Distinct clpP genes control specific adaptive responses in Bacillus thuringiensis

Molecular insights into the dynamic modulation of bacterial ClpP function and oligomerization by peptidomimetic boronate compounds

Bacterial caseinolytic protease P subunit (ClpP) is important and vital for cell survival and infectivity. Recent publications describe and discuss the complex structure-function relationship of ClpP and its processive activity mediated by 14 catalytic sites. Even so, there are several aspects yet to be further elucidated, such as the paradoxical allosteric modulation of ClpP by peptidomimetic boronates. These compounds bind to all catalytic sites, and in specific conditions, they stimulate a dysregulated degradation of peptides and globular proteins, instead of inhibiting the enzymatic activity, as expected for serine proteases in general. Aiming to explore and explain this paradoxical effect, we solved and refined the crystal structure of native ClpP from Staphylococcus epidermidis (Se), an opportunistic pathogen involved in nosocomial infections, as well as ClpP in complex with ixazomib at 1.90 Å and 2.33 Å resolution, respectively. The interpretation of the crystal structures, in combination with complementary biochemical and biophysical data, shed light on how ixazomib affects the ClpP conformational state and activity. Moreover, SEC-SAXS and DLS measurements show, for the first time, that a peptidomimetic boronate compound also induces the assembly of the tetradecameric structure from isolated homomeric heptameric rings of a gram-positive organism.

Identification of ClpP Dual Isoform Disruption as an Anti-sporulation Strategy for Clostridioides difficile

The Gram-positive bacterium Clostridioides difficile is a primary cause of hospital-acquired diarrhea, threatening both immunocompromised and healthy individuals. An important aspect of defining mechanisms that drive C. difficile persistence and virulence relies on developing a more complete understanding of sporulation. C. difficile sporulation is the single determinant of transmission and complicates treatment and prevention due to the chemical and physical resilience of spores. By extension, the identification of druggable targets that significantly attenuate sporulation would have a significant impact on thwarting C. difficile infection. Using a new CRISPR-Cas9 nickase genome editing methodology, stop codons were inserted early in the coding sequence for clpP1 and clpP2 to generate C. difficile mutants that no longer produced the corresponding isoforms of caseinolytic protease P (ClpP). The data show that genetic ablation of ClpP isoforms leads to altered sporulation phenotypes with the clpP1/clpP2 double mutant exhibiting asporogenic behavior. A small screen of known ClpP inhibitors in a fluorescence-based biochemical assay identified bortezomib as an inhibitor of C. difficile ClpP that produces dose-dependent inhibition of purified ClpP. Incubation of C. difficile cultures in the presence of bortezomib reveals anti-sporulation effects approaching that observed in the clpP1/clpP2 double mutant. This work identifies ClpP as a key contributor to C. difficile sporulation and provides compelling support for the pursuit of small molecule ClpP inhibitors as C. difficile anti-sporulating agents. IMPORTANCE Due to diverse roles of ClpP and the reliance of pathogens upon this system for infection, it has emerged as a target for antimicrobial development. Biology regulated by ClpP is organism-dependent and has not been defined in C. difficile. This work identifies ClpP as a key contributor to C. difficile sporulation and provides compelling support for the pursuit of small molecule ClpP inhibitors as anti-sporulating agents. The identification of new approaches and/or drug targets that reduce C. difficile sporulation would be transformative and are expected to find high utility in prophylaxis, transmission attenuation, and relapse prevention. Discovery of the ClpP system as a major driver to sporulation also provides a new avenue of inquiry for advancing the understanding of sporulation.

Loss of the ClpXP Protease Leads to Decreased Resistance to Cell-Envelope Targeting Antimicrobials in Bacillus anthracis Sterne

The ClpX ATPase is critical for resistance to cell envelope targeting antibiotics in Bacillus anthracis, however, it is unclear whether this is due to its function as an independent chaperone or as part of the ClpXP protease. In this study, we demonstrate that antibiotic resistance is due to formation of the ClpXP protease through construction of a ClpX complementation plasmid that is unable to interact with ClpP. Additionally, we genetically disrupted both clpP genes, clpP1 and clpP2, found in B. anthracis Sterne and find that the loss of either increases susceptibility to cell envelope targeting antimicrobials, although neither has as strong of a phenotype as loss of clpX and neither clpP gene is essential for virulence in a G. mellonella model of infection. Lastly, we looked at changes to cell envelope morphology that could contribute to increased antibiotic sensitivity. We find no difference in cell charge or cell lysis, although we do see increased hydrophobicity in the ΔclpX strain, decreased cellular density and slightly thinner cells walls. We also see significant cell division defects in ΔclpX, although only when cells are grown in the mammalian cell culture medium, RPMI. We conclude that the intrinsic resistance of B. anthracis to cell wall active antimicrobials is dependent on formation of the ClpXP protease and that this could be due, at least in part, to the role of ClpX in regulating cell envelope morphology.

Role of the ClpX from Corynebacterium crenatum involved in stress responses and energy metabolism

ClpX and ClpP are involved in many important functions, including stress responses and energy metabolism, in microorganisms. However, the ClpX and ClpP of microbes used in industrial scale have rarely been studied. Industrial bacterial fermentation experiences a variety of stresses, and energy metabolism is extremely important for industrial bacteria. Thus, the role played by the ClpX and ClpP of industrial bacteria in fermentation should be investigated. Most microorganisms have a single clpP gene, while Corynebacterium crenatum AS 1.542 possesses two clpPs. Herein, the clpX, clpP1, and clpP2 of C. crenatum were cloned, and its fusion protein was expressed and characterized. We also constructed clpX deletion mutant and complementation strain. Results indicate that ClpX serves an important function in thermal, pH, and ethanol stresses. It is also involved in NADPH synthesis and glucose consumption during fermentation.

Extreme variation in rates of evolution in the plastid Clp protease complex

Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi-subunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. TheclpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history ofclpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find thatclpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns andRNA-editing sites) within seed plants. AlthoughclpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genusSilene, which has highly elevated and heterogeneous rates ofclpP1 evolution. We confirmed thatclpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergentSilene species. Additionally, there is a tight correlation between amino acid substitution rates inclpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.

CerR, a Single-Domain Regulatory Protein of the LuxR Family, Promotes Cerecidin Production and Immunity in Bacillus cereus

Cerecidins are small lantibiotics from Bacillus cereus that were obtained using a semi-in vitro biosynthesis strategy and showed prominent antimicrobial activities against certain Gram-positive bacteria. However, the parental strain B. cereus As 1.1846 is incapable of producing cerecidins, most probably due to the transcriptional repression of the cerecidin gene cluster. Located in the cerecidin gene cluster, cerR encodes a putative response regulator protein that belongs to the LuxR family transcriptional regulators. CerR (84 amino acids) contains only a conserved DNA binding domain and lacks a conventional phosphorylation domain, which is rarely found in lantibiotic gene clusters. To investigate its function in cerecidin biosynthesis, cerR was constitutively expressed in B. cereus As 1.1846. Surprisingly, Constitutive expression of cerR enabled the production of cerecidins and enhanced self-immunity of B. cereus toward cerecidins. Reverse transcription-PCR analysis and electrophoresis mobility shift assays indicated, respectively, that the cer cluster was transcribed in two transcripts (cerAM and cerRTPFE) and that CerR regulated the cerecidin gene cluster directly by binding to the two predicted promoter regions of cerA and cerR DNase I footprinting experiments further confirmed that CerR specifically bound to the two promoter regions at a conserved inverted repeat sequence that was designated a CerR binding motif (cerR box). The present study demonstrated that CerR, as the first single-domain LuxR family transcriptional regulator, serves as a transcriptional activator in cerecidin biosynthesis and activates the cerecidin gene cluster, which was otherwise cryptic in B. cereusIMPORTANCE Lantibiotics with intriguing and prominent bioactivities are potential peptide antibiotics that could be applied in many areas, including food and pharmaceutical industries. The biosynthesis of lantibiotics is generally controlled by two-component regulatory systems consisting of histidine kinases and response regulators, while some unique and interesting regulatory systems are also revealed with the ever-increasing discovery of lantibiotic gene clusters among diverse microorganisms. Dissection of diverse lantibiotic regulation machineries would permit deep understanding of the biological functions of lantibiotics in different niches and even enable genetic activation of lantibiotic gene clusters that are otherwise cryptic. The significance of our study is to illuminate the regulatory mechanism of a special single-domain protein, CerR, in regulating cerecidin biosynthesis in Bacillus cereus, providing a possible novel approach to activate cryptic lantibiotic clusters.

YhgC protects Bacillus anthracis from oxidative stress

Bacillus anthracis can cause lethal inhalational anthrax and can be used as a bioweapon due to its ability to form spores and to survive under various environmental stress conditions. YhgC in bacilli are structural homologues of TRAP, a protein involved in stress response in staphylococci. To test the role of YhgC in B. anthracis, YhgC gene was deleted in B. anthracis strain Sterne and parent and mutant strains tested. Immunolocalization studies indicated that YhgC is clustered both on the cell surface and within the cytoplasm. Phenotypic analyses indicated that YhgC is an important factor for oxidative stress tolerance and for macrophage infection in vitro. Accordingly, transcriptomics studies indicated that yhgC has a profound effect on genes encoding for stress response regulatory proteins where it negatively regulates the expression of genes encoding for Class I and Class III stress response proteins belonging to the regulons hrcA (hrcA, grpE, dnaK, dnaJ, groEL and groES) and ctsR (ctsR, mcsA, mcsB, clpC/mecB, clpP1). Proteomics studies also indicated that YhgC positively regulates the expression of ClpP-2 and camelysin, which are proteins involved in adaptive responses and pathogenesis in various Gram-positive bacteria. Put together, these results suggest that YhgC is important for the survival of B. anthracis under oxidative stress conditions and thus inhibition of YhgC may compromise the ability of the bacteria to survive within the host.

Genetic evidence that multiple proteases are involved in modulation of heat-induced activation of the sigma factor SigI in Bacillus subtilis

The Bacillus subtilis sigI-rsgI operon encodes the heat-inducible sigma factor SigI and its cognate anti-sigma factor RsgI. The heat-activated SigI positively regulates expression of sigI itself and genes involved in cell wall homeostasis and heat resistance. It remains unknown which protease(s) may contribute to degradation of RsgI and heat-induced activation of SigI. In this study, we found that transcription of sigI from its σI-dependent promoter under heat stress was downregulated in a strain lacking the heat-inducible sigma factor SigB. Deletion of protease-relevant clpP, clpC or rasP severely impaired sigI expression during heat stress, whereas deletion of clpE partially impaired sigI expression. Complementation of mutations with corresponding intact genes restored sigI expression. In a null mutant of rsgI, SigI was activated and sigI expression was strongly upregulated during normal growth and under heat stress. In this rsgI mutant, further inactivation of rasP or clpE did not affect sigI expression, whereas further inactivation of clpP or clpC severely or partially impaired sigI expression. Spx negatively influenced sigI expression during heat stress. Possible implications are discussed. Given that clpC, clpP and spx are directly regulated by SigB, SigB appears to control sigI expression under heat stress via ClpC, ClpP and Spx.

Genome Sequence of Bacillus cereus Phage vB_BceS-MY192

Bacillus cereus is an opportunistic foodborne pathogen. The phage vB_BceS-MY192 was isolated from B. cereus 192 in a cooked rice sample. The temperate phage belongs to the Siphoviridae family, Caudovirales order. Here we announce the phage genome sequence and its annotation, which may expand the understanding of B. cereus siphophages.

A membrane transporter required for 3-hydroxybutyrate uptake during the early sporulation stage in Bacillus subtilis

Exogenous 3-hydroxybutyrate can be utilized by a variety of soil bacteria as a carbon and energy source. However, the membrane transporter responsible for 3-hydroxybutyrate uptake remains unidentified. The Bacillus subtilis strain 168 gene yxjC (herein renamed hbuT) encodes a putative gluconate transporter GntT-type membrane transporter with a previously unknown function. hbuT is organized within the same operon with genes that are used for metabolism of 3-hydroxybutyrate. Here we report that a null mutation of hbuT reduced uptake of 3-hydroxybutyrate by B. subtilis cells grown in nutrient sporulation medium. The SigE-controlled HbuT transporter apparently plays a major role in the uptake of 3-hydroxybutyrate. Uptake of 3-hydroxybutyrate by the HbuT transporter occurred in a specific manner at the early sporulation stage. SigE-controlled hbuT expression and 3-hydroxybutyrate uptake were also subject to CcpA-mediated glucose repression. hbuT expression was not induced by exogenous 3-hydroxybutyrate and B. subtilis cells could not utilize 3-hydroxybutyrate as a sole carbon source for growth. HbuT homologs are present in a wide variety of Gram-positive Bacillus species, some Gram-negative Acinetobacter species and a small group of other bacteria. This is the first tentative identification of a membrane transporter responsible for the uptake of 3-hydroxybutyrate in bacteria.

The two putative comS homologs of the biotechnologically important Bacillus licheniformis do not contribute to competence development

In Bacillus subtilis, natural genetic competence is subject to complex genetic regulation and quorum sensing dependent. Upon extracellular accumulation of the peptide-pheromone ComX, the membrane-bound sensor histidine kinase ComP initiates diverse signaling pathways by activating-among others-DegQ and ComS. While DegQ favors the expression of extracellular enzymes rather than competence development, ComS is crucial for competence development as it prevents proteolytic degradation of ComK, the key transcriptional activator of all genes required for the uptake and integration of DNA. In Bacillus licheniformis, ComX/ComP sensed cell density negatively influences competence development, suggesting differences from the quorum-sensing-dependent control mechanism in Bacillus subtilis. Here, we show that each of six investigated strains possesses both of two different, recently identified putative comS genes. When expressed from an inducible promoter, none of the comS candidate genes displayed an impact on competence development neither in B. subtilis nor in B. licheniformis. Moreover, disruption of the genes did not reduce transformation efficiency. While the putative comS homologs do not contribute to competence development, we provide evidence that the degQ gene as for B. subtilis negatively influences genetic competency in B. licheniformis.

Transcriptional regulation of the l-lactate permease gene lutP by the LutR repressor of Bacillus subtilis RO-NN-1

The Bacillus subtilis lutABC operon encodes three iron–sulfur-containing proteins required for l-lactate utilization and involved in biofilm formation. The transcriptional regulator LutR of the GntR family negatively controls lutABC expression. The lutP gene, which is situated immediately upstream of lutR, encodes an l-lactate permease. Here, we show that lutP expression can be strongly induced by l-lactate and is subject to partial catabolite repression by glucose. Disruption of the lutR gene led to a strong derepression of lutP and no further induction by l-lactate, suggesting that the LutR repressor can also negatively control lutP expression. Electrophoretic mobility shift assay revealed a LutR-binding site located downstream of the promoter of lutA or lutP and containing a consensus inverted repeat sequence 5′-TCATC-N1-GATGA-3′. Reporter gene analysis showed that deletion of each LutR-binding site caused a strong derepression of lutA or lutP. These results indicated that these two LutR-binding sites can function as operators in vivo. Moreover, deletion analysis identified a DNA segment upstream of the lutP promoter to be important for lutP expression. In contrast to the truncated LutR of laboratory strains 168 and PY79, the full-length LutR of the undomesticated strain RO-NN-1, and probably many other B. subtilis strains, can directly and negatively regulate lutP transcription. The absence or presence of the N-terminal 21 aa of the full-length LutR, which encompass a small part of the predicted winged helix–turn–helix DNA-binding motif, may probably alter the DNA-binding specificity or affinity of LutR.

The role of ClpP, RpoS and CsrA in growth and filament formation of Salmonella enterica serovar Typhimurium at low temperature

BACKGROUND

Salmonellae are food-borne pathogens of great health and economic importance. To pose a threat to humans, Salmonellae normally have to cope with a series of stressful conditions in the food chain, including low temperature. In the current study, we evaluated the importance of the Clp proteolytic complex and the carbon starvation protein, CsrA, for the ability of Salmonella Typhimurium to grow at low temperature.

RESULTS

A clpP mutant was severely affected in growth and formed pin point colonies at 10°C. Contrary to this, rpoS and clpP/rpoS mutants were only slightly affected. The clpP mutant formed cold resistant suppressor mutants at a frequency of 2.5 × 10(-3) and these were found not to express RpoS. Together these results indicated that the impaired growth of the clpP mutant was caused by high level of RpoS. Evaluation by microscopy of the clpP mutant revealed that it formed filamentous cells when grown at 10°C, and this phenotype too, disappered when rpoS was mutated in parallel indicating a RpoS-dependency. A csrA (sup) mutant was also growth attenuated a low temperature. An rpoS/csrA (sup) double mutant was also growth attenuated, indicating that the phenotype of the csrA mutant was independent from RpoS.

CONCLUSIONS

The cold sensitivity of clpP mutant was associated with increased levels of RpoS and probably caused by toxic levels of RpoS. Although a csrA mutant also accumulated high level of RpoS, growth impairment caused by lack of csrA was not related to RpoS levels in a similar way.

Contribution of ClpP to stress tolerance and virulence properties of Streptococcus mutans

Abilities to tolerate environmental stresses and to form biofilms on teeth surface are key virulence attributes of Streptococcus mutans, the primary causative agent of human dental caries. ClpP, the chief intracellular protease of S. mutans, along with ATPases degrades altered proteins that might be toxic for bacteria, and thus plays important roles in stress response. To further understand the roles of ClpP in stress response of S. mutans, a ClpP deficient strain was constructed and used for general stress tolerance, autolysis, mutacins production, and virulence assays. Here, we demonstrated that inactivation of ClpP in S. mutans resulted in a sensitive phenotype to several environmental stresses, including acid, cold, thermal, and oxidative stresses. The ClpP deficient strain displayed slow growth rates, poor growth yields, formation of long chains, increased clumping in broth, and reduced capacity to form biofilms in presence of glucose. Mutacins production and autolysis of S. mutans were also impaired by mutation of clpP. Animals study showed that clpP mutation increased virulence of S. mutans but not significant. However, enhanced abilities to survive lethal acid and to form biofilm in sucrose were observed in ClpP deficient strain. Our findings revealed a broad impact of ClpP on several virulence properties of S. mutans and highlighted the relevance of ClpP proteolysis with progression of diseases caused by S. mutans.

Involvement of OpcR, a GbsR-type transcriptional regulator, in negative regulation of two evolutionarily closely related choline uptake genes in Bacillus subtilis

The osmoprotectant glycine betaine can be generated intracellularly from conversion of the exogenous precursor choline by enzymes encoded by the gbsAB operon in Bacillus subtilis. Uptake of choline from outside B. subtilis cells is mediated through two evolutionarily closely related ATP-binding cassette transporters, OpuB and OpuC. Expression of the opuB operon and of the opuC operon is known to be osmoinducible. Here, we show that choline exerts a suppressive effect on opuC expression during normal growth and under osmotic stress. In the absence of the choline-responsive repressor GbsR, opuB expression is also suppressed by choline. We also report that a gene (formerly yvbF, now designated opcR) located immediately upstream of the opuC operon negatively regulates transcription of the opuC operon and, in the absence of GbsR, also that of the opuB operon. An inverted repeat (TTGTAAA-N8-TTTACAA) that overlaps with the -35 hexamer of the promoters of both operons has been identified as the OpcR operator. OpcR belongs to the GbsR-type transcriptional regulators. Its orthologues with unknown function are present in some other Bacillus species. Moreover, deletion analyses revealed that a region located further upstream of the promoters of the opuB operon and the opuC operon is critical for expression of both operons during normal growth and under osmotic stress. Osmotic induction of these two operons appears not to be OpcR mediated. OpcR is not a choline-responsive repressor. The possible biological role of OpcR is discussed.

Reexamining transcriptional regulation of the Bacillus subtilis htpX gene and the ykrK gene, encoding a novel type of transcriptional regulator, and redefining the YkrK operator

HtpX is an integral cytoplasmic membrane metalloprotease well conserved in numerous bacteria. A recent study showed that expression of the Bacillus subtilis htpX gene is under dual negative control by Rok and a novel type of transcriptional regulator, YkrK. Here we report that expression of the B. subtilis htpX gene is strongly heat inducible. Contrary to the previous prediction, ykrK expression has been found to be not subject to autoregulation. We have identified the htpX promoter and the authentic ykrK promoter, which is also distinct from the previously predicted one. We have redefined a conserved inverted repeat sequence to be the YkrK operator, which is somewhat different from the previously proposed one. We provide evidence that YkrK is not a substrate of HtpX and that heat induction of htpX is not YkrK mediated. We have also found that the absence of FtsH or HtpX alone did not impair B. subtilis cell viability on LB agar plates at high temperature, whereas the absence of both FtsH and HtpX caused a severe growth defect under heat stress. This finding supports the notion that FtsH and HtpX may have partially overlapping functions in heat resistance. Finally, we show that htpX expression is subject to transient negative control by sigB under heat stress in a Rok- and YkrK-independent manner. Triple negative control of htpX expression at high temperature by rok, sigB, and ykrK may help cells to prevent uncontrolled and detrimental oversynthesis of the HtpX protease.

AdeR, a PucR-type transcription factor, activates expression of L-alanine dehydrogenase and is required for sporulation of Bacillus subtilis

The Bacillus subtilis ald gene encodes L-alanine dehydrogenase, which catalyzes the NAD(+)-dependent deamination of L-alanine to pyruvate for the generation of energy and is required for normal sporulation. The transcription of ald is induced by alanine, but the mechanism underlying alanine induction remains unknown. Here we report that a gene (formerly yukF and now designated adeR) located upstream of ald is essential for the basal and alanine-inducible expression of ald. The disruption of the adeR gene caused a sporulation defect, whereas the complementation of an adeR mutation with an intact adeR gene restored the sporulation ability. adeR expression was not subject to autoregulation and alanine induction. Deletion and mutation analyses revealed that an inverted repeat, centered at position -74.5 relative to the transcriptional initiation site of ald, was required for ald expression and also likely served as a ρ-independent transcription terminator. Electrophoretic mobility shift assays showed that purified His-tagged AdeR was a specific DNA-binding protein and that this inverted repeat was required for AdeR binding. AdeR shows no significant amino acid sequence similarity to the known transcriptional activators of ald genes from other bacteria. AdeR appears to be a member of the PucR family of transcriptional regulators. Its orthologs of unknown function are present in some other Bacillus species. Collectively, these findings support the notion that AdeR is a transcriptional activator which mediates ald expression in response to alanine availability and is important for normal sporulation in B. subtilis.

How the insect pathogen bacteria Bacillus thuringiensis and Xenorhabdus/Photorhabdus occupy their hosts

Insects are the largest group of animals on earth. Like mammals, virus, fungi, bacteria and parasites infect them. Several tissue barriers and defense mechanisms are common for vertebrates and invertebrates. Therefore some insects, notably the fly Drosophila and the caterpillar Galleria mellonella, have been used as models to study host-pathogen interactions for several insect and mammal pathogens. They are excellent tools to identify pathogen determinants and host tissue cell responses. We focus here on the comparison of effectors used by two different groups of bacterial insect pathogens to accomplish the infection process in their lepidopteran larval host: Bacillus thuringiensis and the nematode-associated bacteria, Photorhabdus and Xenorhabdus. The comparison reveals similarities in function and expression profiles for some genes, which suggest that such factors are conserved during evolution in order to attack the tissue encountered during the infection process.

Validation of the essential ClpP protease in Mycobacterium tuberculosis as a novel drug target

Mycobacterium tuberculosis is a pathogen of major global importance. Validated drug targets are required in order to develop novel therapeutics for drug-resistant strains and to shorten therapy. The Clp protease complexes provide a means for quality control of cellular proteins; the proteolytic activity of ClpP in concert with the ATPase activity of the ClpX/ClpC subunits results in degradation of misfolded or damaged proteins. Thus, the Clp system plays a major role in basic metabolism, as well as in stress responses and pathogenic mechanisms. M. tuberculosis has two ClpP proteolytic subunits. Here we demonstrate that ClpP1 is essential for viability in this organism in culture, since the gene could only be deleted from the chromosome when a second functional copy was provided. Overexpression of clpP1 had no effect on growth in aerobic culture or viability under anaerobic conditions or during nutrient starvation. In contrast, clpP2 overexpression was toxic, suggesting different roles for the two homologs. We synthesized known activators of ClpP protease activity; these acyldepsipeptides (ADEPs) were active against M. tuberculosis. ADEP activity was enhanced by the addition of efflux pump inhibitors, demonstrating that ADEPs gain access to the cell but that export occurs. Taken together, the genetic and chemical validation of ClpP as a drug target leads to new avenues for drug discovery.

PrcR, a PucR-type transcriptional activator, is essential for proline utilization and mediates proline-responsive expression of the proline utilization operon putBCP in Bacillus subtilis

The soil bacterium Bacillus subtilis can utilize exogenous proline as a sole nitrogen or carbon source. The proline-inducible putBCP (formerly ycgMNO) operon encodes proteins responsible for proline uptake and two-step oxidation of proline to glutamate. We now report that a gene (formerly ycgP, now designated prcR) located downstream of the putBCP operon is essential for B. subtilis cells to utilize proline as a sole nitrogen or carbon source. Disruption of the prcR gene also abolished proline induction of putB transcription. prcR expression is not subject to autoregulation and proline induction. The PrcR protein shows no significant amino acid sequence similarity to the known transcriptional activators for proline utilization genes of other bacteria, but it does show partial amino acid sequence similarity to the transcriptional regulator PucR for the purine degradation genes of B. subtilis. PrcR orthologues of unknown function are present in some other Bacillus species. Primer-extension analysis suggests that both putB and prcR are transcribed by a σ(A)-dependent promoter. Deletion and mutation analysis revealed that an inverted repeat (5'-TTGTGG-N5-CCACAA-3') centred at position -76 relative to the transcriptional initiation site of putB is essential for putB expression. Electrophoretic mobility shift assays showed that the purified His-tagged PrcR was capable of binding specifically to this inverted repeat. Altogether, these results suggest that PrcR is a PucR-type transcriptional activator that mediates expression of the B. subtilis putBCP operon in response to proline availability.

Genetic evidence for involvement of the alternative sigma factor SigI in controlling expression of the cell wall hydrolase gene lytE and contribution of LytE to heat survival of Bacillus subtilis

The Bacillus subtilis cell wall hydrolase LytE is involved in cell wall turnover and cell separation during vegetative growth. lytE transcription is known to be driven by a YycF-activated SigA-dependent promoter. The cell wall regulator SigI is an alternative sigma factor that has been shown to be heat stress-inducible and to be essential for survival of B. subtilis at high temperature. However, none of the previously identified target genes of SigI contribute to heat resistance. We now demonstrate that lytE expression is heat-inducible and that heat induction of lytE expression is strongly dependent on SigI. We have also found that the lytE mutant shows the same growth defect at high temperature as the sigI mutant. Introducing an extra copy of lytE into the sigI mutant could rescue its growth defect. Our data strongly suggest that SigI-dependent lytE expression under heat stress is important for heat survival of B. subtilis.

Stress responses in Prochlorococcus MIT9313 vs. SS120 involve differential expression of genes encoding proteases ClpP, FtsH and Lon

Prochlorococcus is a marine cyanobacterium responsible for a significant part of global primary production as well as being one of the most abundant organisms on Earth. Protein turnover is an essential and poorly understood aspect of the cyanobacterial response to environmental stresses. In the present work, cultures of the SS120 and MIT9313 strains were subjected to several conditions, and quantitative real time RT-PCR was used to measure changes in the expression of genes encoding three representative ATP-dependent proteases. We found common responses to conditions such as aging. However, the expression pattern under nutrient starvation was strikingly different in the two strains, probably reflecting the different regulatory backgrounds of the two ecotypes here studied.

Helicobacter pylori mutants defective in the clpP ATP-dependant protease and the chaperone clpA display reduced macrophage and murine survival

The ATP-dependent caseinolytic proteases (Clp) are important in resistance against environmental stresses, antibiotic treatments and host immune defences for a number of pathogenic bacteria. ClpP is the proteolytic subunit, whilst ClpA acts both as a chaperone and as an ATPase driving the degradation of damaged or mis-made proteins. The gastric pathogen Helicobacter pylori infects approximately half of the world's population and can cause gastric or duodenal ulcers, gastric malignancies and mucosa-associated lymphoid tissue lymphomas. The conditions of its in vivo environment expose the organism to host immune cells and upon treatment, antibiotics, conditions likely to cause protein damage. We generated isogenic nonpolar mutants in strain SS1 of clpP and clpA and double mutants with both genes inactivated. Such mutants showed increased sensitivity to antibacterials causing protein damage and/or oxidative stress, in addition to a reduced survival in human macrophages. In the mouse infection model the double mutant SS1 clpAP lacked all ability to colonize the murine host. This suggests that the ability to recover from protein damage is of key importance in the pathogenesis of this organism.

Genetic evidence for the actin homolog gene mreBH and the bacitracin resistance gene bcrC as targets of the alternative sigma factor SigI of Bacillus subtilis

The Bacillus subtilis sigI gene, which is a member of the class VI heat shock genes of the B. subtilis heat shock stimulon, encodes an alternative sigma factor whose regulon is poorly defined. In this study, by using a binary vector system, we showed that B. subtilis SigI could drive expression of a transcriptional fusion between the sigI regulatory region from Bacillus licheniformis, Bacillus sp. strain NRRL B-14911, B. subtilis, or Bacillus thuringiensis and the xylE reporter gene in B. subtilis. The transcriptional initiation sites of these fusions in B. subtilis were mapped by primer extension analyses. A putative consensus promoter sequence probably recognized by the B. subtilis SigI was thus deduced. Using a consensus sequence-based search procedure, we found putative sigmaI promoters preceding the actin homolog gene mreBH and the bacitracin resistance gene bcrC of B. subtilis. Overexpression of the B. subtilis sigI gene could specifically stimulate expression of both an mreBH promoter region-bgaB fusion and a bcrC promoter region-bgaB fusion. Expression of these two fusions at the amyE locus of the B. subtilis chromosome was heat inducible and SigI dependent as revealed by sigI gene disruption experiments. Primer extension analysis showed that the identified mreBH and bcrC transcriptional start sites were at appropriate distances from their sigmaI promoter elements. This further supports the notion that SigI can directly regulate mreBH and bcrC expression. Taken together, these results strongly suggest that mreBH and bcrC are new members of the SigI regulon.

Regulation of the kduID operon of Bacillus subtilis by the KdgR repressor and the ccpA gene: identification of two KdgR-binding sites within the kdgR-kduI intergenic region

Transcription of the Bacillus subtilis kdgRKAT operon, which comprises genes involved in the late stage of galacturonate utilization, is known to be negatively regulated by the KdgR repressor. In this study, Northern analysis was carried out to demonstrate that the kdgR gene also negatively regulates the kduID operon, encoding ketodeoxyuronate isomerase and ketodeoxygluconate reductase. It has also been demonstrated that expression of the kduID operon can be induced by galacturonate and is subject to catabolite repression by glucose. The ccpA gene was found to be involved in this catabolite repression. Primer extension analysis identified a sigma(A)-like promoter sequence preceding kduI. Gel mobility shift assays and DNase I footprinting analyses indicated that KdgR is capable of binding specifically to two sites within the kdgR-kduI intergenic region in vitro. Reporter gene analysis revealed that these two KdgR-binding sites function in vivo. One site is centred 33.5 bp upstream of the translational start site of kdgR and can serve as an operator for controlling expression of the kdgRKAT operon. The other is centred 57.5 bp upstream of the translational start site of kduI and can serve as an operator for controlling expression of the kduID operon. Possible physiological significance of this regulation is discussed.

Exploiting Bifidobacterium genomes: the molecular basis of stress response

Bifidobacteria represent important human commensals because of their perceived contribution to the maintenance of a balanced gastro intestinal tract (GIT). In recent years bifidobacteria have drawn much scientific attention because of their use as live bacteria in numerous food preparations with various health-related claims. For such reasons these bacteria constitute a growing area of interest with respect to genomics, molecular biology and genetics. This review will discuss the current knowledge on the molecular players that allow bifidobacteria to contend with heat-, osmotic-, bile-and acidic stress. Here, we describe the principal molecular chaperones involved in such stresses, as well as their use as phylogenetic markers for gaining insight into the evolutionary history of high G+C Gram positive bacteria.

Identification ofBacillus cereusinternalin and other candidate virulence genes specifically induced during oral infection in insects

Bacillus cereus is an opportunistic bacterium frequently associated with food-borne infections causing gastroenteritis. We developed an in vivo expression technology (IVET), with an insect host, for identification of the B. cereus genes specifically expressed during infection. This IVET-based approach uses site-specific recombinase TnpI to identify transient promoter activation. We constructed a genomic library of B. cereus ATCC14579 by cloning DNA fragments upstream from tnpI. The library was screened in vivo by oral infection of the insect Galleria mellonella. We selected 100 clones from dead larvae. Sequencing of the inserts followed by a second screen for specific in vivo induction led to the identification of 20 in vivo-induced genes (ivi genes). They belonged to several different functional classes: regulation, metabolism, DNA repair and replication, cell division, transport, virulence and adaptation. A strongly induced gene, ivi29, was further analysed. It encodes an internalin-like protein with four distinct domains: an N-terminal signal peptide for export, a NEAT domain thought to be involved in iron transport, a leucine-rich repeat domain that may interact with host cells, and a C-terminal SLH domain presumably binding the protein to the peptidoglycan. As suggested by a Fur box in the promoter, transcriptional analysis showed ivi29 expression to be repressed by iron, suggesting that expression was induced in vivo due to iron deprivation in the host. This iron-regulated, leucine-rich surface protein was designated IlsA. Disruption of ilsA reduced the virulence of the bacteria to the insect larvae indicating its role in the overall pathogenesis of B. cereus.

Identification and characterization of the Bacillus thuringiensis phaZ gene, encoding new intracellular poly-3-hydroxybutyrate depolymerase

A gene that codes for a novel intracellular poly-3-hydroxybutyrate (PHB) depolymerase has now been identified in the genome of Bacillus thuringiensis subsp. israelensis ATCC 35646. This gene, previously annotated as a hypothetical 3-oxoadipate enol-lactonase (PcaD) gene and now designated phaZ, encodes a protein that shows no significant similarity with any known PHB depolymerase. Purified His-tagged PhaZ could efficiently degrade trypsin-activated native PHB granules as well as artificial amorphous PHB granules and release 3-hydroxybutyrate monomer as a hydrolytic product, but it could not hydrolyze denatured semicrystalline PHB. In contrast, purified His-tagged PcaD of Pseudomonas putida was unable to degrade trypsin-activated native PHB granules and artificial amorphous PHB granules. The B. thuringiensis PhaZ was inactive against p-nitrophenylpalmitate, tributyrin, and triolein. Sonication supernatants of the wild-type B. thuringiensis cells exhibited a PHB-hydrolyzing activity in vitro, whereas those prepared from a phaZ mutant lost this activity. The phaZ mutant showed a higher PHB content than the wild type at late stationary phase of growth in a nutrient-rich medium, indicating that this PhaZ can function as a PHB depolymerase in vivo. PhaZ contains a lipase box-like sequence (G-W-S(102)-M-G) but lacks a signal peptide. A purified His-tagged S102A variant had lost the PHB-hydrolyzing activity. Taken together, these results indicate that B. thuringiensis harbors a new type of intracellular PHB depolymerase.

Global transcriptome analysis of Tropheryma whipplei in response to temperature stresses

Tropheryma whipplei, the agent responsible for Whipple disease, is a poorly known pathogen suspected to have an environmental origin. The availability of the sequence of the 0.92-Mb genome of this organism made a global gene expression analysis in response to thermal stresses feasible, which resulted in unique transcription profiles. A few genes were differentially transcribed after 15 min of exposure at 43 degrees C. The effects observed included up-regulation of the dnaK regulon, which is composed of six genes and is likely to be under control of two HspR-associated inverted repeats (HAIR motifs) found in the 5' region. Putative virulence factors, like the RibC and IspDF proteins, were also overexpressed. While it was not affected much by heat shock, the T. whipplei transcriptome was strongly modified following cold shock at 4 degrees C. For the 149 genes that were differentially transcribed, eight regulons were identified, and one of them was composed of five genes exhibiting similarity with genes encoding ABC transporters. Up-regulation of these genes suggested that there was an increase in nutrient uptake when the bacterium was exposed to cold stress. As observed for other bacterial species, the major classes of differentially transcribed genes encode membrane proteins and enzymes involved in fatty acid biosynthesis, indicating that membrane modifications are critical. Paradoxically, the heat shock proteins GroEL2 and ClpP1 were up-regulated. Altogether, the data show that despite the lack of classical regulation pathways, T. whipplei exhibits an adaptive response to thermal stresses which is consistent with its specific environmental origin and could allow survival under cold conditions.

Efficient centrifugal recovery of Bacillus thuringiensis biopesticides from fermented wastewater and wastewater sludge

Studies were conducted on harvesting of Bacillus thuringiensis (Bt)-based biopesticides from fermented broths of starch industry wastewater (SIW), wastewater sludge (raw and hydrolyzed-NH and TH, respectively) and semi-synthetic soyameal to enhance entomotoxicity (Tx) by centrifugation. Pertinent factors influencing Tx, solids concentration, pH, temperature and centrifugal force were investigated. The centrifugate solids concentration beyond 100 g/l did not enhance Tx, instead caused pellet formation. Centrifugation efficiency (Tx recovery) was higher at pH 4, and temperature 20 degrees C for starch wastewater (98%), wastewater sludge (98% and 97.8% for non-hydrolyzed and hydrolyzed, respectively) and soya broth (83%). For maximum Tx recovery (SIW-95%; NH-90%; TH-98% and soya-78%), the centrifugal force and time required was 48,000 g and 30 min, respectively. Losses in recovery efficiency were lower for SIW and wastewater sludge in comparison to soya on adopting commercially recommended centrifugal force of 9000 g. The settling velocity computations for different fermented broths enabled calculation of Sigma factor for continuous commercial centrifuge of a given capacity and hence simulation of power requirements. It was established that power requirements for a given Tx recovery efficiency were highest for conventional medium (soya) in comparison to other waste-based fermented broths.

FlhA influences Bacillus thuringiensis PlcR-regulated gene transcription, protein production, and virulence

Bacillus thuringiensis and Bacillus cereus are closely related. B. thuringiensis is well known for its entomopathogenic properties, principally due to the synthesis of plasmid-encoded crystal toxins. B. cereus appears to be an emerging opportunistic human pathogen. B. thuringiensis and B. cereus produce many putative virulence factors which are positively controlled by the pleiotropic transcriptional regulator PlcR. The inactivation of plcR decreases but does not abolish virulence, indicating that additional factors like flagella may contribute to pathogenicity. Therefore, we further analyzed a mutant (B. thuringiensis 407 Cry(-) DeltaflhA) previously described as being defective in flagellar apparatus assembly and in motility as well as in the production of hemolysin BL and phospholipases. A large picture of secreted proteins was obtained by two-dimensional electrophoresis analysis, which revealed that flagellar proteins are not secreted and that production of several virulence-associated factors is reduced in the flhA mutant. Moreover, we quantified the effect of FlhA on plcA and hblC gene transcription. The results show that the flhA mutation results in a significant reduction of plcA and hblC transcription. These results indicate that the transcription of several PlcR-regulated virulence factors is coordinated with the flagellar apparatus. Consistently, the flhA mutant also shows a strong decrease in cytotoxicity towards HeLa cells and in virulence against Galleria mellonella larvae following oral and intrahemocoelic inoculation. The decrease in virulence may be due to both a lack of flagella and a lower production of secreted factors. Hence, FlhA appears to be an essential virulence factor with a pleiotropic role.

The ClgR protein regulates transcription of the clpP operon in Bifidobacterium breve UCC 2003

Five clp genes (clpC, clpB, clpP1, clpP2, and clpX), representing chaperone- and protease-encoding genes, were previously identified in Bifidobacterium breve UCC 2003. In the present study, we characterize the B. breve UCC 2003 clpP locus, which consists of two paralogous genes, designated clpP1 and clpP2, whose deduced protein products display significant similarity to characterized ClpP peptidases. Transcriptional analyses showed that the clpP1 and clpP2 genes are transcribed in response to moderate heat shock as a bicistronic unit with a single promoter. The role of a clgR homologue, known to control the regulation of clpP gene expression in Streptomyces lividans and Corynebacterium glutamicum, was investigated by gel mobility shift assays and DNase I footprint experiments. We show that ClgR, which in its purified form appears to exist as a dimer, requires a proteinaceous cofactor to assist in specific binding to a 30-bp region of the clpP promoter region. In pull-down experiments, a 56-kDa protein copurified with ClgR, providing evidence that the two proteins also interact in vivo and that the copurified protein represents the cofactor required for ClgR activity. The prediction of the ClgR three-dimensional structure provides further insights into the binding mode of this protein to the clpP1 promoter region and highlights the key amino acid residues believed to be involved in the protein-DNA interaction.

Salt stress induction of glutamyl endopeptidase biosynthesis in Bacillus intermedius

Bacteria from the genus Bacillus have evolved complicated regulatory networks to be protected from various environmental stresses, including sudden increase in salinity. Among these regulatory mechanisms is the DegS-DegU signal transduction system, which controls degradative enzyme synthesis and is involved in sensing salt stress in Bacillus subtilis. We report the study of biosynthesis regulation of Bacillus intermedius glutamyl endopeptidase under salt stress conditions. Salt stress during growth in medium containing 1-2.5 M NaCl, KCl or disodium succinate leads to the induction of glutamyl endopeptidase. Analysis of the regulatory region of the gene for B. intermedius glutamyl endopeptidase revealed the presence of a tentative target sequence for DegU control, AGATN10TTGAG. For the expression of the glutamyl endopeptidase gene, functional DegU protein is required. Thus, we suggest that expression of the gene for B. intermedius glutamyl endopeptidase may be controlled by a regulatory system analogous to DegS-DegU two-component system in B. subtilis.

Characterization of two Bacillus thuringiensis genes identified by in vivo screening of virulence factors

Bacillus thuringiensis vegetative cells are known to be highly pathogenic when injected into the hemocoel of susceptible insect larvae. This pathogenicity is due to the capacity of B. thuringiensis to cause septicemia in the host. We screened a B. thuringiensis mini-Tn10 insertion library for loss of virulence against Bombyx mori larvae on injection into the hemocoel. Three clones with attenuated virulence were isolated, corresponding to two different mini-Tn10 insertions mapping to the yqgB/yqfZ locus. Single disruptions of the yqgB and yqfZ genes did not affect virulence against B. mori. In contrast, the inactivation of both genes simultaneously reproduced the effect of the mini-Tn10 insertion and resulted in a significant delay to infection. The double DeltayqgB DeltayqfZ mutant was also nonmotile, and its growth was affected at 25 degrees C. We analyzed lacZ transcriptional fusions and detected promoter activity upstream from yqgB at 25 and 37 degrees C. Overall, our findings suggest that the yqgB and yqfZ genes encode adaptive factors that may act in synergy, enabling the bacteria to cope with the physical environment in vivo, facilitating colonization of the host.

ClgR, a novel regulator of clp and lon expression in Streptomyces

The clp genes encoding the Clp proteolytic complex are widespread among living organisms. Five clpP genes are present in Streptomyces. Among them, the clpP1 clpP2 operon has been shown to be involved in the Streptomyces growth cycle, as a mutation blocked differentiation at the substrate mycelium step. Four Clp ATPases have been identified in Streptomyces coelicolor (ClpX and three ClpC proteins) which are potential partners of ClpP1 ClpP2. The clpC1 gene appears to be essential, since no mutant has yet been obtained. clpP1 clpP2 and clpC1 are important for Streptomyces growth, and a study of their regulation is reported here. The clpP3 clpP4 operon, which has been studied in Streptomyces lividans, is induced in a clpP1 mutant strain, and regulation of its expression is mediated via PopR, a transcriptional regulator. We report here studies of clgR, a paralogue of popR, in S. lividans. Gel mobility shift assays and DNase I footprinting indicate that ClgR binds not only to the clpP1 and clpC1 promoters, but also to the promoter of the Lon ATP-dependent protease gene and the clgR promoter itself. ClgR recognizes the motif GTTCGC-5N-GCG. In vivo, ClgR acts as an activator of clpC1 gene and clpP1 operon expression. Similarly to PopR, ClgR degradation might be ClpP dependent and could be mediated via recognition of the two carboxy-terminal alanine residues.

Evidence for multiple levels of regulation of Oenococcus oeni clpP-clpL locus expression in response to stress

A locus containing the clpP and clpL genes in the lactic acid bacterium Oenococcus oeni was studied. Real-time reverse transcription-PCR analysis revealed different induction factors involved in expression of these genes during stress. According to the conditions, clpP and clpL genes could be transcripted as two distinct transcripts or cotranscripted. The clpP promoter depended on the CtsR regulator, but surprisingly the clpL promoter did not. The amount of the clpL transcript depended on mRNA stability. This clp ATPase gene is at least controlled at the posttranscriptional level.