Mutational analysis of the early forespore/mother-cell signalling pathway in Bacillus subtilis

Channels modestly impact compartment-specific ATP levels during Bacillus subtilis sporulation and a rise in the mother cell ATP level is not necessary for Pro-σK cleavage

Starvation of Bacillus subtilis initiates endosporulation involving formation of mother cell (MC) and forespore (FS) compartments. During engulfment, the MC membrane migrates around the FS and protein channels connect the two compartments. The channels are necessary for postengulfment FS gene expression, which relieves inhibition of SpoIVFB, an intramembrane protease that cleaves Pro-σ^K , releasing σ^K into the MC. SpoIVFB has an ATP-binding domain exposed to the MC cytoplasm, but the role of ATP in regulating Pro-σ^K cleavage has been unclear, as has the impact of the channels on MC and FS ATP levels. Using luciferase produced separately in each compartment to measure relative ATP concentrations during sporulation, we found that the MC ATP concentration rises about twofold coincident with increasing cleavage of Pro-σ^K , and the FS ATP concentration does not decline. Mutants lacking a channel protein or defective in channel protein turnover exhibited modest and varied effects on ATP levels, which suggested that low ATP concentration does not explain the lack of postengulfment FS gene expression in channel mutants. Furthermore, a rise in the MC ATP level was not necessary for Pro-σ^K cleavage by SpoIVFB, based on analysis of mutants that bypass the need for relief of SpoIVFB inhibition.

RNA dynamics in aging bacterial spores

Upon starvation, the bacterium Bacillus subtilis enters the process of sporulation, lasting several hours and culminating in formation of a spore, the most resilient cell type known. We show that a few days following sporulation, the RNA profile of spores is highly dynamic. In aging spores incubated at high temperatures, RNA content is globally decreased by degradation over several days. This degradation might be a strategy utilized by the spore to facilitate its dormancy. However, spores kept at low temperature exhibit a different RNA profile with evidence supporting transcription. Further, we demonstrate that germination is affected by spore age, incubation temperature, and RNA state, implying that spores can acquire dissimilar characteristics at a time they are considered dormant. We propose that, in contrast to current thinking, entering dormancy lasts a few days, during which spores are affected by the environment and undergo corresponding molecular changes influencing their emergence from quiescence.

Vectorial signalling mechanism required for cell-cell communication during sporulation in Bacillus subtilis

Spore formation in Bacillus subtilis takes place in a sporangium consisting of two chambers, the forespore and the mother cell, which are linked by pathways of cell-cell communication. One pathway, which couples the proteolytic activation of the mother cell transcription factor σ(E) to the action of a forespore synthesized signal molecule, SpoIIR, has remained enigmatic. Signalling by SpoIIR requires the protein to be exported to the intermembrane space between forespore and mother cell, where it will interact with and activate the integral membrane protease SpoIIGA. Here we show that SpoIIR signal activity as well as the cleavage of its N-terminal extension is strictly dependent on the prespore fatty acid biosynthetic machinery. We also report that a conserved threonine residue (T27) in SpoIIR is required for processing, suggesting that signalling of SpoIIR is dependent on fatty acid synthesis probably because of acylation of T27. In addition, SpoIIR localization in the forespore septal membrane depends on the presence of SpoIIGA. The orchestration of σ(E) activation in the intercellular space by an acylated signal protein provides a new paradigm to ensure local transmission of a weak signal across the bilayer to control cell-cell communication during development.

Substrate specificity of SpoIIGA, a signal-transducing aspartic protease in Bacilli

SpoIIGA is a novel type of membrane-associated aspartic protease that responds to a signal from the forespore by cleaving Pro-σ(E) in the mother cell during sporulation of Bacillus subtilis. Very little is known about how SpoIIGA recognizes Pro-σ(E). By co-expressing proteins in Escherichia coli, it was shown that charge reversal substitutions for acidic residues 24 and 25 of Pro-σ(E), and for basic residues 245 and 284 of SpoIIGA, impaired cleavage. These results are consistent with a model predicting possible electrostatic interactions between these residues; however, no charge reversal substitution for residue 245 or residue 284 of SpoIIGA restored cleavage of Pro-σ(E) with a charge reversal substitution for residue 24 or residue 25. Bacillus subtilis SpoIIGA cleaved Pro-σ(E) orthologs from Bacillus licheniformis and Bacillus halodurans, but not from Bacillus cereus. A triple substitution in the pro-sequence of B. cereus Pro-σ(E) allowed cleavage by B. subtilis SpoIIGA, indicating that residues distal from the cleavage site contribute to substrate specificity. Co-expression of SpoIIGA and Pro-σ(E) orthologs in different combinations suggested that B. licheniformis SpoIIGA has a relatively narrow substrate specificity as compared with B. subtilis SpoIIGA, whereas B. cereus SpoIIGA and B. halodurans SpoIIGA appear to have broader substrate specificity.

Loss of compartmentalization of σ(E) activity need not prevent formation of spores by Bacillus subtilis

Compartmentalization of the activities of RNA polymerase sigma factors is a hallmark of formation of spores by Bacillus subtilis. It is initiated soon after the asymmetrically located sporulation division takes place with the activation of σ(F) in the smaller cell, the prespore. σ(F) then directs a signal via the membrane protease SpoIIGA to activate σ(E) in the larger mother cell by processing of pro-σ(E). Here, we show that σ(E) can be activated in the prespore with little effect on sporulation efficiency, implying that complete compartmentalization of σ(E) activity is not essential for spore formation. σ(E) activity in the prespore can be obtained by inducing transcription in the prespore of spoIIGA or of sigE*, which encodes a constitutively active form of σ(E), but not of spoIIGB, which encodes pro-σ(E). We infer that σ(E) compartmentalization is partially attributed to a competition between the compartments for the activation signaling protein SpoIIR. Normally, SpoIIGA is predominantly located in the mother cell and as a consequence confines σ(E) activation to it. In addition, we find that CsfB, previously shown to inhibit σ(G), is independently inhibiting σ(E) activity in the prespore. CsfB thus appears to serve a gatekeeper function in blocking the action of two sigma factors in the prespore: it prevents σ(G) from becoming active before completion of engulfment and helps prevent σ(E) from becoming active at all.

Evidence that the Bacillus subtilis SpoIIGA protein is a novel type of signal-transducing aspartic protease

The bacterium Bacillus subtilis undergoes endospore formation in response to starvation. sigma factors play a key role in spatiotemporal regulation of gene expression during development. Activation of sigma factors is coordinated by signal transduction between the forespore and the mother cell. sigma(E) is produced as pro-sigma(E), which is activated in the mother cell by cleavage in response to a signal from the forespore. We report that expression of SpoIIR, a putative signaling protein normally made in the forespore, and SpoIIGA, a putative protease, is necessary and sufficient for accurate, rapid, and abundant processing of pro-sigma(E) to sigma(E) in Escherichia coli. Modeling and mutational analyses provide evidence that SpoIIGA is a novel type of aspartic protease whose C-terminal half forms a dimer similar to the human immunodeficiency virus type 1 protease. Previous studies suggest that the N-terminal half of SpoIIGA is membrane-embedded. We found that SpoIIGA expressed in E. coli is membrane-associated and that after detergent treatment SpoIIGA was self-associated. Also, SpoIIGA interacts with SpoIIR. The results support a model in which SpoIIGA forms inactive dimers or oligomers, and interaction of SpoIIR with the N-terminal domain of SpoIIGA on one side of a membrane causes a conformational change that allows formation of active aspartic protease dimer in the C-terminal domain on the other side of the membrane, where it cleaves pro-sigma(E).

Sporulation phenotype of a Bacillus subtilis mutant expressing an unprocessable but active sigmaE transcription factor

SigmaE, a sporulation-specific sigma factor of Bacillus subtilis, is formed from an inactive precursor (pro-sigmaE) by a developmentally regulated processing reaction that removes 27 amino acids from the proprotein's amino terminus. A sigE variant (sigE335) lacking 15 amino acids of the prosequence is not processed into mature sigmaE but is active without processing. In the present work, we investigated the sporulation defect in sigE335-expressing B. subtilis, asking whether it is the bypass of proprotein processing or a residual inhibition of sigmaE activity that is responsible. Fluorescence microscopy demonstrated that sigE335-expressing B. subtilis progresses further into sporulation (stage III) than do strains lacking sigmaE activity (stage II). Consistent with its stage III phenotype, and a defect in sigmaE activity rather than its timing, the sigE335 allele did not disturb early sporulation gene expression but did inhibit the expression of late sporulation genes (gerE and sspE). The Spo- phenotype of sigE335 was found to be recessive to wild-type sigE. In vivo assays of sigmaE activity in sigE, sigE335, and merodiploid strains indicate that the residual prosequence on sigmaE335, still impairs its activity to function as a transcription factor. The data suggest that the 11-amino-acid extension on sigmaE335 allows it to bind RNA polymerase and direct the resulting holoenzyme to sigmaE-dependent promoters but reduces the enzyme's ability to initiate transcription initiation and/or exit from the promoter.

Tethering of the Bacillus subtilis sigma E proprotein to the cell membrane is necessary for its processing but insufficient for its stabilization

sigma(E), a sporulation-specific transcription factor of Bacillus subtilis, is synthesized as an inactive proprotein with a 27-amino acid extension at its amino terminus. This "pro" sequence is removed by a developmentally regulated protease, but when present, it blocks sigma(E) activity, tethers sigma(E) to the bacterium's cytoplasmic membrane, and promotes sigma(E) stability. To investigate whether pro-sigma(E) processing and/or stabilization are tied to membrane sequestration, we used fluorescent protein fusions to examine the membrane binding of SigE variants. The results are consistent with membrane association as a prerequisite for pro-sigma(E) processing but not as a sufficient cause for the proprotein's stability.

The Streptomyces coelicolor developmental transcription factor sigmaBldN is synthesized as a proprotein

bldN is one of a set of genes required for the formation of specialized, spore-bearing aerial hyphae during differentiation in the mycelial bacterium Streptomyces coelicolor. Previous analysis (M. J. Bibb et al., J. Bacteriol. 182:4606-4616, 2000) showed that bldN encodes a member of the extracytoplasmic function subfamily of RNA polymerase sigma factors and that translation from the most strongly predicted start codon (GTG(1)) would give rise to a sigma factor having an unusual N-terminal extension of ca. 86 residues. Here, by using a combination of site-directed mutagenesis and immunoblot analysis, we provide evidence that all bldN translation arises from initiation at GTG(1) and that the primary translation product is a proprotein (pro-sigma(BldN)) that is proteolytically processed to a mature species (sigma(BldN)) by removal of most of the unusual N-terminal extension. A time course taken during differentiation of the wild type on solid medium showed early production of pro-sigma(BldN) and the subsequent appearance of mature sigma(BldN), which was concomitant with aerial mycelium formation and the disappearance of pro-sigma(BldN). Two genes encoding members of a family of metalloproteases that are involved in the regulated proteolytic processing of transcription factors in other organisms were identified in the S. coelicolor genome, but their disruption did not affect differentiation or pro-sigma(BldN) processing.

Control of sigma factor activity during Bacillus subtilis sporulation

When starved, Bacillus subtilis undergoes asymmetric division to produce two cell types with different fates. The larger mother cell engulfs the smaller forespore, then nurtures it and, eventually, lyses to release a dormant, environmentally resistant spore. Driving these changes is a programme of transcriptional gene regulation. At the heart of the programme are sigma factors, which become active at different times, some only in one cell type or the other, and each directing RNA polymerase to transcribe a different set of genes. The activity of each sigma factor in the cascade is carefully regulated by multiple mechanisms. In some cases, novel proteins control both sigma factor activity and morphogenesis, co-ordinating the programme of gene expression with morphological change. These bifunctional proteins, as well as other proteins involved in sigma factor activation, and even precursors of sigma factors themselves, are targeted to critical locations, allowing the mother cell and forespore to communicate with each other and to co-ordinate their programmes of gene expression. This signalling can result in proteolytic sigma factor activation. Other mechanisms, such as an anti-sigma factor and, perhaps, proteolytic degradation, prevent sigma factors from becoming active in the wrong cell type. Accessory transcription factors modulate RNA polymerase activity at specific promoters. Negative feedback loops limit sigma factor production and facilitate the transition from one sigma factor to the next. Together, the mechanisms controlling sigma factor activity ensure that genes are expressed at the proper time and level in each cell type.

The Bacillus SpoIIGA protein is targeted to sites of spore septum formation in a SpoIIE-independent manner

The process of bacterial cell division involves the assembly of a complex of proteins at the site of septation that probably provides both the structural and the cytokinetic functions required for elaboration and closure of the septal annulus. During sporulation in Bacillus subtilis, this complex of proteins is modified by the inclusion of a sporulation-specific protein, SpoIIE, which plays a direct role in gene regulation and also has a genetically separable role in determining the gross structural properties of the specialized sporulation septum. We demonstrate by both green fluorescent protein (GFP) fusions and indirect immunofluorescence microscopy that SpoIIGA, a protein required for proteolytic cleavage of pro-sigmaE, is also targeted to the sporulation septum. Septal localization of SpoIIGA-GFP occurred even in the structurally abnormal septum formed by a SpoIIE null mutant. We also report the isolation of a spoIIGA homologue from Bacillus megaterium, a species in which the cells are significantly larger than those of B. subtilis. We have exploited the physical dimensions of the B. megaterium sporangium, in conjunction with wide-field deconvolution microscopy, to construct three-dimensional projections of sporulating cells. These projections indicate that SpoIIGA-GFP is initially localized in an annulus at the septal periphery and is only later localized uniformly throughout the septa. Localization was also detected in a B. subtilis spo0H null strain that fails to construct a spore septum. We propose that SpoIIGA is sequestered in the septum by an interaction with components of the septation machinery and that this interaction begins before the construction of the asymmetric septum.

Activation of the proprotein transcription factor pro-sigmaE is associated with its progression through three patterns of subcellular localization during sporulation in Bacillus subtilis

The activity of the sporulation transcription factor sigmaE in Bacillus subtilis is governed by an intercellular signal transduction pathway that controls the conversion of the inactive proprotein pro-sigmaE to the mature and active form of the factor. Here I use immunofluorescence microscopy to show that the activation of the proprotein is associated with its progression through three patterns of subcellular localization. In the predivisional sporangium, pro-sigmaE was found to be associated with the cytoplasmic membrane. Next, at the stage of asymmetric division, pro-sigmaE accumulated at the sporulation septum. Finally, after processing, mature sigmaE was found to be distributed throughout the mother cell cytoplasm. The results of subcellular fractionation and sedimentation in density gradients of extracts prepared from postdivisional sporangia confirmed that pro-sigmaE was chiefly present in the membrane fraction and that sigmaE was predominantly cytoplasmic, findings that suggest that the pro-amino acid sequence is responsible for the sequestration of pro-sigmaE to the membrane. The results of chemical cross-linking experiments showed that pro-sigmaE was present in a complex with its putative processing protein, SpoIIGA, or with a protein that depended on SpoIIGA. The membrane association of pro-sigmaE was, however, independent of SpoIIGA and other proteins specific to B. subtilis. Likewise, accumulation of pro-sigmaE at the septum did not depend on its interaction with SpoIIGA. Sequestration of pro-sigmaE to the membrane might serve to facilitate its interaction with SpoIIGA and may be important for preventing its premature association with core RNA polymerase. The implications of these findings for the compartmentalization of sigmaE are discussed.