bioRxiv Science⌕ Search

Biology subjects

Setlow, P.

Publications and source records attributed to Setlow, P..

10 recordsLinked to original sources

Pressure-induced membrane tension mechanically opens the germinant receptor GerA ion channel to trigger bacterial spore germination

High pressure (HP) can trigger bacterial spore germination, acting either through germinant receptors (GRs) or the SpoVA channel. However, the mechanism by which HP activates these membrane-embedded proteins remains elusive. Here, using Bacillus subtilis, we demonstrate that the GerA germinant receptor (GR) is the primary target of moderate HP (50-300 MPa). Mutagenesis reveals that pore-lining residues within the GerA ion channel are essential for the pressure response, whereas canonical ligand-binding and intramembrane signaling residues are dispensable. We then propose a s tretch- t o- o pen (STO) model, in which HP differentially compresses the more compliant inner membrane (IM) relative to the rigid spore core, generating lateral membrane tension that promotes opening of the GerA channel. In situ membrane tension measurements indicate HP-induced compression of IM phospholipids and elevated membrane tension. This tension-dependent gating is further supported by the pressure-dependent phenotypic rescue of GerA channel mutants. Consistently, HP increases IM permeability to water-soluble and membrane-impermeable agents (propidium iodide and formaldehyde), an effect potentiated by GerA, indicating concomitant opening of GerA by HP. Furthermore, modulating IM fluidity via heat activation or decoating altered membrane physical properties and delayed HP-induced germination, establishing the IM as the critical mechanical transducer. Additionally, computational modeling and calculations support faster compression of the IM than of the core under HP, rationalizing the source of tensile stress. Together, our findings establish a novel mechanism of HP-induced GerA activation via the STO model: HP compresses the IM, generates lateral tension, and promotes opening of the GerA ion channel to trigger bacterial spore germination.

microbiology↗

GerAB Residues Predicted to Interact with Water Based on MD Simulations Mediate Germinosome Stability in Bacillus subtilis spores

Some species in the Bacillales and Clostridiales orders form spores under unfavourable environmental conditions. These spores are metabolically dormant and highly resistant to extreme stress. The spore core--analogous to the protoplast of vegetative cells--contains only 25-45% water by wet weight, compared to ~80% in vegetative cells. Upon activation by small-molecule nutrients, spores germinate, restoring their core water content, restoring metabolism and becoming easy to kill, while progressing through outgrowth to vegetative growth. GerAB is the B subunit of the prototypical Bacillus subtilis GerA GR (germinant receptor), a membrane protein belonging to the Amino Acid--Polyamine-Organocation (APC) superfamily of transporters. It functions as the L-alanine sensor that initiates germination and was previously predicted, based on molecular dynamics (MD) simulations, to contain a putative water channel. Using MD simulations, we identified low amount of water permeating through GerAB (ranging from 1-121 water molecule/{micro}s in 10 parallel MD simulations), thus revealing a water pathway in GerAB that diverges from the L-alanine binding pocket, suggesting that water transport may play roles in germination beyond facilitating ligand binding. Analysis of water-residue contact frequencies identified eight hydrophilic residues lining this path. Individual substitution of high-contact residues with similarly sized non-polar residues impaired L-alanine germination and disrupted GerAB structural integrity as assessed by Western Blotting. These mutants also respond to the AGFK germinant mixture (L-asparagine, D-glucose, D-fructose and potassium) in slower, yet individually distinct kinetics compared to that of wt spores. These findings prove that water contact residues in GerAB predicted by MD simulations are crucial for the stability of this protein and thus the germinosome complex with all GRs.

microbiology↗

A mathematical kinetic model of memory in Bacillus subtilis spore germination

Dormant Bacillus subtilis spores germinate through interaction of germinants with germinant receptors (GRs). Subsequently, the activated GR signal is transduced to SpoVA proteins that constitute transport channels. The opening of the SpoVA channel then leads to calcium dipicolinic acid (CaDPA) release and then completion of spore germination. Spores are known to exhibit memory in germination, as spores given an initial short germinant pulse respond more readily to a second pulse. We have developed a mathematical model to identify a minimal reconstructed molecular network that is crucial for germination kinetics leading to memory of germinant exposure; the model reproduces experimental double germinant pulse germination curves. Analysis of the reconstructed network indicates that a minimal set of inactive and active GRs and a SpoVA channel in three states - closed inactive, closed active and open - is needed to reproduce memory. Spore germination memory is introduced in the network by the activation and deactivation rates of GRs, and by the interplay between activation of closed SpoVA channels and their rate of opening and closing. Author summaryDormant bacterial spores return to life in germination when exposed to germinants which are recognized by germinant receptors (GRs). Spores have memory of germinant exposure, such that more spores germinate after a 2nd germinant pulse than after the 1st one, if intervals between pulses are short. In this work, a mathematical model has been developed that reproduces experimental memory behavior. Computer simulations of the model reveal the crucial factors in spore memory of germinant exposure as: i) active and inactive GR states and ii) a membrane channel for a major spore core molecule, Ca-dipicolinic acid (CaDPA), with the channel existing in closed inactive, closed active and open states, all of which are indispensable for spore memory. The model will be part of an iterative cycle of modelling of network dynamics and generating hypotheses for further experimentation.

microbiology↗

Identification of key residues in water channel formation in the Bacillus subtilis germinant receptor protein GerAB

Some Bacillales and Clostridiales bacteria form spores in unfavorable environments. These spores are dormant but can rapidly resume metabolism in response to certain small molecule nutrients. This process is termed germination and can be initiated by a variety of low molecular wt nutrients termed germinants. Structural modeling and mutagenesis studies showed that GerAB, an inner membrane (IM) protein of the Bacillus subtilis spore germinant receptor (GR) GerA, is involved in L-alanine-initiated spore germination. A previous molecular simulation study also suggested there is a water channel in GerAB. In the current work, Steered Molecular Dynamics (SMD) simulations were employed to force a single water molecule through GerAB, identifying three key amino acid residues, Y97, L199 and F342, that interfere with water passage. When these residues were altered to alanine, L-alanine germination was minimal in spores with L199A, F342A and triA (Y97A, L199A and F342A triple mutant), while Y97A mutant spores germinated [~]61%. And besides Y97A, all other mutants showed compromised germination triggered by AGFK mixture. Western blotting found reduced levels of the GerA GR in the Y97A mutant, and an absence of the GerA GR in all other mutants. This proved that all three identified residues are crucial to the structural integrity of the GerAB protein and therefore probably the formation of the GR complex, the germinosome.

microbiology↗

Non-mechanical disruption of Bacillus subtilis spores allows sensitive and deep characterization of the minimal proteome for resuming a cellular lifestyle.

In response to extreme conditions, Bacillus subtilis generates highly resilient spores characterized by a unique multilayered structure. This confers resistance against various chemicals and enzymes yet adding complexity to the analysis of the spore proteome. As the first step in bottom-up proteomics, sample preparation poses a significant challenge. We assessed how an optimized protocol for sample preparation by easy extraction and digestion (SPEED) performed compared to previously established methods "One-pot" (OP) and single-pot, solid phase-enhanced sample-preparation (SP3) for the proteomic analysis of B. subtilis cell and spore samples. We found that SPEED outperformed both OP and SP3 in terms of peptides and proteins identified, moreover SPEED highly reproducibly quantified over 1000 proteins in limited input samples as low as 1 OD600 of B. subtilis cells and spores. SPEED was applied to analyze spore samples of different purity by applying sequential purification following harvesting of spores. Comparison of the differential abundance of proteins revealed clusters likely partially stemming from remaining vegetative cells in less purified spore samples. We show that ranking of absolute protein abundance in cellular and spore samples further enables us to rationally differentiate integral spore proteins from vegetative remnants. This is of importance in applications and organisms where highly homogenous spore samples are difficult to obtain. A deep proteomic analysis of spore and vegetative cell samples with the new approach led to the identification of 2447 proteins, 2273 of which were further quantified and compared between B. subtilis spores and cells. Our findings indicate that pathways related to peptidoglycan biosynthesis, glycolysis, carbon metabolism, and biosynthesis of secondary metabolites are shared between cells and spores. This corroborates and extends earlier work stressing that despite marked differences in their physiological states, spores preserve vegetative cell (core) proteins, essential for revival under conditions conducive to growth. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/584050v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@9ac7b1org.highwire.dtl.DTLVardef@1ac35c6org.highwire.dtl.DTLVardef@fe73a4org.highwire.dtl.DTLVardef@15a24e8_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Integrative metabolomics and proteomics allow the global intracellular characterization of Bacillus subtilis cells and spores.

Reliable and comprehensive multi-omics analysis is essential for researchers to understand and explore complex biological systems more completely. Bacillus subtilis is a model organism for Gram-positive spore-forming bacteria, and in-depth insight into the physiology and molecular basis of spore formation and germination in this organism requires advanced multilayer molecular datasets generated from the same sample. In this study, we evaluated two monophasic methods for polar and nonpolar compound extraction (acetonitrile/methanol/water; isopropanol/water, and 60% ethanol), and two biphasic methods (chloroform/methanol/water, and methyl tert-butyl ether/methanol/water) on coefficients of variation of analytes, identified metabolite composition and the quality of proteomics profiles. The analytical workflow comprises (1) parallel metabolite and protein extraction, (2) monophasic or biphasic sample extraction, (3) proteomics comparison and (4) multi-omics-based data visualization. The 60% EtOH protocol proved to be the easiest in sample processing and more amenable to automation. Collectively, we annotated 505 and 484 metabolites and identified 1665 and 1562 proteins in B. subtilis vegetative cells and spores, respectively. We also show differences between vegetative cells and spores from a multi-omics perspective and demonstrated that an integrative multi-omics analysis can be implemented from one sample using the 60% EtOH protocol. Correlation analysis further demonstrated that the metabolome and proteome datasets were highly correlated in content for components annotated to be part of the pyrimidine metabolism pathway. The results obtained by the 60% EtOH protocol provide a comprehensive insight into differences in the metabolic and protein makeup of B. subtilis vegetative cells and spores. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/545067v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@18b0206org.highwire.dtl.DTLVardef@1321433org.highwire.dtl.DTLVardef@cc5e6eorg.highwire.dtl.DTLVardef@14bac12_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Visualization of SpoVAEa protein dynamics in dormant spores of Bacillus cereus and dynamic changes in their germinosomes and SpoVAEa during germination

Bacillus cereus spores, like most Bacillus spores, can survive for years, germinate when their surroundings become suitable, and spore germination proteins play an important role in the initiation of germination. Because germinated spores lose dormant spores extreme resistance, information on the function of germination proteins could be useful in developing new strategies to control B. cereus spores. Prior work has shown that: i) the channel protein SpoVAEa exhibits high frequency movement in the outer leaflet of the inner membrane (IM) in dormant spores of B. subtilis; ii) the formation of the foci termed the germinosome between two germination proteins, the germinant receptor GerR and the scaffold protein GerD, in developing spores of B. cereus is slower than foci formation by GerR and GerD individually. However, the dynamics of movement of SpoVAEa in B. cereus spores, and the behaviour of the germinosome in B. cereus spore germination are unclear. In this study, we found that SpoVAEa fluorescent foci in dormant spores of B. cereus move on the IM, but slower than in B. subtilis spores, and likely colocalize transiently with GerD-mScarlet-I in the germinosome. Our results further indicate that: i) expression of GerR-SGFP2 and SpoVAEa-SGFP2 with GerD-mScarlet-I from a plasmid leads to more heterogeneity and lower efficiency of spore germination in B. cereus; and ii) germinosome foci observed by Fluorescence Resonance Energy Transfer (FRET) between GerR-SGFP2 and GerD-mScarlet-I b can be lost soon after the spore phase transition. However this is not always the case, as some GerR-SGFP2 foci and GerD-mScarlet-I foci continued to exist, colocalize, and even show a weak FRET signal. These data highlight the heterogeneous behaviour of spore germination protein complexes and indicate that some complexes may persist well beyond the initiation of germination. IMPORTANCEBacillus cereus is commonly present in soil and does harm to humans via contaminated food. In this study, we used B. cereus spores to investigate the movement of the spore-specific channel protein SpoVAEa, the interaction between SpoVAEa and the germinosome scaffold protein GerD, as well as the dynamics of a number of germination proteins in spore germination. Our results expand upon observations of the interactions between specific B. cereus spore germination proteins, in particular the GerR germinant receptor A, B and C subunits and GerD, as well as between SpoVAEa and GerD. The approaches used in this work could also be used to examine the interactions between GerD and SpoVAEa and other germination proteins in spores of other Bacillus species.

microbiology↗

Heat activation and inactivation of bacterial spores. Is there an overlap?

Heat activation at a sublethal temperature is widely applied to promote Bacillus species spore germination. This treatment also has potential to be employed in food processing to eliminate undesired bacterial spores by enhancing their germination, and then inactivating the less heat resistant germinated spores at a milder temperature. However, incorrect heat treatment could also generate heat damage in spores, and lead to more heterogeneous spore germination. Here, the heat activation and heat damage profile of Bacillus subtilis spores was determined by testing spore germination and outgrowth at both population and single spore levels. The heat treatments used were 40-80{degrees}C, and for 0-300 min. The results were as follows. 1) Heat activation at 40-70{degrees}C promoted L-valine and L-asparagine-glucose-fructose-potassium (AGFK) induced germination in a time dependent manner. 2) The optimal heat activation temperatures for AGFK and L-valine germination via the GerB plus GerK or GerA germinant receptors were 65 and 50-65{degrees}C, respectively. 3) Heat inactivation of dormant spores appeared at 70{degrees}C, and the heat damage of molecules essential for germination and growth began at 70 and 65{degrees}C, respectively. 4) Heat treatment at 75{degrees}C resulted in both activation of germination and damage to the germination apparatus, and 80{degrees}C treatment caused more pronounced heat damage. 5) For the spores that should withstand adverse environmental temperatures in nature, heat activation seems functional for a subsequent optimal germination process, while heat damage affected both germination and outgrowth.

microbiology↗

Organization and dynamics of the SpoVAEa protein, and its surrounding inner membrane lipids upon germination of Bacillus subtilis spores

The SpoVA proteins make up a channel in the inner membrane (IM) of B. subtilis spore. This channel responds to signals from activated germinant receptors (GRs), and allows release of Ca2+-DPA from the spore core during germination. In the current work, we studied the location and dynamics of SpoVAEa in dormant spores. Notably, the SpoVAEa-SGFP2 proteins were present in a single spot in spores, similar to the complex formed by all GRs. However, while the GRs spot remains in one location, the SpoVAEa-SGFP2 spot in the IM moved randomly with high frequency. The dynamics of the SpoVAEa-SGFP2 and its surrounding IM region as stained by fluorescent dyes were also tracked during spore germination, as the dormant spore IM appeared to have an immobile germination related functional microdomain. This microdomain disappeared around the time of appearance of a germinated spore, the loss of fluorescence of the IM by fluorescent dyes, as well as the appearance of SpoVAEa-SGFP2 peak fluorescent intensity occurred in parallel. These observed events were highly related to the rapid phase darkening, which is considered as the Ca2+DPA rapid release. We also tested the response of SpoVAEa and the IM to thermal treatments at 40-80{degrees}C. Heat treatment triggered an increase of green autofluorescence, which is speculated to be due to coat protein denaturation, and 80{degrees}C treatments induce the appearance of phase-grey-like spores. These spores presumably have a similar intracellular physical state as the phase grey spores detected in the germination but lack the functional proteins for further germination events.

microbiology↗

High resolution analysis of proteome dynamics during Bacillus subtilis sporulation

Bacillus subtilis vegetative cells switch to sporulation upon nutrient limitation. To investigate the proteome dynamics during sporulation, high resolution time-lapse proteomics was performed in a cell population that was induced to sporulate synchronously. Here, we are the first to comprehensively investigate the changeover of sporulation regulatory proteins, coat proteins and other proteins involved in sporulation and spore biogenesis. Protein co-expression analysis revealed four co-expressed modules (blue, brown, green and yellow). Modules brown and green are upregulated during sporulation and contain proteins associated with sporulation. Module blue, is negatively correlated with modules brown and green, and contained ribosomal and metabolic proteins. Finally, module yellow shows co-expression with the three other modules. Notably, several proteins not belonging to any of the known transcription regulons were identified as co-expressed with modules brown and green. We speculate that they may also play roles during sporulation. Finally, levels of some coat proteins, for example morphogenetic coat proteins, decreased late in sporulation. We speculate on their possible role in guiding or helping assembly of other coat proteins, after which they can be disposed of, but such a hypothesis remains to be experimentally addressed.

microbiology↗