of the niche, all enable a minor resident of the initial population to dramatically increase its relative biomass in the ecosystem. This dominance of the grape juice environment is fueled by a rapid launch of glycolysis and energy generation mediated by transport of hexoses and an efficient coupling of transport and catabolism. Fermentation occurs in the presence of molecular oxygen as the choice between respiratory or fermentative growth is regulated by the availability of sugar a phenomenon known as glucose or catabolite repression. Induction of the [GAR + ] prion alters the expression of the major hexose transporter active under these conditions, Hxt3, reducing glycolytic capacity. Bacteria present in the grape juice ecosystem were able to induce the [GAR + ] prion in wine strains of S. cerevisiae. This induction reduced fermentation capacity but did not block it entirely. However, dominance factors such as the rapid depletion of amino acids and other nitrogen sources from the environment were impeded enabling greater access to these substrates for the bacteria. Bacteria associated with arrested commercial wine fermentations were able to induce the prion state, and yeast cells isolated from arrested commercial fermentations were found to be [GAR + ] thus confirming the ecological relevance of prion induction. Subsequent analyses demonstrated that the presence of environmental acetic acid could lead to [GAR + ] induction in yeast strains under certain conditions. The induction of the prion enabled yeast growth on non-preferred substrates, oxidation and reduction products of glucose and fructose, present as a consequence of bacterial energy production. In native ecosystems prion induction never exceeded roughly 50-60% of the population of yeast cells suggesting that the population retains the capacity for maximal fermentation. Thus, the bacterial induction of the [GAR + ] prion represents a novel environmental response: the query of the environment for the presence of competing organisms and the biological decision to temper glucose repression and dominance and enter a metabolic state enabling coexistence.

Importance: Lactobacillus kunkeei, also known as the "ferocious lactobacilli", causes fermentation arrest during wine production 1. L. kunkeei co-evolved with honeybees and is an important probiotic for bee and hive health 2. In the bee ecosystem, L. kunkeei is one of a suite of lactic acid bacteria that protect the bee and hive from pathogens as well as aid in preservation of sugar-rich hive resources. The protection of sugar-rich resources probably uses similar mechanisms to those inhibiting yeast during grape juice fermentation.

SNF3 encodes a low-glucose sensor in Saccharomyces cerevisiae that regulates the expression of a subset of hexose transporter genes. Deletion of SNF3 prevents rapid adaptation to low glucose concentration. Novel spontaneous suppressor mutants of the snf3Delta phenotype were isolated. The mutations isolated fell into one of two groups: those that increase the expression of transporters regulated by Snf3p, and those that show no detectable effect on the regulation of these genes. The physiologic role of one mutation, rgg2 (restoration of growth on glucose), that did not affect HXT gene expression was assessed by transcriptome analysis. Genes involved in glycogen metabolism and cAMP pathways were affected by the rgg2 mutation, suggesting a cellular role as a regulatory protein. Attempts to clone the wild-type RGG2 allele were unsuccessful. The glycogen phenotype and genetic crossing allowed rgg2 to be identified as an allele of the IRA2 gene. Suppression of the snf3 mutant phenotype by deletion of IRA2 was confirmed. A possible mechanism of the suppression of the snf3 growth defect by mutation of ira2 is discussed.