Sequence and arrangement of genes encoding sigma factors in Clostridium acetobutylicum ATCC 824

Expression of germination-related enzymes, CspA, CspB, CspC, SleC, and SleM, of Clostridium perfringens S40 in the mother cell compartment of sporulating cells

In Clostridium perfringens S40, spore germination-specific enzymes are synthesized during sporulation. Previous reports have demonstrated that two cortex-lytic enzymes, SleC and SleM, and a component of germination-specific protease, CspC, are located outside the cortex as an integral part of the dormant spore. In the present study, we examined the time and compartment of these enzymes' gene expression using reverse transcription-PCR (RT-PCR) and fluorescence microscopy on green fluorescence protein (GFP)-fused proteins. These results suggested that CspABC, SleC, and SleM are synthesized in the mother cell compartment of sporulating cells, probably at stages II approximately III of sporulation, and that the expression of cspABC genes is tricistronic.

Transcriptional program of early sporulation and stationary-phase events in Clostridium acetobutylicum

DNA microarray analysis of Clostridium acetobutylicum was used to examine the genomic-scale gene expression changes during the shift from exponential-phase growth and acidogenesis to stationary phase and solventogenesis. Self-organizing maps were used to identify novel expression patterns of functional gene classes, including aromatic and branched-chain amino acid synthesis, ribosomal proteins, cobalt and iron transporters, cobalamin biosynthesis, and lipid biosynthesis. The majority of pSOL1 megaplasmid genes (in addition to the solventogenic genes aad-ctfA-ctfB and adc) had increased expression at the onset of solventogenesis, suggesting that other megaplasmid genes may play a role in stationary-phase phenomena. Analysis of sporulation genes and comparison with published Bacillus subtilis results indicated conserved expression patterns of early sporulation genes, including spo0A, the sigF operon, and putative canonical genes of the sigma(H) and sigma(F) regulons. However, sigE expression could not be detected within 7.5 h of initial spo0A expression, consistent with the observed extended time between the appearance of clostridial forms and endospore formation. The results were compared with microarray comparisons of the wild-type strain and the nonsolventogenic, asporogenous M5 strain, which lacks the pSOL1 megaplasmid. While some results were similar, the expression of primary metabolism genes and heat shock proteins was higher in M5, suggesting a difference in metabolic regulation or a butyrate stress response in M5. The results of this microarray platform and analysis were further validated by comparing gene expression patterns to previously published Northern analyses, reporter assays, and two-dimensional protein electrophoresis data of metabolic genes (including all major solventogenesis genes), sporulation genes, heat shock proteins, and other solventogenesis-induced gene expression.

Initiation of endospore formation in Clostridium acetobutylicum

Endospore formation in bacilli and clostridia shows remarkable similarities in morphology as well as in physiological and molecular biological cellular events. Major differences are the formation of clostridial stage cells and granulose accumulation in clostridia. In both genera, a cascade of sigma factors is activated after septation (by help of sigma(H) and Spo0A approximately P) in the sequence sigma(F), sigma(E), sigma(G), and sigma(K). Of these, sigma(F) and sigma(G) are active inside the forespore and are regulated by anti-sigma factors and anti-anti-sigma factors, whereas sigma(E) and sigma(K) (mother cell-specific sigma factors) are synthesized as precursor proteins and activated by proteolysis. Each of these sigma factors allows transcription of a specific set of genes and operons, thus leading to the orchestral expression of stage-specific proteins required for successful sporulation. Both, the genetic organization of the respective operons and the expression pattern of the sigma factors are very similar in Bacillus subtilis and Clostridium acetobutylicum, the model organisms of the two genera. However, a major regulatory difference is found in initiation of endospore formation. Genome sequencing revealed that clostridia do not contain components of the so-called phosphorelay, with the exception of the essential transcription factor Spo0A. This might reflect recognition of different environmental signals, as for clostridia nutrient limitation is no prerequisite for sporulation. In contrast to Bacillus, the clostridial sigH gene is constitutively expressed at a low level, with no increase at the onset of spore formation. The spo0A gene in C. acetobutylicum is also constitutively expressed, but Spo0A synthesis only occurs during the early and mid-exponential growth phase, indicating a posttranscriptional or cotranslational regulation. Mutational studies revealed an important regulatory function of a dual palindrome region upstream of the spo0A gene of C. acetobutylicum, part of which overlaps with a Spo0A-binding site. In addition to controlling sporulation genes, phosphorylated clostridial Spo0A is involved in regulation of acetone and butanol synthesis.

Northern, morphological, and fermentation analysis of spo0A inactivation and overexpression in Clostridium acetobutylicum ATCC 824

The Clostridium acetobutylicum ATCC 824 spo0A gene was cloned, and two recombinant strains were generated, an spo0A inactivation strain (SKO1) and an spo0A overexpression strain [824(pMPSOA)]. SKO1 was developed by targeted gene inactivation with a replicative plasmid capable of double-crossover chromosomal integration--a technique never used before with solventogenic clostridia. SKO1 was severely deficient in solvent formation: it produced only 2 mM acetone and 13 mM butanol, compared to the 92 mM acetone and 172 mM butanol produced by the parental strain. After 72 h of growth on solid media, SKO1 formed long filaments of rod-shaped cells that failed to septate. SKO1 cells never achieved the swollen clostridial form typical of the parental strain and did not form endospores. No spo0A transcripts were detected in SKO1, while transcription of two solvent formation operons (aad-ctfA-ctfB and adc; both containing 0A boxes in their promoter regions) was limited. Strain 824(pMSPOA) produced higher butanol concentrations than the control strain [824(pIMP1)] and dramatically elevated spo0A transcript levels and displayed a bimodal pattern of spo0A transcription similar to that of B. subtilis. Microscopic studies indicated that sporulation was both enhanced and accelerated due to spo0A overexpression compared to that of both the 824(pIMP1) and parental strains. Consistent with that, expression of the key solvent formation genes (aad-ctfA-ctfB and adc) and three sporulation-specific genes (spoIIGA, sigE, and sigG) was observed earlier in strain 824(pMSPOA) than in the plasmid control. These data support the hypothesis that Spo0A is a transcriptional regulator that positively controls sporulation and solvent production. Its effect on solvent formation is a balancing act in regulating sporulation versus solvent gene expression: its overexpression apparently tips the balance in favor of accelerated and enhanced sporulation at the expense of overall solvent production.

Phylogeny and functional conservation of sigma(E) in endospore-forming bacteria

Conservation of the sporulation processes between Bacillus spp. and Clostridium spp. was investigated through evolutionary and complementation analyses of sigma(E). Alignment of partial predicted sigma(E) amino acid sequences from three Bacillus spp., Paenibacillus polymyxa and five Clostridium spp. revealed that amino acid residues previously reported to be involved in promoter utilization (M124, E119 and N120) and strand opening (C117) are conserved among all these species. Phylogenetic analyses of various sigma factor sequences from endospore-forming bacteria revealed that homologues of sigma(E), sigma(K) and sigma(G) clustered together regardless of genus, suggesting a common origin of sporulation sigma factors. The functional equivalence between Clostridium acetobutylicum sigma(E) and Bacillus subtilis sigma(E) was investigated by complementing a non-polar B. subtilis sigma(E) null mutant with the spoIIG operon from either B. subtilis (spoIIG(Bs)) or C. acetobutylicum (spoIIG(Ca)). Single-copy integration of spoIIG(Bs) into the amyE locus of the sigma(E) null mutant completely restored the wild-type sporulation phenotype, while spoIIG(Ca) only partially restored sporulation. Maximal expression of spoIIG(Ca)-lacZ occurred approximately 12 h later than maximal expression of spoIIG(Bs)-lacZ. Differences in temporal expression patterns for spoIIG(Ca) and spoIIG(Bs) in the B. subtilis background may at least partially explain the observed sporulation complementation phenotypes. This study suggests a common phylogenetic ancestor for sigma(E) in Bacillus spp. and Clostridium spp., although regulation of sigma(E) expression may differ in these two genera.

Two-dimensional gel electrophoresis separation and N-terminal sequence analysis of proteins from Clostridium pasteurianum W5

Proteins from Clostridium pasteurianum were separated by two-dimensional gel electrophoresis. Amino-terminal sequence determination and sequence analysis allowed the identification of 20 proteins, while 11 protein sequences remained unidentified and one protein appeared to have a blocked amino terminus.

Sporulation and time course expression of sigma-factor homologous genes in Clostridium acetobutylicum

The gene for the vegetative sigma factor A of Clostridium acetobutylicum was constitutively transcribed during growth and formed an operon together with dnaE. Sporulation-specific sigma factors E, G, and K were sequentially induced shortly before mature endospores could be detected. Maximal transcription in the course of spore formation was found to be in the order sigE-sigG-sigK, thus matching the pattern described for Bacillus subtilis. From primer extension experiments promoter structures could be deduced with high homology to the Bacillus consensus. Upstream of the spoIIGA-sigE operon a gene with significant similarity to ftsZ could be detected.

Identification and characterization of sporulation-dependent promoters upstream of the enterotoxin gene (cpe) of Clostridium perfringens

Three promoter sites (P1, P2, and P3) responsible for the sporulation-associated synthesis of Clostridium perfringens enterotoxin, a common cause of food poisoning in humans and animals, were identified. Nested and internal deletions of the cpe promoter region were made to narrow down the location of promoter elements. To measure the effects of the deletions on the expression of cpe, translational fusions containing the promoter deletions were made with the gusA gene of Escherichia coli, which codes for beta-glucuronidase; E. coli-C. perfringens shuttle vectors carrying the fusions were introduced into C. perfringens by electroporation. In addition, in vitro transcription assays were performed with the cpe promoter region as the DNA template for extracts made from sporulating cells. DNA sequences upstream of P1 were similar to consensus SigK-dependent promoters, while P2 and P3 were similar to consensus SigE-dependent promoters. SigE and SigK are sporulation-associated sigma factors known to be active in the mother cell compartment of sporulating cells of Bacillus subtilis, the same compartment in which enterotoxin is synthesized in C. perfringens.

Physiology of carbohydrate to solvent conversion by clostridia

The solvent-forming clostridia have attracted interest because of their ability to convert a range of carbohydrates to end-products such as acetone, butanol and ethanol. Polymeric substrates such as cellulose, hemicellulose and starch are degraded by extracellular enzymes. The majority of cellulolytic clostridia, typified by Clostridium thermocellum, produce a multi-enzyme cellulase complex in which the organization of components is critical for activity against the crystalline substrate. A variety of enzymes involved in degradation of hemicellulose and starch have been identified in different strains. The products of degradation, and other soluble substrates, are accumulated via membrane-bound transport systems which are generally poorly characterized. It is clear, however, that the phosphoenolpyruvate-dependent phosphotransferase system (PTS) plays a major role in solute uptake in several species. Accumulated substrates are converted by intracellular enzymes to end-products characteristic of the organism, with production of ATP to support growth. The metabolic pathways have been described, but understanding of mechanisms of regulation of metabolism is incomplete. Synthesis of extracellular enzymes and membrane-bound transport systems is commonly subject to catabolite repression in the presence of a readily metabolized source of carbon and energy. While many genes encoding cellulases, xylanases and amylases have been cloned and sequenced, little is known of control of their expression. Although the mechanism of catabolite repression in clostridia is not understood, some recent findings implicate a role for the PTS as in other low G-C Gram-positive bacteria. Emphasis has been placed on describing the mechanisms underlying the switch of C. acetobutylicum fermentations from acidogenic to solventogenic metabolism at the end of the growth phase. Factors involved include a lowered pH and accumulation of undissociated butyric acid, intracellular concentration of ATP and reduced pyridine nucleotides, nutrient limitation, and the interplay between pathways of carbon and electron flow. Genes encoding enzymes of solvent pathways have been cloned and sequenced, and their expression correlated with the pattern of end-product formation in fermentations. There is evidence that the initiation of solvent formation may be subject to control mechanisms similar to other stationary-phase phenomena, including sporulation. The application of recently developed techniques for genetic manipulation of the bacterium is improving understanding of the regulatory circuits, but a complete molecular description of the control of solvent formation remains elusive. Experimental manipulation of the pathways of electron flow in other species has been shown to influence the range and yield of fermentation end-products. Acid-forming clostridia can, under appropriate conditions, be induced to form atypical solvents as products. While the mechanisms of regulation of gene expression are not at all understood, the capacity to adapt in this way further illustrates the metabolic flexibility of clostridial strains.

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

Intercellular communication is a crucial phenomenon during spore development in Bacillus subtilis. It couples the establishment of a compartment-specific genetic program to the transcriptional activity of a sigma factor in the other compartment. It also keeps sigma factor activation in register with the morphological process. This study used directed mutagenesis to analyse the pathway that couples sigma E activation in the mother-cell to activation of sigma F in the forespore following asymmetric septation. Targets for mutagenesis in SpoIIGA (the receptor) were chosen based on the predicted topology of the protein when associated with the cell membrane. The results showed that a residue near the N terminus (D6), predicted to be exposed outside the cell, is required for receptor activity, whereas the major extracellular loop (between membrane domains IV and V) is dispensable for function. In contrast, mutations in SpoIIR (the signal) that partially blocked protein release (but not membrane translocation) had no effect on signal transduction. These results do not rule out the possibility that uncharacterized molecules intervene in the signalling pathway that establishes the mother-cell-specific developmental program during the early stage of sporulation.

Sigma factor and sporulation genes in Clostridium

The genus Clostridium, represented by Gram-positive, anaerobic, spore-forming bacteria, is well known for its clinical importance and considerable biotechnological potential. Recently, evidence for a functional role of the transcription factors sigma A, sigma E, sigma G, and sigma K in this genus was provided by cloning and sequencing these genes from C. acetobutylicum. In C. kluyveri, a partially sequenced open reading frame was found to encode the N terminus of the putative sigma factor L with significant similarity to members of the sigma 54 family. The identification of sequences with high similarity to the Bacillus sigma F (C. acetobutylicum), sigma H (several clostridial species), and sigma D (C. thermocellum)-controlled consensus promoters renders the existence of these transcription factors in clostridia very likely. These data are in agreement with information obtained by RNA transcript mapping (sigma A, sigma H), heterologous DNA hybridization (sigma D, sigma H), and immuno characterization of purified proteins (sigma A) from various clostridial species. Thus, the picture emerges that a fundamental similarity exists at the genetic level between the regulation of various cellular responses, in particular sporulation, in the genera Bacillus and Clostridium. The different induction patterns of sporulation in Bacillus spp. (nutrient starvation) and many clostridial species (cessation of growth or exposure to oxygen in the presence of excess nutrients) are most interestingly not reflected in the general regulatory features of this developmental process.

The genetic engineering of microbial solvent production

Although the production of acetone and butanol by Clostridium strains was a thriving industrial fermentation process, it is no longer competitive with the chemical synthesis of solvents and has been discontinued. However, studies on the molecular biology of Clostridium strains suggest that genetic engineering for improved solvent production is feasible, and could result in the revival of the industrial fermentation process.