101
|
Castaldo C, Siciliano RA, Muscariello L, Marasco R, Sacco M. CcpA affects expression of the groESL and dnaK operons in Lactobacillus plantarum. Microb Cell Fact 2006; 5:35. [PMID: 17129387 PMCID: PMC1676014 DOI: 10.1186/1475-2859-5-35] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Accepted: 11/27/2006] [Indexed: 11/10/2022] Open
Abstract
Background Lactic acid bacteria (LAB) are widely used in food industry and their growth performance is important for the quality of the fermented product. During industrial processes changes in temperature may represent an environmental stress to be overcome by starters and non-starters LAB. Studies on adaptation to heat shock have shown the involvement of the chaperon system-proteins in various Gram-positive bacteria. The corresponding operons, namely the dnaK and groESL operons, are controlled by a negative mechanism involving the HrcA repressor protein binding to the cis acting element CIRCE. Results We studied adaptation to heat shock in the lactic acid bacterium Lactobacillus plantarum. The LM3-2 strain, carrying a null mutation in the ccpA gene, encoding the catabolite control protein A (CcpA), showed a lower percent of survival to high temperature with respect to the LM3 wild type strain. Among proteins differentially expressed in the two strains, the GroES chaperon was more abundant in the wild type strain compared to the mutant strain under standard growth conditions. Transcriptional studies showed that class I heat shock operons were differentially expressed upon heat shock in both strains. Indeed, the dnaK and groESL operons were induced about two times more in the LM3 strain compared to the LM3-2 strain. Analysis of the regulatory region of the two operons showed the presence of cre sequences, putative binding sites for the CcpA protein. Conclusion The L. plantarum dnaK and groESL operons are characterized by the presence of the cis acting sequence CIRCE in the promoter region, suggesting a negative regulation by the HrcA/CIRCE system, which is a common type of control among the class I heat shock operons of Gram-positive bacteria. We found an additional system of regulation, based on a positive control exerted by the CcpA protein, which would interact with cre sequences present in the regulatory region of the dnaK and groESL operons. The absence of the CcpA protein results in a lower induction of the chaperon coding operons, with a consequent lower percent of survival of the LM3-2 mutant strain population with respect to the wild type when challenged with a heat insult.
Collapse
Affiliation(s)
- Cristiana Castaldo
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy
| | - Rosa A Siciliano
- Centro di Spettrometria di Massa Proteomica e Biomolecolare, Istituto di Scienze dell'Alimentazione, CNR, Avellino, Italy
| | - Lidia Muscariello
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy
| | - Rosangela Marasco
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, Caserta, Italy
| | - Margherita Sacco
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy
| |
Collapse
|
102
|
Thomaides HB, Davison EJ, Burston L, Johnson H, Brown DR, Hunt AC, Errington J, Czaplewski L. Essential bacterial functions encoded by gene pairs. J Bacteriol 2006; 189:591-602. [PMID: 17114254 PMCID: PMC1797375 DOI: 10.1128/jb.01381-06] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To address the need for new antibacterials, a number of bacterial genomes have been systematically disrupted to identify essential genes. Such programs have focused on the disruption of single genes and may have missed functions encoded by gene pairs or multiple genes. In this work, we hypothesized that we could predict the identity of pairs of proteins within one organism that have the same function. We identified 135 putative protein pairs in Bacillus subtilis and attempted to disrupt the genes forming these, singly and then in pairs. The single gene disruptions revealed new genes that could not be disrupted individually and other genes required for growth in minimal medium or for sporulation. The pairwise disruptions revealed seven pairs of proteins that are likely to have the same function, as the presence of one protein can compensate for the absence of the other. Six of these pairs are essential for bacterial viability and in four cases show a pattern of species conservation appropriate for potential antibacterial development. This work highlights the importance of combinatorial studies in understanding gene duplication and identifying functional redundancy.
Collapse
Affiliation(s)
- Helena B Thomaides
- Prolysis Ltd., Begbroke Science Park, Sandy Lane, Yarnton OX5 1PF, Oxfordshire, UK.
| | | | | | | | | | | | | | | |
Collapse
|
103
|
Wang W, Hollmann R, Deckwer WD. Comparative proteomic analysis of high cell density cultivations with two recombinant Bacillus megaterium strains for the production of a heterologous dextransucrase. Proteome Sci 2006; 4:19. [PMID: 17022804 PMCID: PMC1622742 DOI: 10.1186/1477-5956-4-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 10/05/2006] [Indexed: 11/30/2022] Open
Abstract
High cell density cultivations were performed under identical conditions for two Bacillus megaterium strains (MS941 and WH320), both carrying a heterologous dextransucrase (dsrS) gene under the control of the xylA promoter. At characteristic points of the cultivations (end of batch, initial feeding, before and after induction) the proteome was analyzed based on two dimensional gel electrophoresis and mass spectrometric protein identification using the protein database "bmegMEC.v2" recently made available. High expression but no secretion of DsrS was found for the chemical mutant WH320 whereas for MS 941, a defined protease deficient mutant of the same parent strain (DSM319), not even expression of DsrS could be detected. The proteomic analysis resulted in the identification of proteins involved in different cellular pathways such as in central carbon and overflow metabolism, in protein synthesis, protein secretion and degradation, in cell wall metabolism, in cell division and sporulation, in membrane transport and in stress responses. The two strains exhibited considerable variations in expression levels of specific proteins during the different phases of the cultivation process, whereas induction of DsrS production had, in general, little effect. The largely differing behaviour of the two strains with regard to DsrS expression can be attributed, at least in part, to changes observed in the proteome which predominantly concern biosynthetic enzymes and proteins belonging to the membrane translocation system, which were strongly down-regulated at high cell densities in MS941 compared with WH320. At the same time a cell envelope-associated quality control protease and two peptidoglycan-binding proteins related to cell wall turnover were strongly expressed in MS941 but not found in WH320. However, to further explain the very different physiological responses of the two strains to the same cultivation conditions, it is necessary to identify the mutated genes in WH320 in addition to the known lacZ. In view of the results of this proteomic study it seems that at high cell density conditions and hence low growth rates MS941, in contrast to WH320, does not maintain a vegetative growth which is essential for the expression of the foreign dsrS gene by using the xylA promoter. It is conceivable that applications of a promoter which is highly active under nutrient-limited cultivation conditions is necessary, at least for MS941, for the overexpression of recombinant genes in such B. megaterium fed-batch cultivation process. However to obtain a heterologous protein in secreted and properly folded form stills remains a big challenge.
Collapse
Affiliation(s)
- Wei Wang
- Biochemical Engineering, Technical University Braunschweig, GBF/TU-BCE, Mascheroder Weg 1, D-38124 Braunschweig, Germany
| | - Rajan Hollmann
- Biochemical Engineering, Technical University Braunschweig, GBF/TU-BCE, Mascheroder Weg 1, D-38124 Braunschweig, Germany
| | - Wolf-Dieter Deckwer
- Biochemical Engineering, Technical University Braunschweig, GBF/TU-BCE, Mascheroder Weg 1, D-38124 Braunschweig, Germany
| |
Collapse
|
104
|
Abstract
Surface proteins are critical in determining the identifying characteristics of individual bacteria and their interaction with the environment. Because the structure of the cell surface is the major characteristic that distinguishes gram-positive from gram-negative bacteria, the processes used to transport and attach these proteins show significant differences between these bacterial classes. This review is intended to highlight these differences and to focus attention on areas that are ripe for further investigation.
Collapse
Affiliation(s)
- June R Scott
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA.
| | | |
Collapse
|
105
|
Westers H, Westers L, Darmon E, van Dijl JM, Quax WJ, Zanen G. The CssRS two-component regulatory system controls a general secretion stress response in Bacillus subtilis. FEBS J 2006; 273:3816-27. [PMID: 16911528 DOI: 10.1111/j.1742-4658.2006.05389.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacillus species are valuable producers of industrial enzymes and biopharmaceuticals, because they can secrete large quantities of high-quality proteins directly into the growth medium. This requires the concerted action of quality control factors, such as folding catalysts and 'cleaning proteases'. The expression of two important cleaning proteases, HtrA and HtrB, of Bacillus subtilis is controlled by the CssRS two-component regulatory system. The induced CssRS-dependent expression of htrA and htrB has been defined as a protein secretion stress response, because it can be triggered by high-level production of secreted alpha-amylases. It was not known whether translocation of these alpha-amylases across the membrane is required to trigger a secretion stress response or whether other secretory proteins can also activate this response. These studies show for the first time that the CssRS-dependent response is a general secretion stress response which can be triggered by both homologous and heterologous secretory proteins. As demonstrated by high-level production of a nontranslocated variant of the alpha-amylase, AmyQ, membrane translocation of secretory proteins is required to elicit this general protein secretion stress response. Studies with two other secretory reporter proteins, lipase A of B. subtilis and human interleukin-3, show that the intensity of the protein secretion stress response only partly reflects the production levels of the respective proteins. Importantly, degradation of human interleukin-3 by extracellular proteases has a major impact on the production level, but only a minor effect on the intensity of the secretion stress response.
Collapse
Affiliation(s)
- Helga Westers
- Department of Pharmaceutical Biology, University of Groningen, The Netherlands
| | | | | | | | | | | |
Collapse
|
106
|
Brockmeier U, Caspers M, Freudl R, Jockwer A, Noll T, Eggert T. Systematic Screening of All Signal Peptides from Bacillus subtilis: A Powerful Strategy in Optimizing Heterologous Protein Secretion in Gram-positive Bacteria. J Mol Biol 2006; 362:393-402. [PMID: 16930615 DOI: 10.1016/j.jmb.2006.07.034] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 07/21/2006] [Accepted: 07/21/2006] [Indexed: 11/22/2022]
Abstract
Efficient protein secretion is very important in biotechnology as it provides active and stable enzymes, which are an essential prerequisite for successful biocatalysis. Therefore, optimizing enzyme-producing bacterial strains is a major challenge in the field of biotechnology and protein production. In this study, the Gram-positive model bacterium Bacillus subtilis was optimized for heterologous protein secretion using a novel approach. Two lipolytic enzymes, cutinase from Fusarium solani pisi and a cytoplasmatic esterase of metagenomic origin, were chosen as reporters for heterologous protein secretion. In a systematic screening approach, all naturally occurring (non-lipoprotein) Sec-type signal peptides (SPs) from B. subtilis were characterized for their potential in heterologous protein secretion. Surprisingly, optimal SPs in cutinase secretion were inefficient in esterase secretion and vice versa, indicating the importance of an optimal fit between the SP and the respective mature part of the desired secretion target proteins. These results highlight the need for individually optimal signal peptides for every heterologous secretion target. Therefore, the SP library generated in this study represents a powerful tool for secretion optimization in Gram-positive expression hosts.
Collapse
Affiliation(s)
- Ulf Brockmeier
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, im Forschungszentrum Jülich, D-52426 Jülich, Germany
| | | | | | | | | | | |
Collapse
|
107
|
Zhang W, Culley DE, Hogan M, Vitiritti L, Brockman FJ. Oxidative stress and heat-shock responses in Desulfovibrio vulgaris by genome-wide transcriptomic analysis. Antonie van Leeuwenhoek 2006; 90:41-55. [PMID: 16680520 DOI: 10.1007/s10482-006-9059-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 01/17/2006] [Indexed: 10/24/2022]
Abstract
Sulfate-reducing bacteria such as Desulfovibrio vulgaris have developed a set of responses that allow them to survive in hostile environments. To obtain further knowledge of the protective mechanisms employed by D. vulgaris in response to oxidative stress and heat shock, we performed a genome-wide transcriptomic analysis to determine the cellular responses to both stimuli. The results showed that 130 genes were responsive to oxidative stress, while 427 genes were responsive to heat-shock. Functional analyses suggested that the genes regulated were involved in a variety of cellular functions. Amino acid biosynthetic pathways were induced by both oxidative stress and heat shock treatments, while fatty acid metabolism, purine and cofactor biosynthesis were induced by heat shock only. The rubrerythrin gene (rbr) was up-regulated in response to oxidative stress, suggesting an important role for this protein in the oxidative damage resistance response in D. vulgaris. In addition, thioredoxin reductase (trxB) was also responsive to oxidative stress, suggesting that the thiol-specific redox system might also be involved in oxidative protection in this organism. In contrast, the expression of rubredoxin oxidoreductase (rbo), superoxide dismutase (sodB) and catalase (katA) genes were not regulated in response to oxidative stress. Comparison of cellular responses to oxidative stress and heat-shock allowed the identification of 66 genes that showed a similar drastic response to both environmental perturbations, implying that these genes might be part of the general stress response (GSR) network in D. vulgaris. This hypothesis was further supported by the identification of a conserved motif upstream of these stress-responsive genes.
Collapse
Affiliation(s)
- Weiwen Zhang
- Microbiology Department, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA 99352, USA.
| | | | | | | | | |
Collapse
|
108
|
Westers L, Dijkstra DS, Westers H, van Dijl JM, Quax WJ. Secretion of functional human interleukin-3 from Bacillus subtilis. J Biotechnol 2006; 123:211-24. [PMID: 16359746 DOI: 10.1016/j.jbiotec.2005.11.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Revised: 10/20/2005] [Accepted: 11/09/2005] [Indexed: 11/29/2022]
Abstract
The Gram-positive bacterium Bacillus subtilis is well-known for its huge capacity to produce secreted bacterial enzymes. Nevertheless, the secretion of pharmaceutically interesting recombinant proteins by this organism is frequently inefficient. This paper documents for the first time on the optimisation of B. subtilis for the production of human interleukin-3 (hIL-3), a four-helix bundle cytokine, which stimulates the proliferation and differentiation of a broad range of blood cells. By developing a host-vector system on the basis of the multiple protease-deficient B. subtilis strain WB700 and a multicopy plasmid containing two tandemly positioned strong promoters plus an efficient signal sequence, the hIL-3 protein was efficiently produced and secreted into the growth medium. As verified by SDS-PAGE, mass spectrometry and cross-linking experiments with a thiol-specific reagent, intact and properly folded hIL-3 was purified from the B. subtilis growth medium. Bioactivity tests showed that the isolated hIL-3 was able to specifically induce proliferation of the hIL-3-dependent leukaemia cell line MO7e. Using the eight-fold protease-deficient strain WB800 the hIL-3 accumulation in the growth medium was increased to levels up to 100 mg l(-1).
Collapse
Affiliation(s)
- Lidia Westers
- Department of Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | | | | | | |
Collapse
|
109
|
Chitlaru T, Gat O, Gozlan Y, Ariel N, Shafferman A. Differential proteomic analysis of the Bacillus anthracis secretome: distinct plasmid and chromosome CO2-dependent cross talk mechanisms modulate extracellular proteolytic activities. J Bacteriol 2006; 188:3551-71. [PMID: 16672610 PMCID: PMC1482852 DOI: 10.1128/jb.188.10.3551-3571.2006] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 02/19/2006] [Indexed: 12/17/2022] Open
Abstract
The secretomes of a virulent Bacillus anthracis strain and of avirulent strains (cured of the virulence plasmids pXO1 and pXO2), cultured in rich and minimal media, were studied by a comparative proteomic approach. More than 400 protein spots, representing the products of 64 genes, were identified, and a unique pattern of protein relative abundance with respect to the presence of the virulence plasmids was revealed. In minimal medium under high CO(2) tension, conditions considered to simulate those encountered in the host, the presence of the plasmids leads to enhanced expression of 12 chromosome-carried genes (10 of which could not be detected in the absence of the plasmids) in addition to expression of 5 pXO1-encoded proteins. Furthermore, under these conditions, the presence of the pXO1 and pXO2 plasmids leads to the repression of 14 chromosomal genes. On the other hand, in minimal aerobic medium not supplemented with CO(2), the virulent and avirulent B. anthracis strains manifest very similar protein signatures, and most strikingly, two proteins (the metalloproteases InhA1 and NprB, orthologs of gene products attributed to the Bacillus cereus group PlcR regulon) represent over 90% of the total secretome. Interestingly, of the 64 identified gene products, at least 31 harbor features characteristic of virulence determinants (such as toxins, proteases, nucleotidases, sulfatases, transporters, and detoxification factors), 22 of which are differentially regulated in a plasmid-dependent manner. The nature and the expression patterns of proteins in the various secretomes suggest that distinct CO(2)-responsive chromosome- and plasmid-encoded regulatory factors modulate the secretion of potential novel virulence factors, most of which are associated with extracellular proteolytic activities.
Collapse
Affiliation(s)
- Theodor Chitlaru
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona
| | | | | | | | | |
Collapse
|
110
|
Chhabra SR, He Q, Huang KH, Gaucher SP, Alm EJ, He Z, Hadi MZ, Hazen TC, Wall JD, Zhou J, Arkin AP, Singh AK. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J Bacteriol 2006; 188:1817-28. [PMID: 16484192 PMCID: PMC1426554 DOI: 10.1128/jb.188.5.1817-1828.2006] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Desulfovibrio vulgaris Hildenborough belongs to a class of sulfate-reducing bacteria (SRB) and is found ubiquitously in nature. Given the importance of SRB-mediated reduction for bioremediation of metal ion contaminants, ongoing research on D. vulgaris has been in the direction of elucidating regulatory mechanisms for this organism under a variety of stress conditions. This work presents a global view of this organism's response to elevated growth temperature using whole-cell transcriptomics and proteomics tools. Transcriptional response (1.7-fold change or greater; Z >/= 1.5) ranged from 1,135 genes at 15 min to 1,463 genes at 120 min for a temperature up-shift of 13 degrees C from a growth temperature of 37 degrees C for this organism and suggested both direct and indirect modes of heat sensing. Clusters of orthologous group categories that were significantly affected included posttranslational modifications; protein turnover and chaperones (up-regulated); energy production and conversion (down-regulated), nucleotide transport, metabolism (down-regulated), and translation; ribosomal structure; and biogenesis (down-regulated). Analysis of the genome sequence revealed the presence of features of both negative and positive regulation which included the CIRCE element and promoter sequences corresponding to the alternate sigma factors sigma(32) and sigma(54). While mechanisms of heat shock control for some genes appeared to coincide with those established for Escherichia coli and Bacillus subtilis, the presence of unique control schemes for several other genes was also evident. Analysis of protein expression levels using differential in-gel electrophoresis suggested good agreement with transcriptional profiles of several heat shock proteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), and AhpC (DVU2247). The proteomics study also suggested the possibility of posttranslational modifications in the chaperones DnaK, AhpC, GroES (DVU1977), and GroEL (DVU1976) and also several periplasmic ABC transporters.
Collapse
Affiliation(s)
- S R Chhabra
- Biosystems Research Department, Mailstop 9292, Sandia National Laboratory, 7011 East Ave., Livermore, CA 94550, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
111
|
Dalton TL, Collins JT, Barnett TC, Scott JR. RscA, a member of the MDR1 family of transporters, is repressed by CovR and required for growth of Streptococcus pyogenes under heat stress. J Bacteriol 2006; 188:77-85. [PMID: 16352823 PMCID: PMC1317578 DOI: 10.1128/jb.188.1.77-85.2006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of Streptococcus pyogenes (group A streptococcus [GAS]) to respond to changes in environmental conditions is essential for this gram-positive organism to successfully cause disease in its human host. The two-component system CovRS controls expression of about 15% of the GAS genome either directly or indirectly. In most operons studied, CovR acts as a repressor. We previously linked CovRS to the GAS stress response by showing that the sensor kinase CovS is required to inactivate the response regulator CovR so that GAS can grow under conditions of heat, acid, and salt stress. Here, we sought to identify CovR-repressed genes that are required for growth under stress. To do this, global transcription profiles were analyzed by microarrays following exposure to increased temperature (40 degrees C) and decreased pH (pH 6.0). The CovR regulon in an M type 6 strain of GAS was also examined by global transcriptional analysis. We identified a gene, rscA (regulated by stress and Cov), whose transcription was confirmed to be repressed by CovR and activated by heat and acid. RscA is a member of the MDR1 family of ABC transporters, and we found that it is required for growth of GAS at 40 degrees C but not at pH 6.0. Thus, for GAS to grow at 40 degrees C, CovR repression must be alleviated so that rscA can be transcribed to allow the production of this potential exporter. Possible explanations for the thermoprotective role of RscA in this pathogen are discussed.
Collapse
Affiliation(s)
- Tracy L Dalton
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | | | |
Collapse
|
112
|
Vitikainen M, Hyyryläinen HL, Kivimäki A, Kontinen VP, Sarvas M. Secretion of heterologous proteins in Bacillus subtilis can be improved by engineering cell components affecting post-translocational protein folding and degradation. J Appl Microbiol 2006; 99:363-75. [PMID: 16033468 DOI: 10.1111/j.1365-2672.2005.02572.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To explore the potential to enhance secretion of heterologous proteins in Bacillus subtilis by engineering cell factors affecting extracytoplasmic protein folding and degradation. METHODS AND RESULTS Bottleneck components affecting the extracytoplasmic phase of protein secretion were genetically engineered and their effects on the secretion of 11 industrially interesting heterologous proteins were studied by Western blotting and enzymatic assays. Overproduction of PrsA lipoprotein enhanced the secretion of alpha-amylase of Bacillus stearothermophilus (fourfold) and pneumolysin (1.5-fold). Increasing the net negative charge of the cell wall because of lack of the d-alanine substitution of anionic cell wall polymers enhanced the secretion of pneumolysin c. 1.5-fold. Decreasing the level of HtrA-type quality control proteases caused harmful effects on growth and did not enhance secretion. Pertussis toxin subunit, S1 was found to be a substrate for HtrA-type proteases and its secretion was dependent on these proteases. CONCLUSIONS Secretion of heterologous proteins can be enhanced by engineering components involved in late stages of secretion in a protein-dependent manner. SIGNIFICANCE AND IMPACT OF THE STUDY The study revealed both possibilities and limitations of modulating the post-translocational phase of secretion as a means to improve the yield of heterologous proteins.
Collapse
Affiliation(s)
- M Vitikainen
- Vaccine Development Laboratory, National Public Health Institute, Helsinki, Finland
| | | | | | | | | |
Collapse
|
113
|
Kirstein J, Zühlke D, Gerth U, Turgay K, Hecker M. A tyrosine kinase and its activator control the activity of the CtsR heat shock repressor in B. subtilis. EMBO J 2005; 24:3435-45. [PMID: 16163393 PMCID: PMC1276163 DOI: 10.1038/sj.emboj.7600780] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Accepted: 07/20/2005] [Indexed: 11/08/2022] Open
Abstract
The soil bacterium Bacillus subtilis possesses a fine-tuned and complex heat stress response system. The repressor CtsR, whose activity is regulated by its modulators McsA and McsB, controls the expression of the cellular protein quality control genes clpC, clpE and clpP. Here, we show that the interaction of McsA and McsB with CtsR results in the formation of a ternary complex that not only prevents the binding of CtsR to its target DNA, but also results in a subsequent phosphorylation of McsB, McsA and CtsR. We further demonstrate that McsB is a tyrosine kinase that needs McsA to become activated. ClpC inhibits the kinase activity of McsB, indicating a direct role in initiating CtsR-controlled heat shock response. Interestingly, the kinase domain of McsB is homologous to guanidino phosphotransferase domains originating from eukaryotic arginine and creatine kinases. Mutational analysis of key residues of the guanidino kinase domain demonstrated that McsB utilizes this domain to catalyze the tyrosine phosphorylation. McsB represents therefore a new kind of tyrosine kinase, driven by a guanidino phosphotransferase domain.
Collapse
Affiliation(s)
- Janine Kirstein
- Ernst Moritz Arndt Universität Greifswald, Institut für Molekulare Mikrobiologie, Greifswald, Germany.
| | | | | | | | | |
Collapse
|
114
|
Westers H, Braun PG, Westers L, Antelmann H, Hecker M, Jongbloed JDH, Yoshikawa H, Tanaka T, van Dijl JM, Quax WJ. Genes involved in SkfA killing factor production protect a Bacillus subtilis lipase against proteolysis. Appl Environ Microbiol 2005; 71:1899-908. [PMID: 15812018 PMCID: PMC1082511 DOI: 10.1128/aem.71.4.1899-1908.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Accepted: 11/11/2004] [Indexed: 11/20/2022] Open
Abstract
Small lipases of Bacillus species, such as LipA from Bacillus subtilis, have a high potential for industrial applications. Recent studies showed that deletion of six AT-rich islands from the B. subtilis genome results in reduced amounts of extracellular LipA. Here we demonstrate that the reduced LipA levels are due to the absence of four genes, skfABCD, located in the prophage 1 region. Intact skfABCD genes are required not only for LipA production at wild-type levels by B. subtilis 168 but also under conditions of LipA overproduction. Notably, SkfA has bactericidal activity and, probably, requires the SkfB to SkfD proteins for its production. The present results show that LipA is more prone to proteolytic degradation in the absence of SkfA and that high-level LipA production can be improved significantly by employing multiple protease-deficient B. subtilis strains. In conclusion, our findings imply that SkfA protects LipA, directly or indirectly, against proteolytic degradation. Conceivably, SkfA could act as a modulator in LipA folding or as a protease inhibitor.
Collapse
Affiliation(s)
- Helga Westers
- Department of Pharmaceutical Biology, University of Groningen, Hanzeplein 1, P.O. Box 30 001, 9700 RB Groningen, the Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
115
|
Hyyryläinen HL, Sarvas M, Kontinen VP. Transcriptome analysis of the secretion stress response of Bacillus subtilis. Appl Microbiol Biotechnol 2005; 67:389-96. [PMID: 15856219 DOI: 10.1007/s00253-005-1898-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Revised: 12/22/2004] [Accepted: 12/27/2004] [Indexed: 10/25/2022]
Abstract
Transcription profiling of all protein-encoding genes of Bacillus subtilis was carried out under several secretion stress conditions in the exponential growth phase. Cells that secreted AmyQ alpha-amylase at a high level were stressed only moderately: seven genes were induced, most significantly htrA and htrB, encoding quality control proteases, and yqxL, encoding a putative CorA-type Mg(2+) transporter. These three genes were induced more strongly by severe secretion stress (prsA3 mutant secreting AmyQ), suggesting that their expression responds to protein misfolding. In addition, 17 other genes were induced, including the liaIHGFSR (yvqIHGFEC) operon, csaA and ffh, encoding chaperones involved in the pretranslocational phase of secretion, and genes involved in cell wall synthesis/modification. Severe secretion stress caused downregulation of 23 genes, including the prsA paralogue yacD. Analysis of a cssS knockout mutant indicated that the absence of the CssRS two-component system, and consequently the absence of the HtrA and HtrB proteases, caused secretion stress. The results also suggest that the htrA and htrB genes comprise the CssRS regulon. B. subtilis cells respond to secretion/folding stress by various changes in gene expression, which can be seen as an attempt to combat the stress condition.
Collapse
|
116
|
Holtmann G, Brigulla M, Steil L, Schütz A, Barnekow K, Völker U, Bremer E. RsbV-independent induction of the SigB-dependent general stress regulon of Bacillus subtilis during growth at high temperature. J Bacteriol 2004; 186:6150-8. [PMID: 15342585 PMCID: PMC515142 DOI: 10.1128/jb.186.18.6150-6158.2004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
General stress proteins protect Bacillus subtilis cells against a variety of environmental insults. This adaptive response is particularly important for nongrowing cells, to which it confers a multiple, nonspecific, and preemptive stress resistance. Induction of the general stress response relies on the alternative transcription factor, SigB, whose activity is controlled by a partner switching mechanism that also involves the anti-sigma factor, RsbW, and the antagonist protein, RsbV. Recently, the SigB regulon has been shown to be continuously induced and functionally important in cells actively growing at low temperature. With the exception of this chill induction, all SigB-activating stimuli identified so far trigger a transient expression of the SigB regulon that depends on RsbV. Through a proteome analysis and Northern blot and gene fusion experiments, we now show that the SigB regulon is continuously induced in cells growing actively at 51 degrees C, close to the upper growth limit of B. subtilis. This heat induction of SigB-dependent genes requires the environmental stress-responsive phosphatase RsbU, but not the metabolic stress-responsive phosphatase RsbP. RsbU dependence of SigB activation by heat is overcome in mutants that lack RsbV. In addition, loss of RsbV alone or in combination with RsbU triggers a hyperactivation of the general stress regulon exclusively at high temperatures detrimental for cell growth. These new facets of heat induction of the SigB regulon indicate that the current view of the complex genetic and biochemical regulation of SigB activity is still incomplete and that SigB perceives signals independent of the RsbV-mediated signal transduction pathways under heat stress conditions.
Collapse
Affiliation(s)
- Gudrun Holtmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Str., D-35032 Marburg, Federal Republic of Germany
| | | | | | | | | | | | | |
Collapse
|
117
|
Kock H, Gerth U, Hecker M. The ClpP peptidase is the major determinant of bulk protein turnover in Bacillus subtilis. J Bacteriol 2004; 186:5856-64. [PMID: 15317791 PMCID: PMC516825 DOI: 10.1128/jb.186.17.5856-5864.2004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Measurements of overall protein degradation rates in wild-type and clpP mutant Bacillus subtilis cells revealed that stress- or starvation-induced bulk protein turnover depends virtually exclusively on the ClpP peptidase. ClpP is also essential for intracellular protein quality control, and in its absence newly synthesized proteins were highly prone to aggregation even at 37 degrees C. Proteomic comparisons between the wild type and a DeltaclpP mutant showed that the absence of ClpP leads to severe perturbations of "normal" physiology, complicating the detection of ClpP substrates. A pulse-chase two-dimensional gel approach was therefore used to compare wild-type and clpP mutant cultures that had been radiolabeled in mid-exponential phase, by quantifying changes in relative spot intensities with time. The results showed that overall proteolysis is biased toward proteins with vegetative functions which are no longer required (or are required at lower levels) in the nongrowing state. The identified substrate candidates for ClpP-dependent degradation include metabolic enzymes and aminoacyl-tRNA synthetases. Some substrate candidates catalyze the first committed step of certain biosynthetic pathways. Our data suggest that ClpP-dependent proteolysis spans a broad physiological spectrum, with regulatory processing of key metabolic components and regulatory proteins on the one side and general bulk protein breakdown at the transition from growing to nongrowing phases on the other.
Collapse
Affiliation(s)
- Holger Kock
- Ernst-Moritz-Arndt-Universität, Institut für Mikrobiologie, F-L-Jahn-Str. 15, 17487 Greifswald, Germany
| | | | | |
Collapse
|
118
|
Westers H, Darmon E, Zanen G, Veening JW, Kuipers OP, Bron S, Quax WJ, van Dijl JM. The Bacillus secretion stress response is an indicator for alpha-amylase production levels. Lett Appl Microbiol 2004; 39:65-73. [PMID: 15189290 DOI: 10.1111/j.1472-765x.2004.01539.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS Overproduced alpha-amylases in Bacillus subtilis provoke a specific stress response involving the CssRS two-component system, which controls expression of the HtrA and HtrB proteases. Previously, the B. subtilis TepA protein was implicated in high-level alpha-amylase secretion. Our present studies were aimed at investigating a possible role of TepA in secretion stress management, and characterizing the intensity of the secretion stress response in relation to alpha-amylase production. METHODS AND RESULTS The expression of a transcriptional htrB-lacZ gene fusion, and the levels of alpha-amylase production were monitored simultaneously using tepA mutant B. subtilis strains. TepA was shown to be dispensable for secretion stress management. Importantly, however, the levels of htrB-lacZ expression can be correlated with the levels of alpha-amylase production. CONCLUSION Our observations show that the secretion stress response can serve as an indicator for alpha-amylase production levels. SIGNIFICANCE AND IMPACT OF STUDY Conceivably, this stress response can be employed to monitor the biotechnological production of various secretory proteins by the Bacillus cell factory.
Collapse
Affiliation(s)
- H Westers
- Department of Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan, Groningen, the Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
119
|
Tjalsma H, Antelmann H, Jongbloed JDH, Braun PG, Darmon E, Dorenbos R, Dubois JYF, Westers H, Zanen G, Quax WJ, Kuipers OP, Bron S, Hecker M, van Dijl JM. Proteomics of protein secretion by Bacillus subtilis: separating the "secrets" of the secretome. Microbiol Mol Biol Rev 2004; 68:207-33. [PMID: 15187182 PMCID: PMC419921 DOI: 10.1128/mmbr.68.2.207-233.2004] [Citation(s) in RCA: 431] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Secretory proteins perform a variety of important "remote-control" functions for bacterial survival in the environment. The availability of complete genome sequences has allowed us to make predictions about the composition of bacterial machinery for protein secretion as well as the extracellular complement of bacterial proteomes. Recently, the power of proteomics was successfully employed to evaluate genome-based models of these so-called secretomes. Progress in this field is well illustrated by the proteomic analysis of protein secretion by the gram-positive bacterium Bacillus subtilis, for which approximately 90 extracellular proteins were identified. Analysis of these proteins disclosed various "secrets of the secretome," such as the residence of cytoplasmic and predicted cell envelope proteins in the extracellular proteome. This showed that genome-based predictions reflect only approximately 50% of the actual composition of the extracellular proteome of B. subtilis. Importantly, proteomics allowed the first verification of the impact of individual secretion machinery components on the total flow of proteins from the cytoplasm to the extracellular environment. In conclusion, proteomics has yielded a variety of novel leads for the analysis of protein traffic in B. subtilis and other gram-positive bacteria. Ultimately, such leads will serve to increase our understanding of virulence factor biogenesis in gram-positive pathogens, which is likely to be of high medical relevance.
Collapse
Affiliation(s)
- Harold Tjalsma
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Kerklaan 30, 9751 NN Haren, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
120
|
Kock H, Gerth U, Hecker M. MurAA, catalysing the first committed step in peptidoglycan biosynthesis, is a target of Clp-dependent proteolysis in Bacillus subtilis. Mol Microbiol 2004; 51:1087-102. [PMID: 14763982 DOI: 10.1046/j.1365-2958.2003.03875.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The carboxyvinyl transfer from phosphoenolpyruvate to UDP-N-acetylglucosamine is the first committed step in the pathway of peptidoglycan formation. This crucial reaction for bacterial cell growth is catalysed by the MurA enzymes. Gram-negative bacteria carry one murA gene, whereas in a subgroup of Gram-positive bacteria two separate paralogues, MurAA and MurAB, exist. This study provides evidence that in the Gram-positive bacterium Bacillus subtilis, the MurAA protein is specifically degraded by the ClpCP protease. This Clp-dependent degradation is especially enhanced upon entry into stationary phase, thus ensuring an immediate growth arrest due to stalled murein biosynthesis. The MurAA protein can therefore be addressed as a target of Clp-dependent regulatory proteolysis such as the transcriptional regulators CtsR, ComK, Spx in B. subtilis, CtrA in Caulobacter crescentus or RpoS in Escherichia coli. Taking into account all other known regulatory targets of ATP-dependent proteases, MurAA of B. subtilis represents the first example of a metabolic enzyme which is a unique regulatory substrate of Clp-dependent proteolysis. Its function as a regulatory metabolic checkpoint resembles that of homoserine trans-succinylase (MetA) in E. coli which is similarly ATP-dependently degraded.
Collapse
Affiliation(s)
- Holger Kock
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Mikrobiologie und Molekularbiologie, Germany.
| | | | | |
Collapse
|
121
|
Tjalsma H, Koetje EJ, Kiewiet R, Kuipers OP, Kolkman M, van der Laan J, Daskin R, Ferrari E, Bron S. Engineering of quorum-sensing systems for improved production of alkaline protease by Bacillus subtilis. J Appl Microbiol 2004; 96:569-78. [PMID: 14962137 DOI: 10.1111/j.1365-2672.2004.02179.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIM Engineering of Rap-Phr quorum-sensing systems of Bacillus subtilis and subsequent evaluation of the transcription of the aprE gene, encoding a major extracellular alkaline protease. METHODS AND RESULTS Addition of synthetic Phr pentapeptides to the growth medium, or overproduction of pre-Phr peptides, slightly improved the transcription of the aprE gene in B. subtilis. Disruption of certain rap genes similarly improved the transcription of the aprE gene. The production of extracellular proteolytic enzymes was increased when the rapA mutation was combined with a degU32 (Hy) mutation for hyper-secretion. CONCLUSIONS Certain Rap-Phr systems of B. subtilis seem to suppress extracellular AprE production. Although this may be an important feature under natural conditions, repression of AprE production by these systems is not desirable under fermentation conditions. SIGNIFICANCE AND IMPACT OF THE STUDY Although the levels of aprE transcriptional increase in this study are moderate, engineering of Rap-Phr systems may be used to improve the yield of Bacillus strains that are used for the production of the extracellular protease AprE, or Bacillus strains that use of the aprE promoter for the production of a heterologous protein.
Collapse
Affiliation(s)
- H Tjalsma
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Kerklaan, NN Haren, the Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
122
|
Foucaud-Scheunemann C, Poquet I. HtrA is a key factor in the response to specific stress conditions in Lactococcus lactis. FEMS Microbiol Lett 2003; 224:53-9. [PMID: 12855167 DOI: 10.1016/s0378-1097(03)00419-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigated the physiological role of Lactococcus lactis housekeeping surface protease HtrA. It is involved in surface properties under regular growth conditions, as the htrA mutant strain forms longer chains in liquid medium. It participates in cellular defence against environmental stress conditions: compared to the wild-type strain, the htrA mutant strain exhibited increased sensitivity to heat, ethanol, puromycin, and NaCl, but not to pH, H2O2, bile salts or to carbon or nitrogen starvation. htrA transcription in the wild-type strain showed a transient increase under stress conditions determined as requiring htrA, but not under overexpression of a secreted heterologous protein. Our results demonstrate that in L. lactis, htrA is a key factor in the response to specific stress conditions.
Collapse
|
123
|
Antelmann H, Darmon E, Noone D, Veening JW, Westers H, Bron S, Kuipers OP, Devine KM, Hecker M, van Dijl JM. The extracellular proteome of Bacillus subtilis under secretion stress conditions. Mol Microbiol 2003; 49:143-56. [PMID: 12823817 DOI: 10.1046/j.1365-2958.2003.03565.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The accumulation of malfolded proteins in the cell envelope of the Gram-positive eubacterium Bacillus subtilis was previously shown to provoke a so-called secretion stress response. In the present studies, proteomic approaches were employed to identify changes in the extracellular proteome of B. subtilis in response to secretion stress. The data shows that, irrespective of the way in which secretion stress is imposed on the cells, the levels of only two extracellular proteins, HtrA and YqxI, display major variations in a parallel manner. Whereas the extracellular level of the HtrA protease is determined through transcriptional regulation, the level of YqxI in the growth medium is determined post-transcriptionally in an HtrA-dependent manner. In the absence of secretion stress, the extracellular levels of HtrA and YqxI are low because of extracytoplasmic proteolysis. Finally, the protease active site of HtrA is dispensable for post-transcriptional YqxI regulation. It is known that Escherichia coli HtrA has combined protease and chaperone-like activities. As this protein shares a high degree of similarity with B. subtilis HtrA, it can be hypothesized that both activities are conserved in B. subtilis HtrA. Thus, a chaperone-like activity of B. subtilis HtrA could be involved in the appearance of YqxI on the extracellular proteome.
Collapse
Affiliation(s)
- Haike Antelmann
- Institut für Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universität Greifswald, F. -L. -Jahn-Str. 15, D-17487 Greifswald, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
124
|
Abstract
All organisms respond to a sudden increase in temperature by the so-called heat shock response. This response results in the induction of a subset of genes, designated heat shock genes coding for heat shock proteins, which allow the cell to cope with the stress regimen. Research carried out during the last 10 years with eubacteria has revealed that the heat shock genes of a given species fall into different classes (regulons), where each class is regulated by a different transcriptional regulator, which could be an alternative sigma factor, a transcriptional activator, or a transcriptional repressor. All regulons of a single species constitute the heat shock stimulon. In Bacillus subtilis, more than 200 genes representing over 7% of the transcriptionally active genes are induced at least 3-fold in response to a heat shock. This response becomes apparent within the first minute after exposure to heat stress, is transient, and is coordinated by at least 5 transcriptional regulator proteins, including 2 repressors, an alternate sigma-factor, and a 2-component signal transduction system. A detailed analysis of the regulation of all known heat shock genes has shown that they belong to at least 6 regulons that together comprise the B. subtilis heat shock stimulon. Potential thermosensors are discussed in this article.
Collapse
Affiliation(s)
- Wolfgang Schumann
- Institute of Genetics, University of Bayreuth, D-95440 Bayreuth, Germany.
| |
Collapse
|
125
|
|