Protein misfolding in the cell envelope of Escherichia coli: new signaling pathways

Structural characterization of PaFkbA: A periplasmic chaperone from Pseudomonas aeruginosa

Bacterial Mip-like FK506-binding proteins (FKBPs) mostly exhibit peptidyl-prolyl-cis/trans-isomerase (PPIase) and chaperone activities. These activities are associated with various intracellular functions with diverse molecular mechanisms. Herein, we report the PA3262 gene-encoded crystal structure of the Pseudomonas aeruginosa PAO1's Mip-like protein PaFkbA. Biochemical characterization of PaFkbA demonstrated PaFkbA's chaperone activity for periplasmic protein MucD, a negative regulator of alginate biosynthesis. Furthermore, structural analysis of PaFkbA was used to describe the key features of PaFkbA chaperone activity. The outcomes of this analysis showed that the hinge region in the connecting helix of PaFbkA leads to the crucial conformational state transition for PaFkbA activity. Besides, the N-terminal domains participated in dimerization, and revealed its potential connection with FKBP domain and substrate binding. Mutagenesis and chaperone activity assay supported the theory that inter-domain motions are essential for PaFkbA function. These results provide biochemical and structural insights into the mechanism for FKBP's chaperone activity and establish a plausible correlation between PaFkbA and P. aeruginosa MucD.

The novel cis-encoded antisense RNA AsrC positively regulates the expression of rpoE-rseABC operon and thus enhances the motility of Salmonella enterica serovar typhi

Bacterial non-coding RNAs are essential in many cellular processes, including response to environmental stress, and virulence. Deep sequencing analysis of the Salmonella enterica serovar typhi (S. typhi) transcriptome revealed a novel antisense RNA transcribed in cis on the strand complementary to rseC, an activator gene of sigma factor RpoE. In this study, expression of this antisense RNA was confirmed in S. typhi by Northern hybridization. Rapid amplification of cDNA ends and sequence analysis identified an 893 bp sequence from the antisense RNA coding region that covered all of the rseC coding region in the reverse direction of transcription. This sequence of RNA was named as AsrC. After overexpression of AsrC with recombinantant plasmid in S. typhi, the bacterial motility was increased obviously. To explore the mechanism of AsrC function, regulation of rseC and rpoE expression by AsrC was investigated. We found that AsrC increased the levels of rseC mRNA and protein. The expression of rpoE was also increased in S. typhi after overexpression of AsrC, which was dependent on rseC. Thus, we propose that AsrC increased RseC level and indirectly activating RpoE which can initiate fliA expression and promote the motility of S. typhi.

An approach to the production of soluble protein from a fungal gene encoding an aggregation-prone xylanase in Escherichia coli

The development of new procedures and protocols that allow researchers to obtain recombinant proteins is of fundamental importance in the biotechnology field. A strategy was explored to overcome inclusion-body formation observed when expressing an aggregation-prone fungal xylanase in Escherichia coli. pHsh is an expression plasmid that uses a synthetic heat-shock (Hsh) promoter, in which gene expression is regulated by an alternative sigma factor (σ(32)). A derivative of pHsh was constructed by fusing a signal peptide to xynA2 gene to facilitate export of the recombinant protein to the periplasm. The xylanase was produced in a soluble form. Three factors were essential to achieving such soluble expression of the xylanase: 1) the target gene was under the control of the Hsh promoter, 2) the gene product was exported into the periplasm, and 3) gene expression was induced by a temperature upshift. For the first time we report the expression of periplasmic proteins under the control of an Hsh promoter regulated by σ(32). One unique feature of this approach was that over 200 copies of the Hsh promoter in an E. coli cell significantly increased the concentration of σ(32). The growth inhibition of the recombinant cells corresponded to an increase in the levels of soluble periplasmic protein. Therefore, an alternative protocol was designed to induce gene expression from pHsh-ex to obtain high levels of active soluble enzymes.

In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements

Specific promoter recognition by bacterial RNA polymerase is mediated by σ subunits, which assemble with RNA polymerase core enzyme (E) during transcription initiation. However, σ⁷⁰ (the housekeeping σ subunit) and σ^S (an alternative σ subunit mostly active during slow growth) recognize almost identical promoter sequences, thus raising the question of how promoter selectivity is achieved in the bacterial cell. To identify novel sequence determinants for selective promoter recognition, we performed run-off/microarray (ROMA) experiments with RNA polymerase saturated either with σ⁷⁰ (Eσ⁷⁰) or with σ^S (Eσ^S) using the whole Escherichia coli genome as DNA template. We found that Eσ⁷⁰, in the absence of any additional transcription factor, preferentially transcribes genes associated with fast growth (e.g. ribosomal operons). In contrast, Eσ^S efficiently transcribes genes involved in stress responses, secondary metabolism as well as RNAs from intergenic regions with yet-unknown function. Promoter sequence comparison suggests that, in addition to different conservation of the −35 sequence and of the UP element, selective promoter recognition by either form of RNA polymerase can be affected by the A/T content in the −10/+1 region. Indeed, site-directed mutagenesis experiments confirmed that an A/T bias in the −10/+1 region could improve promoter recognition by Eσ^S.

Periplasmic peptidyl-prolyl isomerases SurA and FkpA play an important role in the starvation-stress response (SSR) of Salmonella enterica serovar Typhimurium

Carbon-energy source (C)-starved cells of Salmonella enterica serovar Typhimurium (S. Typhimurium) are remarkably more resistant to stress than actively growing ones. Carbon-starved S. Typhimurium is capable of withstanding extended periods of starvation and assault from a number of different stresses that rapidly kill growing cells. These unique properties of the C-starved cell are the direct result of a series of genetic and physiological adaptations referred to as the starvation-stress response (SSR). Previous work established that the SSR of S. Typhimurium is partially regulated by the extracytoplasmic function sigma factor sigma(E). As part of an effort to identify sigma(E)-regulated SSR genes, we investigated surA and fkpA, encoding two different classes of peptidyl-prolyl isomerase that function in folding cell envelope proteins. Both surA and fkpA are members of the heat-shock-inducible sigma(E) regulon of Escherichia coli. Although both genes are expressed in C-starved Salmonella cells, evidence indicates that surA and fkpA are not C-starvation-inducible. Furthermore, their expression during C-starvation does not appear to be sigma(E)-dependent. Nonetheless, surA and fkpA proved to be important, to differing degrees, for long-term C-starvation survival and for the cross-resistance of C-starved cells to high temperature, acidic pH, and the antimicrobial peptide polymyxin B, but neither were required for cross-resistance to oxidative stress. These results point to fundamental differences between heat-shock-inducible and C-starvation-inducible genes regulated by sigma(E) and suggest that genes other than surA and fkpA are involved in the sigma(E)-regulated branch of the SSR in Salmonella.

Dissection of sigma(E)-dependent cell lysis in Escherichia coli: roles of RpoE regulators RseA, RseB and periplasmic folding catalyst PpiD

To understand the mechanism of sigma(E)-dependent cell lysis, we examined the consequences of deletion derivatives of rpoE regulators rseA, rseB and rseC on sigma(E) transcription, on levels of free versus membrane-bound sigma(E) and on OMP-biogenesis limiting factor(s) that could impact cell lysis. RT-PCR showed that individual nonpolar DeltarseA and DeltarseB increased the rpoE expression to varying extents, with pronounced induction in DeltarseA. Significantly the ratio of soluble (free) versus membrane-bound form of RpoE increased in DeltarseA, however without increase of its total amount, unraveling furthermore complexity in RpoE regulation. Significant characteristics of cell lysis, accompanied by a severe reduction in the levels of periplasmic OMP-folding factor (PpiD), were observed in DeltarseA. The cell-lysis phenotype of DeltarseA was suppressed by either rseA or ppiD plasmids, but neither by rseB nor by rseC clones. However, the cell lysis of the wild-type strain was almost completely repressed not only by the rseA clone but also by the rseB clone, suggesting RseB might be limiting in vivo. Thus, increase in the ratio of free sigma(E) in rseA mutants with a concomitant reduction in PpiD levels can account for sigma(E)-dependent lysis in concert with a potential role of small RNAs on the lysis process.

The proteolytic activity of the HtrA (DegP) protein from Escherichia coli at low temperatures

The HtrA (DegP) protein from Escherichia coli is a periplasmic protease whose function is to protect cells from the deleterious effects of various stress conditions. At temperatures below 28 degrees C the proteolytic activity of HtrA was regarded as negligible and it was believed that the protein mainly plays the role of a chaperone. In the present work we provide evidence that HtrA can in fact act as a protease at low temperatures. Under folding stress, caused by disturbances in the disulfide bond formation, the lack of proteolytic activity of HtrA lowered the survival rates of mutant strains deprived of a functional DsbA/DsbB oxidoreductase system. HtrA degraded efficiently the unfolded, reduced alkaline phosphatase at 20 degrees C, both in vivo and in vitro. The cleavage was most efficient in the case of HtrA deprived of its internal S-S bond; therefore we expect that the reduction of HtrA may play a regulatory role in proteolysis.

The density of negative charge in the cell wall influences two-component signal transduction in Bacillus subtilis

The Dlt system modulates the density of negative charge in the cell wall of Gram-positive bacteria by substituting anionic polymers (wall and lipoteichoic acids) with d-alanine. The htrA and htrB genes, regulated by the CssRS two-component system (TCS) and encoding membrane-associated protein quality control proteases, were expressed at strongly decreased levels in a mutant with defective Dlt (dltD : : miniTn10) as compared to the dlt(+) wild-type strain under a secretion stress condition (hypersecretion of AmyQ alpha-amylase). The level of HtrA protein in the extracellular proteome of the dltD mutant was decreased consistently. Expression from the promoter of the liaIHGFSR (yvqIHGFEC) operon (P(liaI)) is dependent on the LiaRS TCS. The Dlt defect increased the expression from P(liaI) under two stress conditions, AmyQ hypersecretion and treatment with a cationic antimicrobial peptide (LL-37), but decreased the expression in vancomycin-treated cells. Furthermore, Dlt inactivation enhanced the expression of the YxdJK-regulated yxdL gene in LL-37-treated cells. The increased net negative charge of the cell wall seems to cause varied and opposite effects on the expression of CssRS-, LiaRS- and YxdJK-regulated genes under different stress conditions. The results suggest that TCSs which sense misfolded proteins or peptides are modulated by the density of negative charge in the cell wall. The density of negative charge on the outer surface of the cell membrane did not have a similar effect on TCSs.

Effect of heat-shock proteins for relieving physiological stress and enhancing the production of penicillin acylase inEscherichia coli

High-level expression of recombinant penicillin acylase (PAC) using the strong trc promoter system in Escherichia coli is frequently limited by the processing and folding of PAC precursors (proPAC) in the periplasm, resulting in physiological stress and inclusion body formation in this compartment. Periplasmic heat-shock proteins with protease or chaperone activity potentially offer a promise for overcoming this technical hurdle. In this study, the effect of the two genes encoding periplasmic heat-shock proteins, that is degP and fkpA, on pac overexpression was investigated and manipulation of the two genes to enhance the production of recombinant PAC was demonstrated. Both DeltadegP and DeltafkpA mutants showed defective culture performance primarily due to growth arrest. However, pac expression level was not seriously affected by the mutations, indicating that the two proteins were not directly involved in the pathway for periplasmic processing of proPAC. The growth defect caused by the two mutations (i.e., DeltadegP and DeltafkpA) was complemented by either one of the wild-type proteins, implying that the function of the two proteins could partially overlap in cells overexpressing pac. The possible role that the two heat-shock proteins played for suppression of physiological stress caused by pac overexpression is discussed.

The inner cavity of Escherichia coli DegP protein is not essential for molecular chaperone and proteolytic activity

The Escherichia coli DegP protein is an essential periplasmic protein for bacterial survival at high temperatures. DegP has the unusual property of working as a chaperone below 28 degrees C, but efficiently degrading unfolded proteins above 28 degrees C. Monomeric DegP contains a protease domain and two PDZ domains. It oligomerizes into a hexameric cage through the staggered association of trimers. The active sites are located in a central cavity that is only accessible laterally, and the 12 PDZ domains act as mobile sidewalls that mediate opening and closing of the gates. As access to the active sites is restricted, DegP is an example of a self-compartmentalized protease. To determine the essential elements of DegP that maintain the integrity of the hexameric cage, we constructed several deletion mutants of DegP that formed trimers rather than hexamers. We found that residues 39 to 78 within the LA loops, as well as the PDZ2 domains are essential for the integrity of the DegP hexamer. In addition, we asked whether an enclosed cavity or cage of specific dimensions is required for the protease and chaperone activities in DegP. Both activities were maintained in the trimeric DegP mutants without an enclosed cavity and in deletion DegP mutants with significantly reduced dimensions of the cage. We conclude that the functional unit for the protease and chaperone activities of DegP is a trimer and that neither a cavity of specific dimensions nor the presence of an enclosed cavity appears to be essential for the protease and chaperone activities of DegP.

Cell lysis directed by sigmaE in early stationary phase and effect of induction of the rpoE gene on global gene expression in Escherichia coli

It has been shown that Escherichia coli cells with increased expression of the rpoE gene encoding sigma(E) exhibit enhanced cell lysis in early stationary phase. Further analysis of the lysis phenomenon was performed using a transient expression system of the rpoE gene and by DNA microarray. The former analysis revealed a sigma(E)-directed cell lysis, specific for early stationary phase but not for the exponential phase. The microarray analysis with RNAs from exponential and early stationary phase cells revealed that a large number of genes were up- or down-regulated when the rpoE gene was induced, and that several genes were induced in a phase-specific manner. The upregulated genes include many previously identified sigma(E) regulon genes, suggesting that a large number of genes are under the control of sigma(E) in this organism. These genes are involved in various cellular activities, including the cell envelope, cellular processes, regulatory functions, transport and translation. Genes that are presumably related to phase-specific cell lysis in E. coli are discussed.

Osmoregulation of the HtrA (DegP) protease ofEscherichia coli: An Hha–H-NS complex represses HtrA expression at low osmolarity

The HtrA protein of Escherichia coli is a heat-shock inducible periplasmic protease, essential for bacterial survival at high temperatures. Expression of htrA gene depends on the alternative factor sigmaE and on the two-component regulatory system Cpx. These regulators systems respond, among others factors, to overproduction of misfolded proteins in the periplasm or to high level synthesis of various extracytoplasmic proteins. We describe in this report the osmoregulation of the expression of htrA gene. Low osmolarity conditions result in htrA repression. We report, as well, the role of the nucleoid associated proteins H-NS and Hha in the repression of htrA expression at low osmolarity.

Stress and survival of aging Escherichia coli rpoS colonies

In Escherichia coli, the expression of the RpoS regulon is known to be crucial for survival in liquid cultures during stationary phase. By measuring cell viability and by transcriptome analysis, here we show that rpoS cells as well as wild-type cells survive when they form colonies on solid media.

Roles of DegP in prevention of protein misfolding in the periplasm upon overexpression of penicillin acylase in Escherichia coli

Enhancement of the production of soluble recombinant penicillin acylase in Escherichia coli via coexpression of a periplasmic protease/chaperone, DegP, was demonstrated. Coexpression of DegP resulted in a shift of in vivo penicillin acylase (PAC) synthesis flux from the nonproductive pathway to the productive one when pac was overexpressed. The number of inclusion bodies, which consist primarily of protein aggregates of PAC precursors in the periplasm, was highly reduced, and the specific PAC activity was highly increased. DegP was a heat shock protein induced in response to pac overexpression, suggesting that the protein could possibly suppress the physiological toxicity caused by pac overexpression. Coexpression of DegP(S210A), a DegP mutant without protease activity but retaining chaperone activity, could not suppress the physiological toxicity, suggesting that DegP protease activity was primarily responsible for the suppression, possibly by degradation of abnormal proteins when pac was overexpressed. However, a shortage of periplasmic protease activity was not the only reason for the deterioration in culture performance upon pac overexpression because coexpression of a DegP-homologous periplasmic protease, DegQ or DegS, could not suppress the physiological toxicity. The chaperone activity of DegP is proposed to be another possible factor contributing to the suppression.

Internal response correction for fluorescent whole-cell biosensors

Whole-cell biosensors based on reporter genes are finding a variety of applications in analytical chemistry. Despite their ability to selectively recognize the analyte in a complex mixture, few applications of such sensing devices to real sample analysis are reported. This is mainly due to nonspecific effects on the biosensor response caused by components of the sample matrix and by environmental changes. To overcome this problem, a bacterial biosensor with an internal correction mechanism of the analytical response was developed by introducing an additional reporter gene that provides a reference signal of the analytical performance of the biosensor. The first reporter (GFPuv), expressed in response to the concentration of L-arabinose, provides the analytical signal; the second reporter (EYFP), constitutively expressed if a constant amount of IPTG is added to each sample, was used as an internal reference. By inducing the biosensor with varying amounts of L-arabinose and a constant amount of IPTG, it was possible to obtain a dose-response curve for L-arabinose, together with a constant production of EYFP, which allowed for a dynamic evaluation of the metabolic activity of the cell. When tested in nonoptimal conditions (e.g., in the presence of either ethanol or deoxycholic acid at toxic concentrations), the presence of the internal reference system corrected the analytical response due to nonspecific interferences.

PDZ domains facilitate binding of high temperature requirement protease A (HtrA) and tail-specific protease (Tsp) to heterologous substrates through recognition of the small stable RNA A (ssrA)-encoded peptide

The Escherichia coli protease HtrA has two PDZ domains, and sequence alignments predict that the E. coli protease Tsp has a single PDZ domain. PDZ domains are composed of short sequences (80-100 amino acids) that have been implicated in a range of protein:protein interactions. The PDZ-like domain of Tsp may be involved in binding to the extreme COOH-terminal sequence of its substrate, whereas the HtrA PDZ domains are involved in subunit assembly and are predicted to be responsible for substrate binding and subsequent translocation into the active site. E. coli has a system of protein quality control surveillance mediated by the ssrA-encoded peptide tagging system. This system tags misfolded proteins or protein fragments with an 11-amino acid peptide that is recognized by a battery of cytoplasmic and periplasmic proteases as a degradation signal. Here we show that both HtrA and Tsp are able to recognize the ssrA-encoded peptide tag with apparent K(D) values of approximately 5 and 390 nm, respectively, and that their PDZ-like domains mediate this recognition. Fusion of the ssrA-encoded peptide tag to the COOH terminus of a heterologous protein (glutathione S-transferase) renders it sensitive to digestion by Tsp but not HtrA. These observations support the prediction that the HtrA PDZ domains facilitate substrate binding and the differential proteolytic responses of HtrA and Tsp to SsrA-tagged glutathione S-transferase are interpreted in terms of the structure of HtrA.

Regulation of Salmonella enterica serovar Typhimurium mntH transcription by H(2)O(2), Fe(2+), and Mn(2+)

MntH, a bacterial homolog of mammalian natural resistance associated macrophage protein 1 (Nramp1), is a primary transporter for Mn(2+) influx in Salmonella enterica serovar Typhimurium and Escherichia coli. S. enterica serovar Typhimurium MntH contributes to H(2)O(2) resistance and is important for full virulence. Consistent with its phenotype and function, mntH is regulated at the transcriptional level by both H(2)O(2) and substrate cation. We have now identified three trans-acting regulatory factors and the three corresponding cis-acting mntH promoter motifs that mediate this regulation. In the presence of hydrogen peroxide, mntH is activated by OxyR, acting through an OxyR-binding motif centered just upstream of the likely -35 RNA polymerase-binding site. In the presence of Fe(2+), mntH is repressed primarily by Fur, acting through a Fur-binding motif overlapping the -35 region. In the presence of Mn(2+), mntH is repressed primarily by the Salmonella equivalent of E. coli b0817, a distant homolog of the Bacillus subtilis manganese transport repressor, MntR, acting through an inverted-repeat motif located between the likely -10 polymerase binding site and the ribosome binding site. E. coli b0817 was recently shown to bind the identical inverted-repeat motif in the E. coli mntH promoter and hence has been renamed MntR (S. I. Patzer and K. Hantke, J. Bacteriol. 183:4806-4813, 2001). Using Deltafur, DeltamntR, and Deltafur DeltamntR mutant strains as well as mutations in the Fur- and MntR-binding motif elements, we found that Fe(2+) can also mediate repression through the Mn(2+) repressor MntR.

ClpXP protease regulates the signal peptide cleavage of secretory preproteins in Bacillus subtilis with a mechanism distinct from that of the Ecs ABC transporter

Identification and characterization of a suppressor mutation, sup-15, which partially restored secretion in the protein secretion-deficient Bacillus subtilis ecsA26 mutant, led us to discover a novel function of Clp protease. Inactivation of ClpP improved the processing of the precursor of AmyQ alpha-amylase exposed on the outer surface of the cytoplasmic membrane. A similar improvement of AmyQ secretion was conferred by inactivation of the ClpX substrate-binding component of the ClpXP complex. In the absence of ClpXP, the transcription of the sipS, sipT, sipV, and lsp signal peptidase genes was elevated two- to fivefold, a likely cause of the improvement of the processing and secretion of AmyQ and complementation of ecs mutations. Specific overproduction of SipT enhanced the secretion. These findings extend the regulatory roles of ClpXP to protein secretion. ClpXP also influenced the processing of the lipoprotein PrsA. A concerted regulation of signal peptidase genes by a ClpXP-dependent activator is suggested. In contrast, Ecs did not affect transcription of the sip genes, pointing to a different mechanism of secretion regulation.

The starvation-stress response of Salmonella enterica serovar Typhimurium requires sigma(E)-, but not CpxR-regulated extracytoplasmic functions

Starvation of Salmonella enterica serovar Typhimurium (S. Typhimurium) for an exogenous source of carbon and energy (C-starvation) induces the starvation-stress response (SSR). The SSR functions to (i) maintain viability during long-term C-starvation and (ii) generate cross-resistance to other environmental stresses. The SSR is, at least partially, under the control of the alternative sigma factor, sigma(S). It is hypothesized that C-starvation causes cell envelope stresses that could induce the sigma(E) and/or Cpx regulons, both of which control extracytoplasmic functions and, thus, may play a role in the regulation of the SSR. In support of this hypothesis, Western blot analysis showed that the relative levels of sigma(E) increased during C-starvation, peaking after approximately 72 h of C-starvation; in contrast, CpxR levels remained relatively constant from exponential phase up to 72 h of C-starvation. To determine if sigma(E), and thus the regulon it controls, is an essential component of the SSR, several mutant strains were compared for their abilities to survive long-term C-starvation and to develop C-starvation-induced (CSI) cross-resistances. An rpoE mutant strain was significantly impaired in both long-term C-starvation survival (LT-CSS) and in CSI cross-resistance to challenges with 20 mM H(2)O(2) for 40 min, 55 degrees C for 16 min, pH 3.1 for 60 min and 870.2 USP U polymyxin B ml(-1) (PmB) for 60 min, to varying degrees. These results suggest that C-starvation can generate signals that induce the rpoE regulon and that one or more members of the sigma(E) regulon are required for maximal SSR function. Furthermore, evidence suggests that the sigma(E) and sigma(S) regulons function through separate mechanisms in the SSR. In contrast, C-starvation does not appear to generate signals required for Cpx regulon induction which support the findings that it is not required for LT-CSS or cross-resistance to H(2)O(2), pH 3.1 or PmB challenges. However, it was required to achieve maximal cross-resistance to 55 degrees C. Therefore, sigma(E) is a key regulatory component of the SSR and represents an additional sigma factor required for the SSR of Salmonella.

EcfE, a new essential inner membrane protease: its role in the regulation of heat shock response in Escherichia coli

We have identified a new protease in Escherichia coli, which is required for its viability under normal growth conditions. This protease is anchored in the inner membrane and the gene encoding it has been named ecfE, since it is transcribed by Esigma(E) polymerase. Multicopy expression of the ecfE gene was found to turn down expression of both Esigma(E)- and Esigma(32)-transcribed promoters. Purified EcfE degrades both heat shock sigma factors RpoE and RpoH in vitro. EcfE has a zinc binding domain at the N-terminus, a PDZ-like domain in the middle and a highly conserved tripeptide, LDG, at the C-terminus. These features are characteristic of members of a new class of proteases whose activity occurs close to the inner membrane or within the inner membrane. Temperature-sensitive mutants of this gene were isolated mapping to the catalytic site and other domains that exhibited constitutively elevated levels of both heat shock regulons.

A novel two-component regulatory system in Bacillus subtilis for the survival of severe secretion stress

The Gram-positive eubacterium Bacillus subtilis is well known for its high capacity to secrete proteins into the environment. Even though high-level secretion of proteins is an efficient process, it imposes stress on the cell. The present studies were aimed at the identification of systems required to combat this so-called secretion stress. A two-component regulatory system, named CssR-CssS, was identified, which bears resemblance to the CpxR-CpxA system of Escherichia coli. The results show that the CssR/S system is required for the cell to survive the severe secretion stress caused by a combination of high-level production of the alpha-amylase AmyQ and reduced levels of the extracytoplasmic folding factor PrsA. As shown with a prsA3 mutation, the Css system is required to degrade misfolded exported proteins at the membrane-cell wall interface. This view is supported by the observation that transcription of the htrA gene, encoding a predicted membrane-bound protease of B. subtilis, is strictly controlled by CssS. Notably, CssS represents the first identified sensor for extracytoplasmic protein misfolding in a Gram-positive eubacterium. In conclusion, the results show that quality control systems for extracytoplasmic protein folding are not exclusively present in the periplasm of Gram-negative eubacteria, but also in the Gram-positive cell envelope.

Isolation and characterization of a chromosomally encoded disulphide oxidoreductase from Salmonella enterica serovar Typhimurium

In this study, the chromosomally encoded disulphide oxidoreductase dsbA from Salmonella typhimurium was cloned and characterized. A survey of a number of serovars of Salmonella subspecies I showed that dsbA is highly conserved in most, but not all members of this subclass of Salmonella species. Using motility, β-galactosidase, and alkaline phosphatase assays as indirect indicators of disulphide oxidoreductase activity, we demonstrated that DsbA from S. typhimurium LT2 can only partially complement an Escherichia coli dsbA-null strain. This is surprising considering the high degree of conservation between these two DsbA proteins (87% amino acid identity). To determine the contribution of DsbA to the proper folding and assembly of proteins of S. typhimurium, deletion mutants were created in the avirulent strain LT2 and in the virulent strain SL1344. These null alleles were constructed by partial deletion of the dsbA-coding region and then insertion of an antibiotic resistance marker in the gene. Mutants no longer expressing a functional disulphide oxidoreductase exhibit pleitropic effects, including an increase in colony mucoidy, a dramatic decrease in motility, and an increased susceptibility to the cationic peptide protamine sulphate. The disruption of disulphide bond formation was also shown to specifically affect the stability of several proteins secreted into the extracellular environment.Key words: disulphide oxidoreductase, protein folding, Salmonella typhimurium, DsbA.

Biochemical characterization of the thioredoxin domain of Escherichia coli DsbE protein reveals a weak reductant

Thioredoxin (Trx) domain is a typical fold functioning in thiol/disulfide exchange. DsbE protein is one of the Trx-domain containing proteins involved in electron transfer for cytochrome c maturation in the periplasm of Escherichia coli. The soluble C-terminal Trx domain of DsbE protein was overexpressed and purified to homogeneity. We herein report biochemical characterization of the structural and redox properties of this domain. During redox reaction, the domain undergoes a structural transformation resulting in a more stable reduced form with a free energy difference (DeltaDeltaG(Redox)) of ca. 5 kcal/mol, but the thiol/disulfide exchange exhibits very low reactivity. The standard redox potential (E0') for the active thiol/disulfide is -0.175 V and the pK(a) value of the active cysteine is around 6.8, indicating that the domain acts as a weak reductant. This implies that the membrane-anchored DsbE protein may provide driven reducing power for the redox reaction in the thiol/disulfide exchange pathway.

Chaperone function of FkpA, a heat shock prolyl isomerase, in the periplasm of Escherichia coli

The nature of molecular chaperones in the periplasm of Escherichia coli that assist newly translocated proteins to reach their native state has remained poorly defined. Here, we show that FkpA, a heat shock periplasmic peptidyl-prolyl cis/trans isomerase (PPIase), suppresses the formation of inclusion bodies from a defective-folding variant of the maltose-binding protein, MalE31. This chaperone-like activity of FkpA, which is independent of its PPIase activity, requires a full-length structure of the protein. In vitro, FkpA does not catalyse a slow rate-limiting step in the refolding of MalE31, but prevents its aggregation at stoichiometric amounts and promotes the reactivation of denaturated citrate synthase. We propose that FkpA functions as a chaperone for envelope proteins in the bacterial periplasm.

Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome

One of the most salient features of Bacillus subtilis and related bacilli is their natural capacity to secrete a variety of proteins into their environment, frequently to high concentrations. This has led to the commercial exploitation of bacilli as major "cell factories" for secreted enzymes. The recent sequencing of the genome of B. subtilis has provided major new impulse for analysis of the molecular mechanisms underlying protein secretion by this organism. Most importantly, the genome sequence has allowed predictions about the composition of the secretome, which includes both the pathways for protein transport and the secreted proteins. The present survey of the secretome describes four distinct pathways for protein export from the cytoplasm and approximately 300 proteins with the potential to be exported. By far the largest number of exported proteins are predicted to follow the major "Sec" pathway for protein secretion. In contrast, the twin-arginine translocation "Tat" pathway, a type IV prepilin-like export pathway for competence development, and ATP-binding cassette transporters can be regarded as "special-purpose" pathways, through which only a few proteins are transported. The properties of distinct classes of amino-terminal signal peptides, directing proteins into the various protein transport pathways, as well as the major components of each pathway are discussed. The predictions and comparisons in this review pinpoint important differences as well as similarities between protein transport systems in B. subtilis and other well-studied organisms, such as Escherichia coli and the yeast Saccharomyces cerevisiae. Thus, they may serve as a lead for future research and applications.

Function of the sigma(E) regulon in dead-cell lysis in stationary-phase Escherichia coli

Elevation of active sigma(E) levels in Escherichia coli by either repressing the expression of rseA encoding an anti-sigma(E) factor or cloning rpoE in a multicopy plasmid, led to a large decrease in the number of dead cells and the accumulation of cellular proteins in the medium in the stationary phase. The numbers of CFU, however, were nearly the same as those of the wild type or cells devoid of the cloned gene. In the wild-type cells, rpoE expression was increased in the stationary phase and a low-level release of intracellular proteins was observed. These results suggest that dead cell lysis in stationary-phase E. coli occurs in a sigma(E)-dependent fashion. We propose there is a novel physiological function of the sigma(E) regulon that may guarantee cell survival in prolonged stationary phase by providing nutrients from dead cells for the next generation.

Selective degradation of unfolded proteins by the self-compartmentalizing HtrA protease, a periplasmic heat shock protein in Escherichia coli

HtrA, which has a high molecular mass of about 500 kDa, is a periplasmic heat shock protein whose proteolytic activity is essential for the survival of Escherichia coli at high temperatures. To determine the structural organization of HtrA, we have used electron microscopy and chemical cross-linking analysis. The averaged image of HtrA with end-on orientation revealed a six-membered, ring-shaped structure with a central cavity, and its side-on view showed a two-layered structure. Thus, HtrA behaves as a dodecamer consisting of two stacks of hexameric ring. HtrA can degrade thermally unfolded citrate synthase and malate dehydrogenase but cannot when in their native form. HtrA degraded partially unfolded casein more rapidly upon increasing the incubation temperature. However, it hydrolyzed oxidized insulin B-chain, which is fully unfolded, at nearly the same rate at all of the temperatures tested. HtrA also rapidly degraded reduced insulin B-chain generated by treatment of insulin with dithiothreitol but not A-chain or intact insulin. Moreover, HtrA degraded fully unfolded alpha-lactalbumin, of which all four disulfide bonds were reduced, but not the native alpha-lactalbumin and its unfolded intermediates containing two or three disulfide bonds. These results indicate that unfolding of the protein substrates, such as by exposure to high temperatures or reduction of disulfide bonds, is essential for their access into the inner chamber of the double ring-shaped HtrA, where cleavage of peptide bonds may occur. Thus, HtrA with a self-compartmentalizing structure may play an important role in elimination of unfolded proteins in the periplasm of Escherichia coli.

In vivo and in vitro function of the Escherichia coli periplasmic cysteine oxidoreductase DsbG

We have characterized in vivo and in vitro the recently identified DsbG from Escherichia coli. In addition to sharing sequence homology with the thiol disulfide exchange protein DsbC, DsbG likewise was shown to form a stable periplasmic dimer, and it displays an equilibrium constant with glutathione comparable with DsbA and DsbC. DsbG was found to be expressed at approximately 25% the level of DsbC. In contrast to earlier results (Andersen, C. L., Matthey-Dupraz, A., Missiakas, D., and Raina, S. (1997) Mol. Microbiol. 26, 121-132), we showed that dsbG is not essential for growth and that dsbG null mutants display no defect in folding of multiple disulfide-containing heterologous proteins. Overexpression of DsbG, however, was able to restore the ability of dsbC mutants to express heterologous multidisulfide proteins, namely bovine pancreatic trypsin inhibitor, a protein with three disulfides, and to a lesser extent, mouse urokinase (12 disulfides). As in DsbC, the putative active site thiols in DsbG are completely reduced in vivo in a dsbD-dependent fashion, as would be expected if DsbG is acting as a disulfide isomerase or reductase. However, the latter is not likely because DsbG could not catalyze insulin reduction in vitro. Overall, our results indicate that DsbG functions primarily as a periplasmic disulfide isomerase with a narrower substrate specificity than DsbC.

Negative regulation of bacterial heat shock genes

The expression of eubacterial heat shock genes is efficiently controlled at the transcriptional level by both positive and negative mechanisms. Positive control operates by the use of alternative sigma factors that target RNA polymerase to heat shock gene promoters. Alternatively, bacteria apply repressor-dependent mechanisms, in which transcription of heat shock genes is initiated from a classical housekeeping promoter and cis-acting DNA elements are used in concert with a cognate repressor protein to limit transcription under physiological conditions. Eight examples of negative regulation will be presented, among them the widespread CIRCE/HrcA system and the control by HspR in Streptomyces. Both mechanisms are designed to permit simple feedback control at the level of gene expression. Many bacteria have established sophisticated regulatory networks, often combining positive and negative mechanisms, in order to allow fine-tuned heat shock gene expression in an environmentally responsive way.

Molecular characterization of a stress-inducible gene from Lactobacillus helveticus

A gene (htrA) coding for a stress-inducible HtrA-like protein from Lactobacillus helveticus CNRZ32 was cloned, sequenced, and characterized. The deduced amino acid sequence of the gene exhibited 30% identity with the HtrA protein from Escherichia coli; the putative catalytic triad and a PDZ domain that characterize the HtrA family of known bacterial serine proteases were also found in the sequence. Expression of the L. helveticus htrA gene in a variety of stress conditions was analyzed at the transcriptional level. The strongest induction, resulting in over an eightfold increase in the htrA transcription level, was found in growing CNRZ32 cells exposed to 4% (wt/vol) NaCl. Enhanced htrA mRNA expression was also seen in CNRZ32 cells after exposure to puromycin, ethanol, or heat. The reporter gene gusA was integrated in the Lactobacillus chromosome downstream of the htrA promoter by a double-crossover event which also interrupted the wild-type gene. The expression of gusA in the stress conditions tested was similar to that of htrA itself. In addition, the presence of an intact htrA gene facilitated growth under heat stress but not under salt stress.

Oral vaccination against tetanus: comparison of the immunogenicities of Salmonella strains expressing fragment C from the nirB and htrA promoters

We have found the in vivo-regulated nirB promoter (PnirB) to be effective for directing expression of a number of antigens in salmonella in vivo. We wished to determine if other in vivo-regulated promoters have utility for antigen expression in salmonella and to compare the effectiveness of these promoters with that of PnirB. To this end, we have devised a scheme that allows the promoter element of the PnirB-fragment C plasmid pTETnir15 to be swapped with other promoters of interest. We demonstrate the usefulness of this system by replacing PnirB with PhtrA to create plasmid pTEThtrA1. htrA is a stress response gene that is required for virulence of salmonella in mice and survival within macrophages. Expression of fragment C in Salmonella typhimurium BRD509 (aroA aroD) harboring pTEThtrA1 (strain BRD937) correlated with growth temperature in vitro. A comparison was made of the immune responses to fragment C elicited in mice immunized orally with BRD937 or BRD847 (BRD509/pTETnir15) or subcutaneously with purified fragment C plus alhydrogel. High levels of anti-fragment C antibodies that persisted for at least 12 weeks were present in all groups of mice. Vaccination with BRD937 was the most effective means of immunization: the serum immunoglobulin G (IgG), IgA, and IgM anti-fragment C titers were higher in the BRD937-immunized mice throughout the duration of the study than in mice in the other groups. The kinetics of the serum anti-fragment C responses were different in different groups. The response was most rapid in the BRD937 group, with the titers almost at peak levels at 2 weeks postimmunization. Only the mice immunized with BRD937 or BRD847 developed an intestinal IgA response to fragment C. Again, the response was superior in the BRD937 group. The peak of the intestinal response was delayed with respect to the serum response. Analysis of the IgG subtype response to fragment C revealed a dominant IgG2a response in the salmonella-immunized mice, indicating a type 1 helper T-cell response to fragment C, whereas the major subtype in the group parenterally immunized with fragment C plus alhydrogel was IgG1. The IgG1/IgG2a ratio was much higher in sera of BRD937-immunized mice than in sera of BRD847-immunized mice. At 15 to 20 weeks after immunization, the mice immunized with BRD937 or BRD847 were solidly immune to tetanus toxin and salmonella. The immune responses to fragment C seen in mice immunized with BRD937 are the strongest we have observed and indicate that the htrA promoter may be very useful for expressing foreign antigens in salmonella vaccine strains.

Degradation versus aggregation of misfolded maltose-binding protein in the periplasm of Escherichia coli

The periplasmic fates of misfolded MalE31, a defective folding mutant of the maltose-binding protein, were determined by manipulating two cellular activities affecting the protein folding pathway in host cells: (i) the malEp promoter activity, which is controlled by the transcriptional activator MalT, and (ii) the DegP and Protease III periplasmic proteolytic activity. At a low level of expression, the degradation of misfolded MalE31 was partially impaired in cells lacking DegP or Protease III. At a high level of expression, misfolded MalE31 rapidly formed periplasmic inclusion bodies and thus escaped degradation. However, the manipulated host cell activities did not enhance the production of periplasmic, soluble MalE31. A kinetic competition between folding, aggregation, and degradation is proposed as a general model for the biogenesis of periplasmic proteins.

Proteolysis and chaperones: the destruction/reconstruction dilemma

Cytoplasmic proteases, although necessary for proper cell functioning, must be strictly regulated. In fact, they resemble chaperones, ancient protein folding devices. These molecules recognise exposed hydrophobic regions of unfolded or denatured proteins. For most substances it is not known how the cell chooses between the refolding and proteolytic pathways. In Escherichia coli, however, a carboxy-terminal proteolysis tag and binding site for the chaperone DnaK have recently been identified.

Ero1p: a novel and ubiquitous protein with an essential role in oxidative protein folding in the endoplasmic reticulum

The structure of many proteins entering the secretory pathway is dependent on stabilization by disulfide bonds. To support disulfide-linked folding, the endoplasmic reticulum (ER) must maintain a strongly oxidizing environment compared to the highly reduced environment of the cytosol. We report here the identification and characterization of Ero1p, a novel and essential ER-resident protein. Mutations in Ero1p cause extreme sensitivity to the reducing agent DTT, whereas overexpression confers DTT resistance. Strikingly, compromised Ero1p function results in ER retention of disulfide-stabilized proteins in a reduced, nonnative form, while not affecting structural maturation of a disulfide-free protein. We conclude that there exists a specific cellular redox machinery required for disulfide-linked protein folding in the ER and that Ero1p is an essential component of this machinery.

Catalysis of protein folding by parvulin

Recently a new family of prolyl isomerases was discovered, which is unrelated with the cyclophilins or the FK-506 binding proteins. Parvulin, the smallest member of this new family, is a protein with only 92 residues, but parvulin-like domains occur in several large proteins that are apparently involved in protein folding or activation processes. We show here that, in addition to its activity in assays with proline-containing tetrapeptides, parvulin catalyzes the proline-limited folding of a variant of ribonuclease T1 with a kcat/Km value of 30,000 M-1 s-1. This value is much smaller than the kcat/Km value of 1.1x10(7) M-1 s-1 determined for the parvulin-catalyzed prolyl isomerization in the tetrapeptide succinyl-Ala-Leu-Pro-Phe-4-nitroanilide. Parvulin itself unfolds and refolds reversibly in a simple two-state reaction with a Gibbs free energy of stabilization of 28 kJ/mol at 10 degrees C. Most of the unfolded parvulin molecules refold in a slow reaction that involves prolyl isomerization and is catalyzed by cyclophilin, another prolyl isomerase. Moreover, parvulin accelerates its own refolding in an autocatalytic fashion, and the rate of refolding increases tenfold when the concentration of parvulin is increased from 0.5 to 3.0 microM. Apparently, small single-domain prolyl isomerases catalyze prolyl isomerization much better in short peptides than in protein folding reactions, presumably because the prolyl bonds are less accessible in refolding protein chains. It is possible that the additional domains of the large prolyl isomerases improve the affinity for protein substrates.