Thermolability of the stringent factor in rel mutants of Escherichia coli

The stringent factor extracted from several independently isolated rel^- mutants is more thermolabile than the stringent factor extracted from the parental rel⁺ strain. This thermolability is characteristically different in each of the mutants. This strongly suggests that the stringent factor is the product of the rel gene.     

Evidence of a conserved intrinsically disordered region in the C-terminus of the stringent response protein Rel from mycobacteria

The RelA/SpoT enzyme produces (p)ppGpp that helps the bacterium survive during stress. The domains present in it are interspersed with connecting linkers whose functions have been poorly elucidated. We rationally analyzed the sequence and structural property of the regulatory C-terminal region in the Rel family of proteins and report the presence of an intrinsically disordered region between two successive domains in this region that are separated by a defined amino acid sequence length. We show that the length and secondary structure of this linker are conserved in Rel proteins, further signifying its importance in rendering flexibility for domain movement and domain–domain interaction.     

ppGpp: stringent response and survival

Adaptation to any undesirable change in the environment dictates the survivability of many microorganisms, with such changes generating a quick and suitable response, which guides the physiology of bacteria. During nutritional deprivation, bacteria show a stringent response, as characterized by the accumulation of (p)ppGpp, resulting in the repression of stable RNA species, such as rRNA and tRNA, with a concomitant change in colony morphology. However, genes involved in amino acid biosynthesis become over-expressed to help bacteria survive under such conditions. The survivability of pathogenic bacteria inside a host cell also depends upon the stringent response demonstrated. Therefore, an understanding of the physiology of stringent conditions becomes very interesting in regulation of the growth and persistence of such invading pathogens.     

Phenotypic heterogeneity in mycobacterial stringent response

Background  

A common survival strategy of microorganisms subjected to stress involves the generation of phenotypic heterogeneity in the isogenic microbial population enabling a subset of the population to survive under stress. In a recent study, a mycobacterial population of M. smegmatis was shown to develop phenotypic heterogeneity under nutrient depletion. The observed heterogeneity is in the form of a bimodal distribution of the expression levels of the Green Fluorescent Protein (GFP) as reporter with the gfp fused to the promoter of the rel gene. The stringent response pathway is initiated in the subpopulation with high rel activity.     

Nitrofurantoin prompts the stringent response in Bacillus subtilis

Nitrofurantoin causes the stringent response in Bacillus subtilis. After exposure of a stringent strain to this drug, the intracellular concentrations of guanosine 3'-diphosphate 5'-diphosphate (ppGpp), guanosine 3'-diphosphate 5'-triphosphate (pppGpp) and ATP increased, while that of GTP decreased. In a relaxed strain no accumulation of ppGpp or pppGpp was observed, but both GTP and ATP declined after the addition of nitrofurantoin. Protein synthesis was equally sensitive to nitrofurantoin in both the stringent and relaxed strains, but the drug inhibited RNA accumulation only in the stringent strain, not in the relaxed strain. Nitrofurantoin also caused the accumulation of ppGpp in Escherichia coli and Serratia marcescens.     

Revisiting the stringent response, ppGpp and starvation signaling

Microbial adaptation to environmental stress plays an important role in survival. It is necessary to understand the mechanisms underlying the survival of microbes under stress, as they may eventually aid in the successful control of the growth and persistence of these organisms. During nutrient starvation, Escherichia coli elicits a stringent response to conserve energy. The hallmark of the stringent response is the accumulation of guanosine tetra- (ppGpp) and pentaphosphates (pppGpp), which probably bind RNA polymerase to regulate gene expression at certain promoters. Recently, there has been renewed interest in the stringent responses of other microbes, with a view to correlating it with sporulation, virulence and long-term persistence.     

Polyphosphate and stress response in mycobacteria

Polyphosphate (poly P) is present in every living cell. Long considered a 'molecular fossil', its role in cell physiology has been neglected. However, in the last few years it has become clear that poly P plays a role in multiple physiological functions, the best characterized of which is rpoS and recA induction during the Escherichia coli stringent response. Sureka et al. in this issue of Molecular Microbiology investigate the role of poly P in mycobacterial stress response and describe its participation in a novel regulatory pathway involving the two-component system MprAB, the alternative sigma factor sigma(E) and Rel, the enzyme responsible for (p)ppGpp metabolism in mycobacteria.     

Positive feedback in aquatic ecosystems

Aquatic ecosystems offer striking examples of how positive feedback can be integral to the dynamics of complex communities. In particular, microorganisms (bacteria and protozoa) introduce a multitude of positive feedback pathways by rapidly recycling nutrients at the very base of many aquatic food webs. The relatively large magnitude of fluxes being shunted through this 'microbial loop' allows an accumulation of nutrients in localized areas, promotes a general build-up of biomass, and acts as a 'life-support system' in harsh environments. In contrast to customary notions which portray positive feedback effects as undesirable, a reassessment indicates that this 'bootstrapping' can often be advantageous for many organisms.     

Positive feedback circuits and memory

The concept of regulatory feedback circuit refers to oriented cyclic interactions between elements of a system. There are two classes of circuits, positive and negative, whose properties are in striking contrast. Positive circuits are a prerequisite for the occurrence of multiple steady states (multistationarity), and hence, they are involved in all processes showing hysteresis or memory. Endogenous or exogenous perturbations can lead the system to exhibit or to evoke one particular stable regime. The role of positive circuits in cell differentiation and in immunology is well documented. Negative circuits are involved in homeostatic regulation, with or without oscillations. The aim of this paper is to show: a) that positive circuits account for many features of memory stricto sensu (i.e., neural memory and mnesic evocation) as well as largo sensu (e.g. differentiation or immunological memory); and b) that simple combinations of positive and negative circuits provide powerful regulatory modules, which can also be associated in batteries. These entities have vast dynamical possibilities in the field of neurobiology, as well as in the fields of differentiation and immunology. Here we consider a universal minimal regulatory module, for which we suggest to adopt the term 'logical regulon', which can be considered as an atom of Jacob's integron. It comprises a positive and a negative circuit in its interaction matrix, and we recall the main results related to the simultaneous presence of these circuits. Finally, we give three applications of this type of interaction matrix. The first two deal with the coexistence of multiple stable steady states and periodicity in differentiation and in an immunological system showing hysteretic properties. The third deals with the dual problems of synchronization and desynchronization of a neural model for hippocampus memory evocation processes.     

Metabolic stringent response in intracellular stages of Leishmania

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The dormancy regulator DosR controls ribosome stability in hypoxic mycobacteria

It is thought that during latent infection, Mycobacterium tuberculosis bacilli are retained within granulomas in a low-oxygen environment. The dormancy survival (Dos) regulon, regulated by the response regulator DosR, appears to be essential for hypoxic survival in M. tuberculosis, but it is not known how the regulon promotes survival. Here we report that mycobacteria, in contrast to enteric bacteria, do not form higher-order structures (e.g. ribosomal dimers) upon entry into stasis. Instead, ribosomes are stabilized in the associated form (70S). Using a strategy incorporating microfluidic, proteomic, and ribosomal profiling techniques to elucidate the fate of mycobacterial ribosomes during hypoxic stasis, we show that the dormancy regulator DosR is required for optimal ribosome stabilization. We present evidence that the majority of this effect is mediated by the DosR-regulated protein MSMEG_3935 (a S30AE domain protein), which is associated with the ribosome under hypoxic conditions. A Δ3935 mutant phenocopies the ΔdosR mutant during hypoxia, and complementation of ΔdosR with the MSMEG_3935 gene leads to complete recovery of dosR mutant phenotypes during hypoxia. We suggest that this protein is named ribosome-associated factor under hypoxia (RafH) and that it is the major factor responsible for DosR-mediated hypoxic survival in mycobacteria.     

Positive feedback in cellular control systems

Feedback loops have been identified in a variety of regulatory systems and organisms. While feedback loops of the same type (negative or positive) tend to have properties in common, they can play distinctively diverse roles in different regulatory systems, where they can affect virulence in a pathogenic bacterium, maturation patterns of vertebrate oocytes and transitions through cell cycle phases in eukaryotic cells. This review focuses on the properties and functions of positive feedback in biological systems, including bistability, hysteresis and activation surges.