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Our interests center on fundamental mechanisms that mediate bacterial physiological transitions between growth during good times and bad. Growth during good times involves an intricate balance of synthetic, degradative and transport processes mediated by global gene expression that ensures exponential growth. Bad times consist of stress occasioned by nutrient limitation or physical or biological harm that can come from: heat, cold, acidity, osmotic, radiation, oxidants, viruses, toxins, foreign DNA and host cell defenses. Recent discoveries suggest emerging “nucleotide-centric” regulation across all biological kingdoms that involve phosphate blocked analogs of ribonucleotides that cannot be used for RNA synthesis. The block can be with monocyclic, dicyclic or heterodicyclic nucleotides as well as blocked with polyphosphates such as ppGpp and pppGpp (p)ppGpp or (p)ppApp. We first published our discovery of (p)ppGpp fifty years ago. Ever since we have studied how stress triggers its abundance and how this helps cells adjust gene expression and metabolism to favor surviving the stress. The (p)ppGpp analogs are present in bacterial and plant kingdoms but not in archea, yeast or animals. We use E. coli as a model. It is becoming clear that these analogs do function in animal cells, where their presence is due to commensal relationships with bacteria.

The (p)ppGpp analogs can be viewed as hormone-like signals, whose varied functions ensure stress survival. Subtle deficiencies in metabolic sources for amino acids, lipids or carbohydrates are sensed to elevate (p)ppGpp either by stimulating synthesis, inhibiting hydrolysis or both. Accumulation then triggers regulation that curtails synthetic processes activated not needed during luxurious growth (eg. DNA, RNA, protein, lipid synthesis) but sparing enough residual activity to enable stress-specific remedial functions. Sensing stress is extraordinarily sensitive. An inability to make any one of 20 different amino acid charged-tRNA molecules is sensed by codon anti-codon mismatching. Matching occurs about 20 times per second for each ribosome of the 15,000 cellular ribosomes. For lipids an inability to synthesize and covalently bind a lipid chain to acyl carrier protein (ACP) is sensed (about 2/sec for about 1,500 ACP molecules/cell). Unbound ACP leads to inhibiting hydrolysis and stimulating (p)ppGpp synthesis. Oxidative stress leads to (p)ppGpp stimulation of peroxidases; heat shock to elevated protective heat shock proteins, and so on. Elevated (p)ppGpp leads to adaptive changes of expression for about 20% of all E. coli genes. These seemingly esoteric fundamental findings turn out to be of considerable practical consequence. A transient metabolic dormancy due to high (p)ppGpp protects microbial pathogens from many host defenses, making them more pathogenic. Rare spontaneous spikes of ppGpp levels render pathogens resistant to antibiotics that target active metabolism. When (p)ppGpp is totally absent, most pathogens are attenuated and carrier states are minimized. These properties are being exploited in order to find new antibiotics.

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