Physiological responses of Bacteroides and Clostridium strains to environmental stress factors

Genome-Wide Transcriptomic Analysis of n-Caproic Acid Production in Ruminococcaceae Bacterium CPB6 with Lactate Supplementation

n-Caproic acid (CA) is gaining increased attention due to its high value as a chemical feedstock. Ruminococcaceae bacterium strain CPB6 is an anaerobic mesophilic bacterium that is highly prolific in its ability to perform chain elongation of lactate to CA. However, little is known about the genome-wide transcriptional analysis of strain CPB6 for CA production triggered by the supplementation of exogenous lactate. In this study, cultivation of strain CPB6 was carried out in the absence and presence of lactate. Transcriptional profiles were analyzed using RNA-seq, and differentially expressed genes (DEGs) between the lactate-supplemented cells and control cells without lactate were analyzed. The results showed that lactate supplementation led to earlier CA p,roduction, and higher final CA titer and productivity. 295 genes were substrate and/or growth dependent, and these genes cover crucial functional categories. Specifically, 5 genes responsible for the reverse β-oxidation pathway, 11 genes encoding ATP-binding cassette (ABC) transporters, 6 genes encoding substrate-binding protein (SBP), and 4 genes encoding phosphotransferase system (PTS) transporters were strikingly upregulated in response to the addition of lactate. These genes would be candidates for future studies aiming at understanding the regulatory mechanism of lactate conversion into CA, as well as for the improvement of CA production in strain CPB6. The findings presented herein reveal unique insights into the biomolecular effect of lactate on CA production at the transcriptional level.

Sporulation in solventogenic and acetogenic clostridia

The Clostridium genus harbors compelling organisms for biotechnological production processes; while acetogenic clostridia can fix C1-compounds to produce acetate and ethanol, solventogenic clostridia can utilize a wide range of carbon sources to produce commercially valuable carboxylic acids, alcohols, and ketones by fermentation. Despite their potential, the conversion by these bacteria of carbohydrates or C1 compounds to alcohols is not cost-effective enough to result in economically viable processes. Engineering solventogenic clostridia by impairing sporulation is one of the investigated approaches to improve solvent productivity. Sporulation is a cell differentiation process triggered in bacteria in response to exposure to environmental stressors. The generated spores are metabolically inactive but resistant to harsh conditions (UV, chemicals, heat, oxygen). In Firmicutes, sporulation has been mainly studied in bacilli and pathogenic clostridia, and our knowledge of sporulation in solvent-producing or acetogenic clostridia is limited. Still, sporulation is an integral part of the cellular physiology of clostridia; thus, understanding the regulation of sporulation and its connection to solvent production may give clues to improve the performance of solventogenic clostridia. This review aims to provide an overview of the triggers, characteristics, and regulatory mechanism of sporulation in solventogenic clostridia. Those are further compared to the current knowledge on sporulation in the industrially relevant acetogenic clostridia. Finally, the potential applications of spores for process improvement are discussed.Key Points• The regulatory network governing sporulation initiation varies in solventogenic clostridia.• Media composition and cell density are the main triggers of sporulation.• Spores can be used to improve the fermentation process.

CRISPR-Cas9-Based Toolkit for Clostridium botulinum Group II Spore and Sporulation Research

The spores of Clostridium botulinum Group II strains pose a significant threat to the safety of modern packaged foods due to the risk of their survival in pasteurization and their ability to germinate into neurotoxigenic cultures at refrigeration temperatures. Moreover, spores are the infectious agents in wound botulism, infant botulism, and intestinal toxemia in adults. The identification of factors that contribute to spore formation is, therefore, essential to the development of strategies to control related health risks. Accordingly, development of a straightforward and versatile gene manipulation tool and an efficient sporulation-promoting medium is pivotal. Our strategy was to employ CRISPR-Cas9 and homology-directed repair (HDR) to replace targeted genes with mutant alleles incorporating a unique 24-nt "bookmark" sequence that could act as a single guide RNA (sgRNA) target for Cas9. Following the generation of the sporulation mutant, the presence of the bookmark allowed rapid generation of a complemented strain, in which the mutant allele was replaced with a functional copy of the deleted gene using CRISPR-Cas9 and the requisite sgRNA. Then, we selected the most appropriate medium for sporulation studies in C. botulinum Group II strains by measuring the efficiency of spore formation in seven different media. The most effective medium was exploited to confirm the involvement of a candidate gene in the sporulation process. Using the devised sporulation medium, subsequent comparisons of the sporulation efficiency of the wild type (WT), mutant and "bookmark"-complemented strain allowed the assignment of any defective sporulation phenotype to the mutation made. As a strain generated by complementation with the WT gene in the original locus would be indistinguishable from the parental strain, the gene utilized in complementation studies was altered to contain a unique "watermark" through the introduction of silent nucleotide changes. The mutagenesis system and the devised sporulation medium provide a solid basis for gaining a deeper understanding of spore formation in C. botulinum, a prerequisite for the development of novel strategies for spore control and related food safety and public health risk management.

Oxygen-mediated growth enhancement of an obligate anaerobic archaeon Thermococcus onnurineus NA1

Thermococcus onnurineus NA1, an obligate anaerobic hyperthermophilic archaeon, showed variable oxygen (O₂) sensitivity depending on the types of substrate employed as an energy source. Unexpectedly, the culture with yeast extract as a sole energy source showed enhanced growth by 2-fold in the presence of O₂. Genome-wide transcriptome analysis revealed the upregulation of several antioxidant-related genes encoding thioredoxin peroxidase (TON_0862), rubrerythrin (TON_0864), rubrerythrin-related protein (TON_0873), NAD(P)H rubredoxin oxidoreductase (TON_0865), or thioredoxin reductase (TON_1603), which can couple the detoxification of reactive oxygen species with the regeneration of NAD(P)⁺ from NAD(P)H. We present a plausible mechanism by which O₂ serves to maintain the intracellular redox balance. This study demonstrates an unusual strategy of an obligate anaerobe underlying O₂-mediated growth enhancement despite not having heme-based or cytochrome-type proteins.

The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis

Endospores formed by Bacillus subtilis are encased in a tough protein shell known as the coat, which consists of at least 70 different proteins. We investigated the process of spore coat morphogenesis using a library of 40 coat proteins fused to green fluorescent protein and demonstrate that two successive steps can be distinguished in coat assembly. The first step, initial localization of proteins to the spore surface, is dependent on the coat morphogenetic proteins SpoIVA and SpoVM. The second step, spore encasement, requires a third protein, SpoVID. We show that in spoVID mutant cells, most coat proteins assembled into a cap at one side of the developing spore but failed to migrate around and encase it. We also found that SpoIVA directly interacts with SpoVID. A domain analysis revealed that the N-terminus of SpoVID is required for encasement and is a structural homologue of a virion protein, whereas the C-terminus is necessary for the interaction with SpoIVA. Thus, SpoVM, SpoIVA and SpoVID are recruited to the spore surface in a concerted manner and form a tripartite machine that drives coat formation and spore encasement.

O2 and reactive oxygen species detoxification complex, composed of O2-responsive NADH:rubredoxin oxidoreductase-flavoprotein A2-desulfoferrodoxin operon enzymes, rubperoxin, and rubredoxin, in Clostridium acetobutylicum

Clostridium acetobutylicum, an obligate anaerobe, grows normally under continuous-O(2)-flow culture conditions, where the cells consume O(2) proficiently. An O(2)-responsive NADH:rubredoxin oxidoreductase operon composed of three genes (nror, fprA2, and dsr), encoding NROR, functionally uncharacterized flavoprotein A2 (FprA2), and the predicted superoxide reductase desulfoferrodoxin (Dsr), has been proposed to participate in defense against O(2) stress. To functionally characterize these proteins, native NROR from C. acetobutylicum, recombinant NROR (rNROR), FprA2, Dsr, and rubredoxin (Rd) expressed in Escherichia coli were purified. Purified native NROR and rNROR both exhibited weak H(2)O(2)-forming NADH oxidase activity that was slightly activated by Rd. A mixture of NROR, Rd, and FprA2 functions as an efficient H(2)O-forming NADH oxidase with a high affinity for O(2) (the K(m) for O(2) is 2.9 +/- 0.4 microM). A mixture of NROR, Rd, and Dsr functions as an NADH-dependent O(2)(-) reductase. A mixture of NROR, Rd, and rubperoxin (Rpr, a rubrerythrin homologue) functions as an inefficient H(2)O-forming NADH oxidase but an efficient NADH peroxidase with a low affinity for O(2) and a high affinity for H(2)O(2) (the K(m)s for O(2) and H(2)O(2) are 303 +/- 39 microM and <or=1 microM, respectively). A gene encoding Rd is dicistronically transcribed with a gene encoding a glutaredoxin (Gd) homologue, and the expression levels of the genes encoding Gd and Rd were highly upregulated upon exposure to O(2). Therefore, nror operon enzymes, together with Rpr, efficiently function to scavenge O(2), O(2)(-), and H(2)O(2) by using an O(2)-responsive rubredoxin as a common electron carrier protein.

Adaptive responses to oxygen stress in obligatory anaerobes Clostridium acetobutylicum and Clostridium aminovalericum

Clostridium acetobutylicum and Clostridium aminovalericum, both obligatory anaerobes, grow normally after growth conditions are changed from anoxic to microoxic, where the cells consume oxygen proficiently. In C. aminovalericum, a gene encoding a previously characterized H2O-forming NADH oxidase, designated noxA, was cloned and sequenced. The expression of noxA was strongly upregulated within 10 min after the growth conditions were altered to a microoxic state, indicating that C. aminovalericum NoxA is involved in oxygen metabolism. In C. acetobutylicum, genes suggested to be involved in oxygen metabolism and genes for reactive oxygen species (ROS) scavenging were chosen from the genome database. Although no clear orthologue of C. aminovalericum NoxA was found, Northern blot analysis identified many O2-responsive genes (e.g., a gene cluster [CAC2448 to CAC2452] encoding an NADH rubredoxin oxidoreductase-A-type flavoprotein-desulfoferrodoxin homologue-MerR family-like protein-flavodoxin, an operon [CAC1547 to CAC1549] encoding a thioredoxin-thioredoxin reductase-glutathione peroxidase-like protein, an operon [CAC1570 and CAC1571] encoding two glutathione peroxidase-like proteins, and genes encoding thiol peroxidase, bacterioferritin comigratory proteins, and superoxide dismutase) whose expression was quickly and synchronously upregulated within 10 min after flushing with 5% O2. The corresponding enzyme activities, such as NAD(P)H-dependent peroxide (H2O2 and alkyl hydroperoxides) reductase, were highly induced, indicating that microoxic growth of C. acetobutylicum is associated with the expression of a number of genes for oxygen metabolism and ROS scavenging.

Identification of O2-induced peptides in an obligatory anaerobe, Clostridium acetobutylicum

Clostridium acetobutylicum DSM792 (=ATCC824), a solvent producing obligate anaerobe, grew well after a shift in growth conditions from anoxic to microoxic at the mid exponential phase. In two-dimensional gel electrophoresis, a spot migrating at 45 kDa and three spots at 23 kDa accumulated after 30 min of flushing with 5% O(2)/95% N(2). Based on peptide mass fingerprints, the 45 kDa polypeptide was determined to be NP_347663 (A-type flavoprotein homologue) and the 23 kDa polypeptides were determined to be NP_350180 or NP_350181 (novel type rubrerythrin homologue). Northern blot analysis indicated that the expressions of these peptide transcripts were upregulated within 10 min after flushing with 5% O(2)/95% N(2).

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.

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.

Cloning and sequencing of a chromosomal fragment from Clostridium acetobutylicum strain ABKn8 conferring chemical-damaging agents and UV resistance to E. coli recA strains

A 3.3-kb DNA fragment of Clostridium acetobutylicum conferred methyl methane sulfonate (MMS), mitomycin C (MC), and UV resistance to recA strains of E. coli when cloned on the pUC19 plasmid. Analysis of the nucleotide sequence of the total insert and results of in vitro transcription-translation experiments showed that the insert directed the synthesis of three polypeptides referred to as ORFa, ORFb, and ORFc of 23.6, 15.3, and 21 kDa, respectively. None of the polypeptides presented a relationship with the RecA protein of E. coli or products of genes involved in the SOS response. The deduced amino acid sequence of ORFb and ORFc are highly homologous to those deduced from two genes specifying resistance to tellurium salts present on plasmid pMER610 harbored by Alcaligenes sp.strains and to an AMP-binding protein (CABP1) found in Dictyostelium discoideum. The existence of these homologous proteins suggests that they may perform a similar key function in the three unrelated organisms.

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.

Microbial stress proteins

There is general agreement that a function, perhaps the major function, of stress proteins under normal physiological conditions is to help assembly and disassembly of protein complexes and to catalyse protein-translocation processes. It remains unclear, however, as to what role these processes play in stressed cells. It could be that cells under stress produce abnormal, misfolded or otherwise damaged proteins and that increased synthesis of stress proteins is required to counter protein modifications. A role for stress proteins in recovery of cells from stress, as opposed to a role in helping cells to withstand a lethal stress, is thus suggested. The intracellular location of stress proteins, in the unstressed and stressed cell, is worthy of further studies. Members of the hsp70 family are associated with the cytosol, mitochondria and endoplasmic reticulum. There is evidence, particularly from studies on mammalian cells (Tanguay, 1985; Welch and Mizzen, 1988; Arrigo et al., 1988), that following stress hsps migrate to various cellular compartments and subsequently delocalize after stress. However, there is little comparable data from microbial systems for this phenomenon (e.g. Rossi and Lindquist, 1989). The question as to the role of stress proteins in the transient acquisition of thermotolerance remains to be answered. It is insufficient to equate the kinetics of stress-protein synthesis with acquisition of thermotolerance. Quantitative data on the amount of stress protein present at various times, including the recovery period, is required. The demonstration that microbial stress proteins are important antigenic determinants of micro-organisms causing major debilitating diseases in the world is an exciting observation. Studies on the interplay of pathogen and host, both carrying similar antigenic hsp determinants, will be a challenging area for future research. It is likely that E. coli and Sacch. cerevisiae, with their well-established biochemical and genetic properties, will continue to be the experimental systems of choice for studies on stress proteins. On the other hand, it is encouraging that studies on other micro-organisms have expanded in the past few years and have made substantial contributions towards our understanding of the stress response. The ubiquitous nature of the stress response and the remarkable evolutionary conservation of the stress proteins continue to be attractive areas for research.

The acetone-butanol-ethanol fermentation

Renewed interest in the acetone-butanol-ethanol (ABE) fermentation as a route for industrial production of butanol has been evident since the oil crisis of the 1970s. The present review includes an historical recap of the traditional industrial process and culturing practices useful in maintaining viable solvent-producing cultures, and then summarizes new and exciting research on the physiology and genetics of the microorganisms as well as process design. Most of these reports relate to improvements in solvent yield and the overall process, since traditional production is not efficient under present economic conditions. Conclusions are then made on future developments necessary for the establishment of an economically viable industrial process.

Cloning and expression in Escherichia coli of a recA-like gene from Bacteroides fragilis

The recombinant plasmid pHG100, containing a 5.2-kb DNA fragment from Bacteroides fragilis, complemented defects in homologous recombination, DNA repair and prophage induction to various levels in an Escherichia coli recA mutant strain. There was no DNA homology between the cloned B. fragilis recA-like gene and E. coli chromosomal DNA. pHG100 produced two proteins with Mr of approx. 39,000 and 37,000 which cross-reacted with antibodies raised against E. coli RecA protein. The production of these proteins was not increased after UV induction. The cloned B. fragilis recA-like gene product did not enhance the production of native but defective E. coli RecA protein after UV irradiation.