Symposium on bacterial spores: V. Germination and outgrowth: effect of inhibitors

Dormant bacterial spores encrypt a long-lasting transcriptional program to be executed during revival

Sporulating bacteria can retreat into long-lasting dormant spores that preserve the capacity to germinate when propitious. However, how the revival transcriptional program is memorized for years remains elusive. We revealed that in dormant spores, core RNA polymerase (RNAP) resides in a central chromosomal domain, where it remains bound to a subset of intergenic promoter regions. These regions regulate genes encoding for most essential cellular functions, such as rRNAs and tRNAs. Upon awakening, RNAP recruits key transcriptional components, including sigma factor, and progresses to express the adjacent downstream genes. Mutants devoid of spore DNA-compacting proteins exhibit scattered RNAP localization and subsequently disordered firing of gene expression during germination. Accordingly, we propose that the spore chromosome is structured to preserve the transcriptional program by halting RNAP, prepared to execute transcription at the auspicious time. Such a mechanism may sustain long-term transcriptional programs in diverse organisms displaying a quiescent life form.

Arginine dephosphorylation propels spore germination in bacteria

Bacterial spores can remain dormant for years but possess the remarkable ability to germinate, within minutes, once nutrients become available. However, it still remains elusive how such instant awakening of cellular machineries is achieved. Utilizing Bacillus subtilis as a model, we show that YwlE arginine (Arg) phosphatase is crucial for spore germination. Accordingly, the absence of the Arg kinase McsB accelerated the process. Arg phosphoproteome of dormant spores uncovered a unique set of Arg-phosphorylated proteins involved in key biological functions, including translation and transcription. Consequently, we demonstrate that during germination, YwlE dephosphorylates an Arg site on the ribosome-associated chaperone Tig, enabling its association with the ribosome to reestablish translation. Moreover, we show that Arg dephosphorylation of the housekeeping σ factor A (SigA), mediated by YwlE, facilitates germination by activating the transcriptional machinery. Subsequently, we reveal that transcription is reinitiated at the onset of germination and its recommencement precedes that of translation. Thus, Arg dephosphorylation elicits the most critical stages of spore molecular resumption, placing this unusual post-translational modification as a major regulator of a developmental process in bacteria.

The molecular timeline of a reviving bacterial spore

The bacterial spore can rapidly convert from a dormant to a fully active cell. Here we study this remarkable cellular transition in Bacillus subtilis and reveal the identity of the newly synthesized proteins throughout spore revival. Our analysis uncovers a highly ordered developmental program that correlates with the spore morphological changes and reveals the spatial and temporal molecular events fundamental to reconstruct a cell. As opposed to current knowledge, we found that translation takes place during the earliest revival event, termed germination, a process hitherto considered to occur without the need for any macromolecule synthesis. Furthermore, we demonstrate that translation is required for execution of germination and relies on the bona fide translational factors RpmE and Tig. Our study sheds light on the spore revival process and on the vital building blocks underlying cellular awakening, thereby paving the way for designing new antimicrobial agents to eradicate spore-forming pathogens.

•

We reveal the identity of the newly synthesized proteins throughout spore revival

•

We define the timeline of molecular events occurring during spore revival

•

Protein synthesis occurs during germination and is essential for its execution

•

RpmE and Tig are required for protein synthesis during germination

Potential use of inhibitors of bacteria spore germination in the prophylactic treatment of anthrax andClostridium difficile-associated disease

Spore germination is the first step in establishing Bacillus and Clostridium infections. Germination is triggered by the binding of small molecules by the resting spore. Subsequently, the activated spore secretes dipicolinic acid and calcium, the spore core is rehydrated and spore structures are degraded. Inhibition of any of the germination-related events will prevent development to the vegetative stage. Inhibition of spore germination has been studied intensively in the prevention of food spoilage. In this perspective, we propose that similar approaches could be used in the prophylactic control of Bacillus anthracis and Clostridium difficile infections. Inhibition of B. anthracis spore germination could protect military and first-line emergency personnel at high risk for anthrax exposure. Inhibition of C. difficile could prevent human C. difficile-associated disease during antibiotic treatment of immunocompromised patients.

Analysis of the action of compounds that inhibit the germination of spores of Bacillus species

AIMS

To determine the mechanism of action of inhibitors of the germination of spores of Bacillus species, and where these inhibitors act in the germination process.

METHODS AND RESULTS

Spores of various Bacillus species are significant agents of food spoilage and food-borne disease, and inhibition of spore germination is a potential means of reducing such problems. Germination of the following spores was studied: (i) wild-type B. subtilis spores; (ii) B. subtilis spores with a nutrient receptor variant allowing recognition of a novel germinant; (iii) B. subtilis spores with elevated levels of either the variant nutrient receptor or its wild-type allele; (iv) B. subtilis spores lacking all nutrient receptors and (v) wild-type B. megaterium spores. Spores were germinated with a variety of nutrient germinants, Ca2+-dipicolinic acid (DPA) and dodecylamine for B. subtilis spores, and KBr for B. megaterium spores. Compounds tested as inhibitors of germination included alkyl alcohols, a phenol derivative, a fatty acid, ion channel blockers, enzyme inhibitors and several other compounds. Assays used to assess rates of spore germination monitored: (i) the fall in optical density at 600 nm of spore suspensions; (ii) the release of the dormant spore's large depot of DPA; (iii) hydrolysis of the dormant spore's peptidoglycan cortex and (iv) generation of CFU from spores that lacked all nutrient receptors. The results with B. subtilis spores allowed the assignment of inhibitory compounds into two general groups: (i) those that inhibited the action of, or response to, one nutrient receptor and (ii) those that blocked the action of, or response to, several or all of the nutrient receptors. Some of the compounds in groups 1 and 2 also blocked action of at least one cortex lytic enzyme, however, this does not appear to be the primary site of their action in inhibiting spore germination. The inhibitors had rather different effects on germination of B. subtilis spores with nutrients or non-nutrients, consistent with previous work indicating that germination of B. subtilis spores by non-nutrients does not involve the spore's nutrient receptors. In particular, none of the compounds tested inhibited spore germination with dodecylamine, and only three compounds inhibited Ca2+-DPA germination. In contrast, all compounds had very similar effects on the germination of B. megaterium spores with either glucose or KBr. The effects of the inhibitors tested on spores of both Bacillus species were largely reversible.

CONCLUSIONS

This work indicates that inhibitors of B. subtilis spore germination fall into two classes: (i) compounds (most alkyl alcohols, N-ethylmaleimide, nifedipine, phenols, potassium sorbate) that inhibit the action of, or response to, primarily one nutrient receptor and (ii) compounds [amiloride, HgCl2, octanoic acid, octanol, phenylmethylsulphonylfluoride (PMSF), quinine, tetracaine, tosyl-l-arginine methyl ester, trifluoperazine] that inhibit the action of, or response to, several nutrient receptors. Action of these inhibitors, is reversible. The similar effects of inhibitors on B. megaterium spore germination by glucose or KBr indicate that inorganic salts likely trigger germination by activating one or more nutrient receptors. The lack of effect of all inhibitors on dodecylamine germination suggests that this compound stimulates germination by creating channels in the spore's inner membrane allowing DPA release.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work provides new insight into the steps in spore germination that are inhibited by various chemicals, and the mechanism of action of these inhibitors. The work also provides new insights into the process of spore germination itself.

Transcriptional responses during outgrowth of Bacillus subtilis endospores

The Bacillus subtilis 168 genome contains an array of alternative sigma factors, many of which play important roles in reprogramming expression during stress and sporulation. The role of the different sigma factors during outgrowth, when the germinated endospore is converted back to a vegetative cell, is less well characterized. The activity of the alternative sigma factors sigmaB, sigmaD and sigmaH during endospore outgrowth was analysed by Northern blotting and lacZ reporter assays. While sigmaD and sigmaH were transcriptionally active during outgrowth, sigmaB-dependent transcription was not observed until after the first cell division, when growth slowed. Using an IPTG-controllable copy of sigA, an optimal level of expression was required to maintain growth rate at the end of outgrowth. The genes encoding the putative extracytoplasmic function (ECF) sigma factors sigmaI, sigmaV, sigmaW, sigmaZ and YlaC were insertionally inactivated using pMUTIN4. These strains, together with sigM and sigX mutants, were tested to determine their role and measure their expression during endospore outgrowth. Transcripts or beta-galactosidase activity were observed for each of the ECF sigma factors early after germination. With the exception of MJH003 (sigM), which showed an exacerbated salt stress defect, inactivation of the ECF sigma factor genes did not affect outgrowth in the conditions tested.

Bacterial spores and chemical sporicidal agents

Bacterial spores are among the most resistant of all living cells to biocides, although the response depends on the stage of sporulation. The development of resistance to some agents such as chlorhexidine occurs much earlier in sporulation than does resistance to glutaraldehyde, which is a very late event. During germination or outgrowth or both, resistance is lost and the cells become as susceptible to biocides as nonsporulating bacteria. Mechanisms of spore resistance to, and the action of, biocides are discussed, and possible means of enhancing antispore activity are considered. The clinical and other uses of sporicidal and sporostatic chemical agents are described.

The use of inhibitors to identify early events during Bacillus megaterium KM spore germination

The germination response of spores of Bacillus megaterium KM, as measured by loss of A600, is more than 95% inhibited by 1 mM-HgCl2. Two Hg2+-sensitive sites (referred to as 'sites I and II') have been identified during germination. Site I represents a pre-commitment event and can be protected from HgCl2 by 50 mM-D-alanine, whereas site II represents a post-commitment event and is not D-alanine-protectable. At 1 mM-HgCl2, 25% of the spore population becomes committed to germinate, but an A600 loss of less than 5% occurs. In this system, loss of heat resistance was associated with commitment, whereas selective cortex hydrolysis, release of pyridine-2,6-dicarboxylic acid, Zn2+ and soluble peptidoglycan, as well as loss of refractility, were identified as post-commitment events. The commitment event was reversibly inhibited by several proteinase inhibitors and a membrane bulking agent. A model of spore germination based on these results is presented.

Inhibition of Bacillus subtilis spore germination by various hydrophobic compounds: demonstration of hydrophobic character of the L-alanine receptor site

L-Alanine-initiated germination of Bacillus subtilis spores was inhibited by various kinds of hydrophobic compounds. Good correlation of inhibitory effect with hydrophobicity of the compound was demonstrated by using regression analysis in which the hydrophobic character was expressed by the partition coefficient in an octyl alcohol-water system. The correlation coefficient for 20 alcohols was 0.959, and that for 19 miscellaneous compounds was 0.906. Regression lines of the alcohols and other hydrophobic compounds were almost identical, showing that hydrophobic interaction played an important role in inhibition. Diphenylamine was one of the most effective inhibitors examined. n-Octyl, n-nonyl, and n-decyl alcohols were the most effective alcohols. The mode of inhibition by diphenylamine and n-octyl alcohol was a "mixed type" (competitive plus noncompetitive type) with respect to L-alanine; that by D-alanine was competitive inhibition. Sites for diphenylamine, n-octyl alcohol, and D-alanine may have overlapped. Inhibition was reversible by washing; heat resistance, stainability, and germination rate of the washed spores remained unaltered. Thus, we confirmed that the inhibition may occur before the initial trigger reaction of germination and that it may be due to the interaction between a hydrophobic compound and a hydrophobic region closely associated with the L-alanine receptor site on the spore.

Germination and peptidoglycan solubilization in Bacillus megaterium spores

During initiation of Bacillus megaterium QM B1551 spore germination, trichloroacetic acid-soluble, nondialyzable peptidoglycan fragments with an average molecular weight of 20,000 were excreted. This solubilization of peptidoglycan was measured in vitro as the amount of trichloroacetic acid-soluble hexosamine released from a suspension of broken spores. HgC12, a potent inhibitor of initiation, had no effect on the in vitro solubilization of peptidoglycan. In vivo, HgC12 had no effect on peptidoglycan release from spores that had lost heat resistance, but HgC12 did block complete absorbance loss. These results suggest that mercury inhibits some reactions that normally occur before loss in heat resistance but not the subsequent peptidoglycan release, and mercury inhibits other reactions involved with complete absorbance loss.

Spores of microorganisms. XXVI. Synthetic activities of germinating spores of Bacillus cereus prevented from outgrowth

Spores of Bacillus cereus were germinated in a germination limited medium (GL-medium) which facilitates only germination but not the postgerminative development of spores. Under these conditions a limited protein synthesis occurs. However, this protein synthesis is stopped after a short time interval. The rate of synthesis of new proteins, as well as their total amount, is influenced by the length of the activation heat shock. Synthesis of the wall material continues for several hours and thick-walled cells with a changed ultrastructure are formed. Synthesis of the diaminopimelic acid (dap) containing material of the cell wall is sensitive to actinomycin D and relatively resistant to chloramphenicol. Similarly, protein synthesis is relatively chlorapmhenicol-resistant but is fully inhibited by azauracil or spiramycin. Whereas RNA formed in the control culture is partially decomposed after 30 min of incubation, chloramphenicol accelerates its synthesis and prevents its decay. Exudate components apparently stimulate synthesis of ribonucleic acid, proteins and the wall material. The 14-C-dap containing material released by prelabelled spores in the form of the exudate during the germination is not re-utilized by the spores germinated in the GL-medium. The results are discussed with respect to the atypical primary synthetic activities of spores under conditions when the postgerminative development is prevented and from the point of view of participation of the germination exudate during these syntheses.

Initiation of spore germination in Bacillus subtilis: relationship to inhibition of L-alanine metabolism

The inhibitory effects of anthranilic acid esters (methyl anthranilate and N-methyl anthranilate) on the l-alanine-induced initiation of spore germination was examined in Bacillus subtilis 168. Methyl anthranilate irreversibly inhibited alanine initiation by a competitive mechanism. In its presence, the inhibition could be reversed only by the combined addition of d-glucose, d-fructose, and K(+). Both l-alanine dehydrogenase and l-glutamate-pyruvate transaminase, enzymes which catalyze the first reaction in l-alanine metabolism, were competitively inhibited by methyl anthranilate. The K(i) values for germination initiation (0.053 mM) and of l-glutamate-pyruvate transaminase (0.068 mM) were similar, whereas that for l-alanine dehydrogenase (0.4 mM) was six to seven times higher. Since a mutant lacking l-alanine dehydrogenase activity germinated normally in l-alanine alone, it is speculated that the major pathway of l-alanine metabolism during initiation may be via transmination reaction.

The effect of temperature and of cetrimide on the rate of loss of refractility of spores of Bacillus megaterium

The rate of germination of spores of Bacillus megaterium at 30° is not significantly different from the rate at 37° but the onset of germination is delayed; outgrowth is normal. At 45° germination of some spores occurs but the rate is much slower than at 37°, and there is no lag; emergence occurs from only a proportion of the germinated spores and after 3 or 4 vegetative cells have been produced, replication ceases. A single regression equation can represent the germination rate of the spores at 37° in the presence of from 0.0005 to 0.02% w/v of cetrimide and in its absence. In 0.0005% w/v of cetrimide, germ cells emerge from some of the germinated spores but many of them become swollen and disintegrate. Concentrations of 0.00125% w/v or more progressively inhibit swelling and completely inhibit emergence.