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Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that demonstrate that families of mRNAs show non-trivial sub-cellular distributions raise the question of how localization may affect the regulatory activity of sRNAs. Here we address this question within a simple mathematical model. We show that the non-uniform spatial distributions of mRNA can alter the threshold-linear response that characterizes sRNAs that act stoichiometrically, and modulate the hierarchy among targets co-regulated by the same sRNA. We also identify conditions where the sub-cellular organization of cofactors in the sRNA pathway can induce spatial heterogeneity on sRNA targets. Our results suggest that under certain conditions, interpretation and modeling of natural and synthetic gene regulatory circuits need to take into account the spatial organization of the transcripts of participating genes.

Acridine dye binding by cells of Escherichia coli has been characterized in terms of a number of parameters. There is a temperature-dependent, readily reversible binding of acriflavine which occurs to a greater extent with acridine-sensitive mutants of E. coli K-12 than with wild-type E. coli B or K-12. There is an essentially irreversible internal binding of acriflavine which occurs when the cellular permeability barriers are destroyed or altered by heat-treatment, elevated pH, treatment with toluene or phenethyl alcohol, or infection with bacteriophage T2 or T4. Both the reversible and the irreversible binding of acridines occurs more effectively with the acridine dye acriflavine than with the related dye proflavine, and still less effectively with 9-aminoacridine and quinacrine. These properties of acridine binding can be correlated with various inhibitory effects of the dyes on the cells.

Infection of Escherichia coli by bacteriophage T2 was accompanied by a rapid but transient increase in the rate of loss of small molecules from the bacterial cells. This transient leakage was studied with radioactive labels such as (42)K and (28)Mg. Bacteriophage-induced leakage was dependent on the ratio of phage to bacteria: the higher the multiplicity of infection, the greater the leakage. No leakage occurred at 4 C [when adsorption proceeds but injection of phage deoxyribonucleic acid (DNA) is blocked]. Leakage was caused by heavily irradiated phage as well as by normal phage; therefore, the intracellular functioning of the bacteriophage DNA was not required. This conclusion was supported by experiments which showed phage-induced leakage in the presence of chloramphenicol or sodium cyanide. Leakage could be prevented by infecting the bacteria with phage in the presence of high magnesium concentrations. Phage-induced leakage was terminated by a "sealing" reaction, after which potassium turnover by infected and uninfected cells was very similar. The sealing reaction occurred even in the presence of chloramphenicol, suggesting that the sealing is controlled by bacterial and not bacteriophage genes. We were not able to detect any effect of normal bacteriophage infection on the influx (active transport) of potassium and magnesium into the cells.

The steroidal diamine irehdiamine A (IDA) is a potent inhibitor of bacteriophage growth and macromolecular synthesis in Escherichia coli. By using radioactive (42)K and (14)C-thiomethylgalactoside (TMG), rapid effects of IDA and related steroids, both on the influx of potassium and TMG via their respective transport systems and on the efflux (leakage) of radioactivity from the treated cells, have been measured. IDA affects both the influx and efflux of (42)K at concentrations of steroid as low as 2 x 10(-5)m. Because of the increased leakage, it is not possible to tell whether there is a direct effect reducing the rate of active transport of potassium. The primary diamine, IDA, and its bis-secondary, bis-tertiary, and bis-quaternary diamine analogues are decreasingly effective in altering cell permeability properties in the order 1 degrees > 2 degrees > 3 degrees > 4 degrees . The effects of IDA on potassium transport are mirrored by similar effects on the transport of TMG. Therefore, the action of IDA is on the cell membrane and not directly on one or another transport system. The effects of IDA on cell permeability can reasonably explain the inhibitory actions of the drugs on bacteriophage growth and cellular metabolism.

Levine, Elliot M. (Yale University, New Haven, Conn.) and Sofia Simmonds. Effect of cultural conditions on growth and metabolite uptake by serine-glycine auxotrophs of Escherichia coli. J. Bacteriol. 84:683-693. 1962.-A study was made of the effect of environmental conditions on the growth and metabolite uptake by Escherichia coli strain S/G (a serine-glycine auxotroph) and strain S (a serine-glycine auxotroph lacking a normal transport system for glycine). The induction in strain S of the glycine transport system, which occurs during growth in a glycine-containing medium, was prevented by l-asparagine; the "repression" appeared to result from the endogenous formation of glycine from asparagine (through homoserine and threonine) via a pathway in which serine was not an obligatory intermediate. The response of both strains to glycine appeared to be determined by the amount of l-serine or glycine present in the media (containing asparagine) in which the cells were grown prior to testing. Preliminary growth in the presence of low concentrations of exogenous glycine, which should produce cells with small endogenous "glycine-serine pools," favored the induction of a functional glycine transport system in cells of strain S. Cells of strain S/G grown under similar conditions subsequently showed an enhanced ability to take up C(14)-labeled glycine. With both strains, preliminary growth conditions leading to the formation of large endogenous "glycine-serine pools" (e.g., growth in the presence of high concentrations of exogenous serine) produced cells exhibiting a glycine uptake rate that was not commensurate with the rate at which these cells grew on glycine. The growth response apparently depends not only on the ability of the cells to transport glycine but also on the size of the endogenous "glycine-serine pools"; inocula composed of cells having a limited capacity to accumulate labeled glycine showed significant growth in glycine-containing media if the cells had large "glycine-serine pools." The growth and uptake responses to glycylglycine appear to be governed, in part, by the same factors that control the responses to free glycine.

Levine, Elliot M. (National Institutes of Health, Bethesda, Md.). Protein turnover in Escherichia coli as measured with an equilibration apparatus. J. Bacteriol. 90:1578-1588. 1965.-Intercellular protein turnover (the reutilization by one cell of amino acids derived from the protein of another cell) occurs at a rate of 0.16 to 0.18% per hour in nongrowing cultures of Escherichia coli, as determined in an apparatus that rapidly equilibrates the culture fluids of two separated bacterial suspensions.