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Evaluation of temperature, pH and nutrient conditions in bacterial growth and extracellular hydrolytic activities of two Alicyclobacillus spp. strains. Arch Microbiol 2021; 203:4557-4570. [PMID: 34159433 DOI: 10.1007/s00203-021-02332-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 12/16/2022]
Abstract
Extremophile bacteria have developed the metabolic machinery for living in extreme temperatures, pH, and high-salt content. Two novel bacterium strains Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2, were isolated from crater lake El Chichon in Chiapas, Mexico. Phylogenetic tree analysis based on the 16SrRNA gene sequence revealed that the strain Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2 were closely related to Alicyclobacillus species (98% identity and 94.73% identity, respectively). Both strains were Gram variable, and colonies were circular, smooth and creamy. Electron microscopy showed than Alicyclobacillus sp. PA1 has a daisy-like form and Alicyclobacillus sp. PA2 is a regular rod. Both strains can use diverse carbohydrates and triglycerides as carbon source and they also can use organic and inorganic nitrogen source. But, the two strains can grow without any carbon or nitrogen sources in the culture medium. Temperature, pH and nutrition condition affect bacterial growth. Maximum growth was produced at 65 °C for Alicyclobacillus sp. PA1 (0.732 DO600) at pH 3 and Alicyclobacillus sp. PA2 (0.725 DO600) at pH 5. Inducible extracellular extremozyme activities were determined for β-galactosidase (Alicyclobacillus sp. PA1: 88.07 ± 0.252 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), cellulose (Alicyclobacillus sp. PA1: 141.20 ± 0.585 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), lipase (Alicyclobacillus sp. PA1: 138.25 ± 0.600 U/mg, Alicyclobacillus sp. PA2: 175.75 ± 1.387 U/mg), xylanase (Alicyclobacillus sp. PA1: 174.72 ± 1.746 U/mg, Alicyclobacillus sp. PA2: 172.69 ± 0.855U/mg), and protease (Alicyclobacillus sp. PA1: 15.12 ± 0.121 U/mg, Alicyclobacillus sp. PA2: 15.33 ± 0.284 U/mg). These results provide new insights on extreme enzymatic production on Alicyclobacillus species.
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Schilling T, Dietrich S, Hoppert M, Hertel R. A CRISPR-Cas9-Based Toolkit for Fast and Precise In Vivo Genetic Engineering of Bacillus subtilis Phages. Viruses 2018; 10:v10050241. [PMID: 29734705 PMCID: PMC5977234 DOI: 10.3390/v10050241] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/29/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
Phages are currently under discussion as a solution for the antibiotic crisis, as they may cure diseases caused by multi-drug-resistant pathogens. However, knowledge of phage biology and genetics is limited, which impedes risk assessment of therapeutic applications. In order to enable advances in phage genetic research, the aim of this work was to create a toolkit for simple and fast genetic engineering of phages recruiting Bacillus subtilis as host system. The model organism B. subtilis represents a non-pathogenic surrogate of its harmful relatives, such as Bacillus anthracis or Bacillus cereus. This toolkit comprises the application CutSPR, a bioinformatic tool for rapid primer design, and facilitates the cloning of specific CRISPR-Cas9-based mutagenesis plasmids. The employment of the prophage-free and super-competent B. subtilis TS01 strain enables an easy and fast introduction of specific constructs for in vivo phage mutagenesis. Clean gene deletions and a functional clean gene insertion into the genome of the model phage vB_BsuP-Goe1 served as proof of concept and demonstrate reliability and high efficiency. The here presented toolkit allows comprehensive investigation of the diverse phage genetic pool, a better understanding of phage biology, and safe phage applications.
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Affiliation(s)
- Tobias Schilling
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany.
| | - Sascha Dietrich
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany.
| | - Michael Hoppert
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany.
| | - Robert Hertel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany.
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Takada H, Shiwa Y, Takino Y, Osaka N, Ueda S, Watanabe S, Chibazakura T, Su'etsugu M, Utsumi R, Yoshikawa H. Essentiality of WalRK for growth in Bacillus subtilis and its role during heat stress. MICROBIOLOGY-SGM 2018; 164:670-684. [PMID: 29465029 DOI: 10.1099/mic.0.000625] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
WalRK is an essential two-component signal transduction system that plays a central role in coordinating cell wall synthesis and cell growth in Bacillus subtilis. However, the physiological role of WalRK and its essentiality for growth have not been elucidated. We investigated the behaviour of WalRK during heat stress and its essentiality for cell proliferation. We determined that the inactivation of the walHI genes which encode the negative modulator of WalK, resulted in growth defects and eventual cell lysis at high temperatures. Screening of suppressor mutations revealed that the inactivation of LytE, an dl-endopeptidase, restored the growth of the ΔwalHI mutant at high temperatures. Suppressor mutations that reduced heat induction arising from the walRK regulon were also mapped to the walK ORF. Therefore, we hypothesized that overactivation of LytE affects the phenotype of the ΔwalHI mutant. This hypothesis was corroborated by the overexpression of the negative regulator of LytE, IseA and PdaC, which rescued the growth of the ΔwalHI mutant at high temperatures. Elucidating the cause of the temperature sensitivity of the ΔwalHI mutant could explain the essentiality of WalRK. We proved that the constitutive expression of lytE or cwlO using a synthetic promoter uncouples these expressions from WalRK, and renders WalRK nonessential in the pdaC and iseA mutant backgrounds. We propose that the essentiality of WalRK is derived from the coordination of cell wall metabolism with cell growth by regulating dl-endopeptidase activity under various growth conditions.
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Affiliation(s)
- Hiraku Takada
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan.,Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yuta Takino
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Natsuki Osaka
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shuhei Ueda
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, 3327-204 Nakamachi, Nara-shi, Nara 631-8505, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Taku Chibazakura
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masayuki Su'etsugu
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Ryutaro Utsumi
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, 3327-204 Nakamachi, Nara-shi, Nara 631-8505, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.,Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
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4
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Phan T, Huynh P, Truong T, Nguyen H. A Generic Protocol for Intracellular Expression of Recombinant Proteins in Bacillus subtilis. Methods Mol Biol 2017; 1586:325-334. [PMID: 28470615 DOI: 10.1007/978-1-4939-6887-9_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Bacillus subtilis (B. subtilis) is a potential and attractive host for the production of recombinant proteins. Different expression systems for B. subtilis have been developed recently, and various target proteins have been recombinantly synthesized and purified using this host. In this chapter, we introduce a generic protocol to express a recombinant protein in B. subtilis. It includes protocols for (1) using our typical expression vector (plasmid pHT254) to introduce a target gene, (2) transformation of the target vector into B. subtilis, and (3) evaluation of the actual expression of a recombinant protein.
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Affiliation(s)
- Trang Phan
- VNUHCM-University of Science, 227 Nguyen Van Cu, District 5, Hochiminh City, Vietnam
| | - Phuong Huynh
- VNUHCM-University of Science, 227 Nguyen Van Cu, District 5, Hochiminh City, Vietnam
| | - Tuom Truong
- VNUHCM-University of Science, 227 Nguyen Van Cu, District 5, Hochiminh City, Vietnam
| | - Hoang Nguyen
- VNUHCM-University of Science, 227 Nguyen Van Cu, District 5, Hochiminh City, Vietnam.
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Brumm PJ, De Maayer P, Mead DA, Cowan DA. Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. Front Microbiol 2015; 6:430. [PMID: 26029180 PMCID: PMC4428132 DOI: 10.3389/fmicb.2015.00430] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/22/2015] [Indexed: 11/13/2022] Open
Abstract
In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan.
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Affiliation(s)
- Phillip J. Brumm
- C5•6 TechnologiesMiddleton, WI, USA
- Great Lakes Bioenergy Research Center, University of WisconsinMadison, WI, USA
| | - Pieter De Maayer
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
- Department of Microbiology and Plant Pathology, University of PretoriaPretoria, South Africa
| | - David A. Mead
- C5•6 TechnologiesMiddleton, WI, USA
- Great Lakes Bioenergy Research Center, University of WisconsinMadison, WI, USA
- Lucigen CorporationMiddleton, WI, USA
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
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Krajewski SS, Joswig M, Nagel M, Narberhaus F. A tricistronic heat shock operon is important for stress tolerance of Pseudomonas putida and conserved in many environmental bacteria. Environ Microbiol 2014; 16:1835-53. [PMID: 24612349 DOI: 10.1111/1462-2920.12432] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 02/13/2014] [Indexed: 11/28/2022]
Abstract
Small heat shock proteins (sHsps) including the well-studied IbpA protein from Escherichia coli are molecular chaperones that bind to non-native proteins and prevent them from aggregation. We discovered an entirely unexplored tricistronic small heat shock gene cluster in Pseudomonas putida. The genes pp3314, pp3313 and pp3312 (renamed to hspX, hspY and hspZ respectively) are transcribed in a single transcript. In addition to σ(32) -dependent transcriptional control, translation of the first and second gene of the operon is controlled by RNA thermometers with novel architectures. Biochemical analysis of HspY, HspZ and P. putida IbpA demonstrated that they assemble into homo-oligomers of different sizes whose quaternary structures alter in a temperature-dependent manner. IbpA and HspY are able to prevent the model substrate citrate synthase from thermal aggregation in vitro. Increased stress sensitivity of a P. putida strain lacking HspX, HspY and HspZ revealed an important role of these sHsps in stress adaptation. The hspXYZ operon is conserved among metabolically related bacteria that live in hostile environments including polluted soils. This heat shock operon might act as a protective system to promote survival in such ecological niches.
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In Silico Analysis of β-Galactosidases Primary and Secondary Structure in relation to Temperature Adaptation. JOURNAL OF AMINO ACIDS 2014; 2014:475839. [PMID: 24790757 PMCID: PMC3982409 DOI: 10.1155/2014/475839] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/06/2014] [Indexed: 11/18/2022]
Abstract
β -D-Galactosidases (EC 3.2.1.23) hydrolyze the terminal nonreducing β -D-galactose residues in β -D-galactosides and are ubiquitously present in all life forms including extremophiles. Eighteen microbial β -galactosidase protein sequences, six each from psychrophilic, mesophilic, and thermophilic microbes, were analyzed. Primary structure reveals alanine, glycine, serine, and arginine to be higher in psychrophilic β -galactosidases whereas valine, glutamine, glutamic acid, phenylalanine, threonine, and tyrosine are found to be statistically preferred by thermophilic β -galactosidases. Cold active β -galactosidase has a strong preference towards tiny and small amino acids, whereas high temperature inhabitants had higher content of basic and aromatic amino acids. Thermophilic β -galactosidases have higher percentage of α -helix region responsible for temperature tolerance while cold loving β -galactosidases had higher percentage of sheet and coil region. Secondary structure analysis revealed that charged and aromatic amino acids were significant for sheet region of thermophiles. Alanine was found to be significant and high in the helix region of psychrophiles and valine counters in thermophilic β -galactosidase. Coil region of cold active β -galactosidase has higher content of tiny amino acids which explains their high catalytic efficiency over their counterparts from thermal habitat. The present study has revealed the preference or prevalence of certain amino acids in primary and secondary structure of psychrophilic, mesophilic, and thermophilic β -galactosidase.
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Polysaccharide-degrading thermophiles generated by heterologous gene expression in Geobacillus kaustophilus HTA426. Appl Environ Microbiol 2013; 79:5151-8. [PMID: 23793634 DOI: 10.1128/aem.01506-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Thermophiles have important advantages over mesophiles as host organisms for high-temperature bioprocesses, functional production of thermostable enzymes, and efficient expression of enzymatic activities in vivo. To capitalize on these advantages of thermophiles, we describe here a new inducible gene expression system in the thermophile Geobacillus kaustophilus HTA426. Six promoter regions in the HTA426 genome were identified and analyzed for expression profiles using β-galactosidase reporter assay. This analysis identified a promoter region upstream of a putative amylose-metabolizing gene cluster that directed high-level expression of the reporter gene. The expression was >280-fold that without a promoter and was further enhanced 12-fold by maltose addition. In association with a multicopy plasmid, this promoter region was used to express heterologous genes. Several genes, including a gene whose product was insoluble when expressed in Escherichia coli, were successfully expressed as soluble proteins, with yields of 0.16 to 59 mg/liter, and conferred new functions to G. kaustophilus strains. Remarkably, cellulase and α-amylase genes conferred the ability to degrade cellulose paper and insoluble starch at high temperatures, respectively, generating thermophiles with the potential to degrade plant biomass. Our results demonstrate that this novel expression system expands the potential applications of G. kaustophilus.
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Krajewski SS, Nagel M, Narberhaus F. Short ROSE-like RNA thermometers control IbpA synthesis in Pseudomonas species. PLoS One 2013; 8:e65168. [PMID: 23741480 PMCID: PMC3669281 DOI: 10.1371/journal.pone.0065168] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 04/22/2013] [Indexed: 11/18/2022] Open
Abstract
The bacterial small heat shock protein IbpA protects client proteins from aggregation. Due to redundancy in the cellular chaperone network, deletion of the ibpA gene often leads to only a mild or no phenotypic defect. In this study, we show that a Pseudomonas putida ibpA deletion mutant has a severe growth defect under heat stress conditions and reduced survival during recovery revealing a critical role of IbpA in heat tolerance. Transcription of the ibpA gene depends on the alternative heat shock sigma factor σ32. Production of IbpA protein only at heat shock temperatures suggested additional translational control. We conducted a comprehensive structural and functional analysis of the 5′ untranslated regions of the ibpA genes from P. putida and Pseudomonas aeruginosa. Both contain a ROSE-type RNA thermometer that is substantially shorter and simpler than previously reported ROSE elements. Comprised of two hairpin structures only, they inhibit translation at low temperature and permit translation initiation after a temperature upshift. Both elements regulate reporter gene expression in Escherichia coli and ribosome binding in vitro in a temperature-dependent manner. Structure probing revealed local melting of the second hairpin whereas the first hairpin remained unaffected. High sequence and structure conservation of pseudomonal ibpA untranslated regions and their ability to confer thermoregulation in vivo suggest that short ROSE-like thermometers are commonly used to control IbpA synthesis in Pseudomonas species.
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Affiliation(s)
| | - Miriam Nagel
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
- * E-mail:
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10
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Yang M, Zhang W, Ji S, Cao P, Chen Y, Zhao X. Generation of an artificial double promoter for protein expression in Bacillus subtilis through a promoter trap system. PLoS One 2013; 8:e56321. [PMID: 23409173 PMCID: PMC3568030 DOI: 10.1371/journal.pone.0056321] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 01/08/2013] [Indexed: 11/28/2022] Open
Abstract
Bacillus subtilis is an attractive host for production of recombinant proteins. Promoters and expression plasmid backbones have direct impacts on the efficiency of gene expression. To screen and isolate strong promoters, a promoter trap vector pShuttleF was developed in this study. Using the vector, approximately 1000 colonies containing likely promoters from Bacillus licheniformis genomic DNA were obtained. Amongst them, pShuttle-09 exhibited the highest β-Gal activities in both Escherichia coli and B. subtilis. The activity of pShuttle-09 in B. subtilis was eight times of that of the P43 promoter, a commonly used strong promoter for B. subtilis. A sequence analysis showed that pShuttle-09 contained PluxS and truncated luxS in-frame fused with the reporter gene as well as another fragment upstream of PluxS containing a putative promoter. This putative promoter was a hybrid promoter and its β-Gal activity was higher than PluxS. Reconstructing the hybrid promoter from pShuttle-09 to PlapS further improved the β-Gal production by 60%. The usefulness of our promoter trap system is likely due to random shuffling and recombination of DNA fragments and adoption of a rapid and high-throughput screening. Thus, our data provide additional evidence to support the concept of using a promoter trap system to create new promoters.
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Affiliation(s)
- Mingming Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People's Republic of China
| | - Weiwei Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People's Republic of China
| | - Shengyue Ji
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People's Republic of China
| | - Pinghua Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People's Republic of China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People's Republic of China
- * E-mail: (YC); (XZ)
| | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People's Republic of China
- Department of Animal Science, McGill University, Quebec, Canada
- * E-mail: (YC); (XZ)
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Expression of a cryptic secondary sigma factor gene unveils natural competence for DNA transformation in Staphylococcus aureus. PLoS Pathog 2012; 8:e1003003. [PMID: 23133387 PMCID: PMC3486894 DOI: 10.1371/journal.ppat.1003003] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 09/17/2012] [Indexed: 12/19/2022] Open
Abstract
It has long been a question whether Staphylococcus aureus, a major human pathogen, is able to develop natural competence for transformation by DNA. We previously showed that a novel staphylococcal secondary sigma factor, SigH, was a likely key component for competence development, but the corresponding gene appeared to be cryptic as its expression could not be detected during growth under standard laboratory conditions. Here, we have uncovered two distinct mechanisms allowing activation of SigH production in a minor fraction of the bacterial cell population. The first is a chromosomal gene duplication rearrangement occurring spontaneously at a low frequency [≤10−5], generating expression of a new chimeric sigH gene. The second involves post-transcriptional regulation through an upstream inverted repeat sequence, effectively suppressing expression of the sigH gene. Importantly, we have demonstrated for the first time that S. aureus cells producing active SigH become competent for transformation by plasmid or chromosomal DNA, which requires the expression of SigH-controlled competence genes. Additionally, using DNA from the N315 MRSA strain, we successfully transferred the full length SCCmecII element through natural transformation to a methicillin-sensitive strain, conferring methicillin resistance to the resulting S. aureus transformants. Taken together, we propose a unique model for staphylococcal competence regulation by SigH that could help explain the acquisition of antibiotic resistance genes through horizontal gene transfer in this important pathogen. Staphylococcus aureus is a major human pathogen responsible for a broad spectrum of infections, emphasized by the emergence of multiple antibiotic-resistant strains with up to 60% of strains worldwide resistant to methicillin (Methicillin Resistant Staphylococcus aureus or MRSA). Indeed, MRSA-related infections are now one of the leading causes of death in the USA, highlighting the growing threat this bacterium poses to human health. Many bacteria have the ability to acquire novel genetic characteristics, including antibiotic resistance, through the uptake of extracellular DNA, a phenomenon known as natural genetic transformation or competence. We have shown that the SigH staphylococcal sigma factor is a likely key component for competence development, but that its gene is not expressed under standard laboratory conditions. Here, we have uncovered two distinct mechanisms allowing activation of SigH production in S. aureus: a chromosomal gene duplication rearrangement and post-transcriptional regulation through an upstream inverted repeat sequence. Importantly, we have demonstrated for the first time that S. aureus cells producing active SigH become competent for natural transformation by plasmid or chromosomal DNA, and we were able to confer methicillin resistance to a methicillin-sensitive strain by transformation with chromosomal DNA. SigH-dependent competence development in S. aureus could help explain the acquisition of antibiotic resistance genes and the rise of the so-called “superbug."
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Counterselection system for Geobacillus kaustophilus HTA426 through disruption of pyrF and pyrR. Appl Environ Microbiol 2012; 78:7376-83. [PMID: 22885745 DOI: 10.1128/aem.01669-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Counterselection systems facilitate marker-free genetic modifications in microbes by enabling positive selections for both the introduction of a marker gene into the microbe and elimination of the marker from the microbe. Here we report a counterselection system for Geobacillus kaustophilus HTA426, established through simultaneous disruption of the pyrF and pyrR genes. The pyrF gene, essential for pyrimidine biosynthesis and metabolization of 5-fluoroorotic acid (5-FOA) to toxic metabolites, was disrupted by homologous recombination. The resultant MK54 strain (ΔpyrF) was auxotrophic for uracil and resistant to 5-FOA. MK54 complemented with pyrF was prototrophic for uracil but insensitive to 5-FOA in the presence of uracil. To confer 5-FOA sensitivity, the pyrR gene encoding an attenuator to repress pyrimidine biosynthesis by sensing uracil derivatives was disrupted. The resultant MK72 strain (ΔpyrF ΔpyrR) was auxotrophic for uracil and resistant to 5-FOA. MK72 complemented with pyrF was prototrophic for uracil and 5-FOA sensitive even in the presence of uracil. The results suggested that pyrF could serve as a counterselection marker in MK72, which was demonstrated by efficient marker-free integrations of heterologous β-galactosidase and α-amylase genes. The integrated genes were functionally expressed in G. kaustophilus and conferred new functions on the thermophile. This report describes the first establishment of a pyrF-based counterselection system in a Bacillus-related bacterium, along with the first demonstration of homologous recombination and heterologous gene expression in G. kaustophilus. Our results also suggest a new strategy for establishment of counterselection systems.
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Zhang WW, Gao QR, Yang MM, Liu H, Wang D. Assay and characterization of an osmolarity inducible promoter newly isolated from Bacillus subtilis. Mol Biol Rep 2012; 39:7347-53. [DOI: 10.1007/s11033-012-1566-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 01/25/2012] [Indexed: 11/30/2022]
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14
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Welsch N, Homuth G, Schweder T. Suitability of different β-galactosidases as reporter enzymes in Bacillus subtilis. Appl Microbiol Biotechnol 2011; 93:381-92. [PMID: 22052389 DOI: 10.1007/s00253-011-3645-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 09/27/2011] [Accepted: 10/12/2011] [Indexed: 11/30/2022]
Abstract
The suitability of three β-galactosidases as reporter enzymes for promoter expression analyses was investigated in Bacillus subtilis with respect to various temperature conditions during cultivation and assay procedures. Starting from the hypothesis that proteins derived from diverse habitats have different advantages as reporters at different growth temperatures, the beta-galactosidases from the thermophilic organism Bacillus stearothermophilus, from the mesophilic bacterium Escherichia coli and from the psychrophilic organism Pseudoalteromonas haloplanktis TAE79 were analysed under control of the constitutive B. subtilis lepA promoter. Subsequent expression of the β-galactosidase genes and determination of specific activities was performed at different cultivation and assay temperatures using B. subtilis as host. Surprisingly, the obtained results demonstrated that the highest activities over a broad cultivation temperature range were obtained using the β-galactosidase from the mesophilic bacterium E. coli whereas the enzymes from the thermophilic and psychrophilic bacteria revealed a more restricted usability in terms of cultivation temperature.
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Affiliation(s)
- Norma Welsch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Greifswald, Germany
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Oliveira C, Guimarães PM, Domingues L. Recombinant microbial systems for improved β-galactosidase production and biotechnological applications. Biotechnol Adv 2011; 29:600-9. [DOI: 10.1016/j.biotechadv.2011.03.008] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 01/24/2011] [Accepted: 03/31/2011] [Indexed: 11/28/2022]
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Kortmann J, Sczodrok S, Rinnenthal J, Schwalbe H, Narberhaus F. Translation on demand by a simple RNA-based thermosensor. Nucleic Acids Res 2010; 39:2855-68. [PMID: 21131278 PMCID: PMC3074152 DOI: 10.1093/nar/gkq1252] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Structured RNA regions are important gene control elements in prokaryotes and eukaryotes. Here, we show that the mRNA of a cyanobacterial heat shock gene contains a built-in thermosensor critical for photosynthetic activity under stress conditions. The exceptionally short 5′-untranslated region is comprised of a single hairpin with an internal asymmetric loop. It inhibits translation of the Synechocystis hsp17 transcript at normal growth conditions, permits translation initiation under stress conditions and shuts down Hsp17 production in the recovery phase. Point mutations that stabilized or destabilized the RNA structure deregulated reporter gene expression in vivo and ribosome binding in vitro. Introduction of such point mutations into the Synechocystis genome produced severe phenotypic defects. Reversible formation of the open and closed structure was beneficial for viability, integrity of the photosystem and oxygen evolution. Continuous production of Hsp17 was detrimental when the stress declined indicating that shutting-off heat shock protein production is an important, previously unrecognized function of RNA thermometers. We discovered a simple biosensor that strictly adjusts the cellular level of a molecular chaperone to the physiological need.
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Affiliation(s)
- Jens Kortmann
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, 44780 Bochum, Germany
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17
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Differential responses of Bacillus subtilis rRNA promoters to nutritional stress. J Bacteriol 2010; 193:723-33. [PMID: 21097612 DOI: 10.1128/jb.00708-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The in vivo expression levels of four rRNA promoter pairs (rrnp(1)p(2)) of Bacillus subtilis were determined by employing single-copy lacZ fusions integrated at the amyE locus. The rrnO, rrnJ, rrnD, and rrnB promoters displayed unique growth rate regulation and stringent responses. Both lacZ activity and mRNA levels were highest for rrnO under all growth conditions tested, while rrnJ, rrnB, and rrnD showed decreasing levels of activity. During amino acid starvation induced by serine hydroxamate (SHX), only the strong rrnO and rrnJ promoters demonstrated stringent responses. Under the growth conditions used, the rrn promoters showed responses similar to the responses to carbon source limitation induced by α-methyl glucoside (α-MG). The ratio of P2 to P1 transcripts, determined by primer extension analysis, was high for the strong rrnO and rrnJ promoters, while only P2 transcripts were detected for the weak rrnD and rrnB promoters. Cloned P1 or P2 promoter fragments of rrnO or rrnJ were differentially regulated. In wild-type (relA(+)) and suppressor [relA(S)] strains under the conditions tested, only P2 responded to carbon source limitation by a decrease in RNA synthesis, correlating with an increase in (p)ppGpp levels and a decrease in the GTP concentration. The weak P1 promoter elements remain relaxed in the three genetic backgrounds [relA(+), relA, relA(S)] in the presence of α-MG. During amino acid starvation, P2 was stringently regulated in relA(+) and relA(S) cells, while only rrnJp(1) was also regulated, but to a lesser extent. Both the relA(+) and relA(S) strains showed (p)ppGpp accumulation after α-MG treatment but not after SHX treatment. These data reveal the complex nature of B. subtilis rrn promoter regulation in response to stress, and they suggest that the P2 promoters may play a more prominent role in the stringent response.
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Ming YM, Wei ZW, Lin CY, Sheng GY. Development of a Bacillus subtilis expression system using the improved Pglv promoter. Microb Cell Fact 2010; 9:55. [PMID: 20618987 PMCID: PMC2908567 DOI: 10.1186/1475-2859-9-55] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 07/10/2010] [Indexed: 11/12/2022] Open
Abstract
Background B. subtilis is an important organism in the biotechnological application. The efficient expression system is desirable in production of recombinant gene products in B. subtilis. Recently, we developed a new inducible expression system in B. subtilis, which directed by B. subtilis maltose utilization operon promoter Pglv. The system demonstrated high-level expression for target proteins in B. subtilis when induced by maltose. However, the system was markedly repressed by glucose. This limited the application of the system as a high-expression tool in biotechnology field. The aim of this study was to further improve the Pglv promoter system and enhance its expression strength. Results Here, site-directed mutagenesis was facilitated to enhance the expression strength of Pglv. The transcription level from four mutants was increased. Production of β-Gal from the mutants reached the maximum 1.8 times as high as that of wildtype promoter. When induced by 5% maltose, the production of β-Gal from two mutants reached 14.3 U/ml and 13.8 U/ml, 63.5% and 57.5% higher than wildtype promoter (8.8 U/ml) respectively. Thus, site-directed mutagenesis alleviated the repression of glucose and improved the expression activity. To further improve the promoter system, the B. subtilis expression host was reconstructed, in which B. subtilis well-characterized constitutive promoter P43 replaced the promoter of the glv operon in B. subtilis chromosome through a double crossover event. The β-galactosidase production from the improved system (21.1 U/mL) increased compared to that from origin system. Meanwhile, the repression caused by glucose was further alleviated. Conclusions In this study, we obtained a mutated promoter Pglv-M1 through site-directed mutagenesis, which demonstrated high expression strength and alleviated the repression caused by glucose. Moreover, we alleviated the repression and enhanced the expression activity of the Pglv-M1 promoter system via reconstruction of the B. subtilis host. Thus, we provided a valuable expression system in B. subtilis.
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Affiliation(s)
- Yang M Ming
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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Heterogeneous Properties of Individual Molecules of β-Galactosidase from the Thermophilic Bacteria Geobacillus stearothermophilus. Protein J 2010; 29:55-61. [DOI: 10.1007/s10930-009-9220-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Calvez S, Prévost H, Drider D. Identification of a new molecular target of class IIa bacteriocins in Listeria monocytogenes EGDe. Folia Microbiol (Praha) 2008; 53:417-22. [DOI: 10.1007/s12223-008-0063-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 04/14/2008] [Indexed: 11/30/2022]
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Chen W, Chen H, Xia Y, Zhao J, Tian F, Zhang H. Production, Purification, and Characterization of a Potential Thermostable Galactosidase for Milk Lactose Hydrolysis from Bacillus stearothermophilus. J Dairy Sci 2008; 91:1751-8. [DOI: 10.3168/jds.2007-617] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Nguyen HD, Phan TTP, Schumann W. Expression vectors for the rapid purification of recombinant proteins in Bacillus subtilis. Curr Microbiol 2007; 55:89-93. [PMID: 17624574 DOI: 10.1007/s00284-006-0419-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2006] [Accepted: 10/20/2006] [Indexed: 10/23/2022]
Abstract
We describe the construction of six novel plasmid-based IPTG-inducible expression vectors for Bacillus subtilis and related species. While one vector allows intracellular production of recombinant proteins, the second provides a strong secretion signal. The third vector allows addition of the c-Myc epitope tag, and the remaining three vectors provide the purification tags His and Strep. The versatility of all six vectors was demonstrated by the insertion of several reporter genes and by their regulated overexpression. Recombinant proteins with a His- or Strep-tag could be purified to near homogeneity in a single step.
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Affiliation(s)
- Hoang Duc Nguyen
- Institute of Genetics, University of Bayreuth, D-95440, Bayreuth, Germany
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23
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Li W, Li HX, Ji SY, Li S, Gong YS, Yang MM, Chen YL. Characterization of two temperature-inducible promoters newly isolated from B. subtilis. Biochem Biophys Res Commun 2007; 358:1148-53. [PMID: 17521615 DOI: 10.1016/j.bbrc.2007.05.064] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Accepted: 05/10/2007] [Indexed: 11/30/2022]
Abstract
Here, two temperature sensitive promoters, P2 and P7, isolated from Bacillus subtilis, were characterized. The production of beta-galactosidase driven by these promoters was much higher at 45 degrees C than that at 37 degrees C both in Escherichia coli and B. subtilis and that the P2 promoter showed higher expression strength in B. subtilis at 45 degrees C. Thereby, an efficient temperature-inducible expression system was constructed by using P2 promoter in B. subtilis. Thus, we isolated and characterized a newly temperature inducible promoter and exploited it as a potential expression element in B. subtilis.
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Affiliation(s)
- Wang Li
- College of Animal Sciences, Northwest A&F University, Yangling 712100, People's Republic of China
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24
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Parche S, Amon J, Jankovic I, Rezzonico E, Beleut M, Barutçu H, Schendel I, Eddy MP, Burkovski A, Arigoni F, Titgemeyer F. Sugar transport systems of Bifidobacterium longum NCC2705. J Mol Microbiol Biotechnol 2007; 12:9-19. [PMID: 17183207 DOI: 10.1159/000096455] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Here we present the complement of the carbohydrate uptake systems of the strictly anaerobic probiotic Bifidobacterium longum NCC2705. The genome analysis of this bacterium predicts that it has 19 permeases for the uptake of diverse carbohydrates. The majority belongs to the ATP-binding cassette transporter family with 13 systems identified. Among them are permeases for lactose, maltose, raffinose, and fructooligosaccharides, a commonly used prebiotic additive. We found genes that encode a complete phosphotransferase system (PTS) and genes for three permeases of the major facilitator superfamily. These systems could serve for the import of glucose, galactose, lactose, and sucrose. Growth analysis of NCC2705 cells combined with biochemical characterization and microarray data showed that the predicted substrates are consumed and that the corresponding transport and catabolic genes are expressed. Biochemical analysis of the PTS, in which proteins are central in regulation of carbon metabolism in many bacteria, revealed that B. longum has a glucose-specific PTS, while two other species (Bifidobacterium lactis and Bifidobacterium bifidum) have a fructose-6-phosphate-forming fructose-PTS instead. It became obvious that most carbohydrate systems are closely related to those from other actinomycetes, with a few exceptions. We hope that this report on B. longum carbohydrate transporter systems will serve as a guide for further in-depth analyses on the nutritional lifestyle of this beneficial bacterium.
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Affiliation(s)
- Stephan Parche
- Nestlé Research Center, Vers-chez-les-Blanc, Lausanne, Switzerland
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25
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Zhang AL, Liu H, Yang MM, Gong YS, Chen H. Assay and characterization of a strong promoter element from B. subtilis. Biochem Biophys Res Commun 2007; 354:90-5. [PMID: 17210127 DOI: 10.1016/j.bbrc.2006.12.137] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 12/18/2006] [Indexed: 11/26/2022]
Abstract
A new strong promoter fragment isolated from Bacillus subtilis was identified and characterized. Using the heat stable beta-galactosidase as reporter, the promoter fragment exhibited high expression strength both in Escherichia coli and B. subtilis. The typical prokaryotic promoter conservation regions were found in the promoter fragment and the putative promoter was identified as the control element of yxiE gene via sequencing assay and predication of promoter. To further verify and characterize the cloned strong promoter, the putative promoter was sub-cloned and the beta-Gal directed by the promoters was high-level expressed both in E. coli and B. subtilis. By means of the isolated promoter, an efficient expression system was developed in B. subtilis and the benefit and usefulness was demonstrated through expression of three heterologous and homogenous proteins. Thus, we identified a newly strong promoter of B. subtilis and provided a robust expression system for genetic engineering of B. subtilis.
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Affiliation(s)
- Ai-Ling Zhang
- College of Animal Sciences, Northwest A and F University, Yangling 712100, People's Republic of China
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26
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Asai K, Ootsuji T, Obata K, Matsumoto T, Fujita Y, Sadaie Y. Regulatory role of RsgI in sigI expression in Bacillus subtilis. MICROBIOLOGY-SGM 2007; 153:92-101. [PMID: 17185538 DOI: 10.1099/mic.0.29239-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes. The B. subtilis sigI gene is considered to constitute an operon with rsgI (regulation of sigI, formerly ykrI). As little is known about either the structure and function of the sigI-rsgI operon or the SigI regulons, the role of RsgI in heat-inducible transcription of the sigI-rsgI operon was investigated, using Northern analysis and a heat-stable beta-galactosidase reporter assay. Heat-inducible, SigI-dependent transcription of the sigI-rsgI operon was stimulated greatly by disrupting rsgI. Yeast two-hybrid analysis showed direct interaction between the N-terminal portion of the presumed RsgI protein and SigI. Without RsgI function, induction of transcription of the sigI-rsgI operon upon transient heat stress depended on dnaK activity. However, transcription of the operon was induced during growth at prolonged higher temperature even without DnaK function. Without RsgI function, sigI-rsgI operon transcription was induced after the end of growth independent of any temperature shift in a sporulation medium and toward the end of growth in a rich complex medium. Furthermore, glucose addition resulted in a strong suppression of sigI-rsgI transcription. Therefore it is hypothesized that transcription of the sigI-rsgI operon of B. subtilis is negatively regulated by the putative transmembrane protein RsgI, which moderates SigI's sensitivity to heat shock or nutritional stress.
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Affiliation(s)
- Kei Asai
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Saitama, Japan
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Koga K, Ikegami A, Nakasone K, Murayama R, Akanuma G, Natori Y, Nanamiya H, Kawamura F. Construction of Bacillus subtilis strains carrying the transcriptional bgaB fusion with the promoter region of each rrn operon and their differential transcription during spore development. J GEN APPL MICROBIOL 2006; 52:119-24. [PMID: 16778356 DOI: 10.2323/jgam.52.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Keiko Koga
- Laboratory of Molecular Genetics and Frontier Project 'Life's Adaptation Strategies to Environmental Changes', College of Science, Rikkyo University, Japan
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28
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Ming-Ming Y, Wei-Wei Z, Xi-Feng Z, Pei-Lin C. Construction and characterization of a novel maltose inducible expression vector in Bacillus subtilis. Biotechnol Lett 2006; 28:1713-8. [PMID: 17001500 DOI: 10.1007/s10529-006-9146-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Accepted: 06/23/2006] [Indexed: 10/24/2022]
Abstract
A maltose-inducible expression vector in Bacillus subtilis has been developed and characterized. The vector permitted beta-galactosidase expression at a high level (maximum activity, 8.16 U/ml) when induced and its expression was markedly repressed by glucose. Using this vector, we successfully expressed the other two genes, bioA and vgb. This thus provided a potential expression system for cloned genes in B. subtilis.
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Affiliation(s)
- Yang Ming-Ming
- Institute of Biochemical Engineering, College of Material Science and Chemical Engineering, Zhejiang University, Hangzhou 310027, P.R. China
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29
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Grandvalet C, Coucheney F, Beltramo C, Guzzo J. CtsR is the master regulator of stress response gene expression in Oenococcus oeni. J Bacteriol 2005; 187:5614-23. [PMID: 16077106 PMCID: PMC1196072 DOI: 10.1128/jb.187.16.5614-5623.2005] [Citation(s) in RCA: 50] [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
Although many stress response genes have been characterized in Oenococcus oeni, little is known about the regulation of stress response in this malolactic bacterium. The expression of eubacterial stress genes is controlled both positively and negatively at the transcriptional level. Overall, negative regulation of heat shock genes appears to be more widespread among gram-positive bacteria. We recently identified an ortholog of the ctsR gene in O. oeni. In Bacillus subtilis, CtsR negatively regulates expression of the clp genes, which belong to the class III family of heat shock genes. The ctsR gene of O. oeni is cotranscribed with the downstream clpC gene. Sequence analysis of the O. oeni IOB 8413 (ATCC BAA-1163) genome revealed the presence of potential CtsR operator sites upstream from most of the major molecular chaperone genes, including the clp genes and the groES and dnaK operons. Using B. subtilis as a heterologous host, CtsR-dependent regulation of O. oeni molecular chaperone genes was demonstrated with transcriptional fusions. No alternative sigma factors appear to be encoded by the O. oeni IOB 8413 (ATCC BAA-1163) genome. Moreover, apart from CtsR, no known genes encoding regulators of stress response, such as HrcA, could be identified in this genome. Unlike the multiple regulatory mechanisms of stress response described in many closely related gram-positive bacteria, this is the first example where dnaK and groESL are controlled by CtsR but not by HrcA.
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Affiliation(s)
- Cosette Grandvalet
- Laboratoire de Microbiologie, UMR UB/INRA 1232, ENSBANA, Université de Bourgogne, 1 Esplanade Erasme, F-21000 Dijon, France.
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Bae T, Schneewind O. Allelic replacement in Staphylococcus aureus with inducible counter-selection. Plasmid 2005; 55:58-63. [PMID: 16051359 DOI: 10.1016/j.plasmid.2005.05.005] [Citation(s) in RCA: 492] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Revised: 05/13/2005] [Accepted: 05/19/2005] [Indexed: 02/03/2023]
Abstract
A method for rapid selection of allelic replacement mutations in the chromosome of Staphylococcus aureus is described. Plasmid pKOR1, an Escherichia coli/S. aureus shuttle vector, permits rapid cloning via lambda recombination and ccdB selection. Plasmid transformation of staphylococci and growth at 43 degrees C, a non-permissive condition for pKOR1 replication, selects for homologous recombination and pKOR1 integration into the bacterial chromosome. Anhydrotetracycline-mediated induction of pKOR1-encoded secY antisense transcripts via the Pxyl/tetO promoter, a condition that is not compatible with staphylococcal growth, selects for chromosomal excision and loss of plasmid. Using this strategy, allelic replacements in S. aureus rocA were generated at frequencies that obviated the need for antibiotic marker selection.
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Affiliation(s)
- Taeok Bae
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
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Arnaud M, Chastanet A, Débarbouillé M. New vector for efficient allelic replacement in naturally nontransformable, low-GC-content, gram-positive bacteria. Appl Environ Microbiol 2005; 70:6887-91. [PMID: 15528558 PMCID: PMC525206 DOI: 10.1128/aem.70.11.6887-6891.2004] [Citation(s) in RCA: 733] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A shuttle vector designated pMAD was constructed for quickly generating gene inactivation mutants in naturally nontransformable gram-positive bacteria. This vector allows, on X-Gal (5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside) plates, a quick colorimetric blue-white discrimination of bacteria which have lost the plasmid, greatly facilitating clone identification during mutagenesis. The plasmid was used in Staphylococcus aureus, Listeria monocytogenes, and Bacillus cereus to efficiently construct mutants with or without an associated antibiotic resistance gene.
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Affiliation(s)
- Maryvonne Arnaud
- Unité de Biologie des Bactéries Pathogènes à Gram Positif, Institut Pasteur, Paris, France
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33
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Pysz MA, Conners SB, Montero CI, Shockley KR, Johnson MR, Ward DE, Kelly RM. Transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium Thermotoga maritima. Appl Environ Microbiol 2004; 70:6098-112. [PMID: 15466556 PMCID: PMC522082 DOI: 10.1128/aem.70.10.6098-6112.2004] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Thermotoga maritima, a fermentative, anaerobic, hyperthermophilic bacterium, was found to attach to bioreactor glass walls, nylon mesh, and polycarbonate filters during chemostat cultivation on maltose-based media at 80 degrees C. A whole-genome cDNA microarray was used to examine differential expression patterns between biofilm and planktonic populations. Mixed-model statistical analysis revealed differential expression (twofold or more) of 114 open reading frames in sessile cells (6% of the genome), over a third of which were initially annotated as hypothetical proteins in the T. maritima genome. Among the previously annotated genes in the T. maritima genome, which showed expression changes during biofilm growth, were several that corresponded to biofilm formation genes identified in mesophilic bacteria (i.e., Pseudomonas species, Escherichia coli, and Staphylococcus epidermidis). Most notably, T. maritima biofilm-bound cells exhibited increased transcription of genes involved in iron and sulfur transport, as well as in biosynthesis of cysteine, thiamine, NAD, and isoprenoid side chains of quinones. These findings were all consistent with the up-regulation of iron-sulfur cluster assembly and repair functions in biofilm cells. Significant up-regulation of several beta-specific glycosidases was also noted in biofilm cells, despite the fact that maltose was the primary carbon source fed to the chemostat. The reasons for increased beta-glycosidase levels are unclear but are likely related to the processing of biofilm-based polysaccharides. In addition to revealing insights into the phenotype of sessile T. maritima communities, the methodology developed here can be extended to study other anaerobic biofilm formation processes as well as to examine aspects of microbial ecology in hydrothermal environments.
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Affiliation(s)
- Marybeth A Pysz
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
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Fedhila S, Guillemet E, Nel P, Lereclus D. Characterization of two Bacillus thuringiensis genes identified by in vivo screening of virulence factors. Appl Environ Microbiol 2004; 70:4784-91. [PMID: 15294815 PMCID: PMC492376 DOI: 10.1128/aem.70.8.4784-4791.2004] [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] [Indexed: 11/20/2022] Open
Abstract
Bacillus thuringiensis vegetative cells are known to be highly pathogenic when injected into the hemocoel of susceptible insect larvae. This pathogenicity is due to the capacity of B. thuringiensis to cause septicemia in the host. We screened a B. thuringiensis mini-Tn10 insertion library for loss of virulence against Bombyx mori larvae on injection into the hemocoel. Three clones with attenuated virulence were isolated, corresponding to two different mini-Tn10 insertions mapping to the yqgB/yqfZ locus. Single disruptions of the yqgB and yqfZ genes did not affect virulence against B. mori. In contrast, the inactivation of both genes simultaneously reproduced the effect of the mini-Tn10 insertion and resulted in a significant delay to infection. The double DeltayqgB DeltayqfZ mutant was also nonmotile, and its growth was affected at 25 degrees C. We analyzed lacZ transcriptional fusions and detected promoter activity upstream from yqgB at 25 and 37 degrees C. Overall, our findings suggest that the yqgB and yqfZ genes encode adaptive factors that may act in synergy, enabling the bacteria to cope with the physical environment in vivo, facilitating colonization of the host.
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Affiliation(s)
- Sinda Fedhila
- Unité Grénétique microbienne et Environnement, La Miniére, 78285 Guyancourt cedex, France
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Bertram R, Schlicht M, Mahr K, Nothaft H, Saier MH, Titgemeyer F. In silico and transcriptional analysis of carbohydrate uptake systems of Streptomyces coelicolor A3(2). J Bacteriol 2004; 186:1362-73. [PMID: 14973030 PMCID: PMC344420 DOI: 10.1128/jb.186.5.1362-1373.2004] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Streptomyces coelicolor is the prototype for the investigation of antibiotic-producing and differentiating actinomycetes. As soil bacteria, streptomycetes can metabolize a wide variety of carbon sources and are hence vested with various specific permeases. Their activity and regulation substantially determine the nutritional state of the cell and, therefore, influence morphogenesis and antibiotic production. We have surveyed the genome of S. coelicolor A3(2) to provide a thorough description of the carbohydrate uptake systems. Among 81 ATP-binding cassette (ABC) permeases that are present in the genome, we found 45 to encode a putative solute binding protein, an essential feature for carbohydrate permease function. Similarity analysis allowed the prediction of putative ABC systems for transport of cellobiose and cellotriose, alpha-glucosides, lactose, maltose, maltodextrins, ribose, sugar alcohols, xylose, and beta-xylosides. A novel putative bifunctional protein composed of a substrate binding and a membrane-spanning moiety is likely to account for ribose or ribonucleoside uptake. Glucose may be incorporated by a proton-driven symporter of the major facilitator superfamily while a putative sodium-dependent permease of the solute-sodium symporter family may mediate uptake of galactose and a facilitator protein of the major intrinsic protein family may internalize glycerol. Of the predicted gene clusters, reverse transcriptase PCRs showed active gene expression in 8 of 11 systems. Together with the previously surveyed permeases of the phosphotransferase system that accounts for the uptake of fructose and N-acetylglucosamine, the genome of S. coelicolor encodes at least 53 potential carbohydrate uptake systems.
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Affiliation(s)
- Ralph Bertram
- Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
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36
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Chastanet A, Derre I, Nair S, Msadek T. clpB, a novel member of the Listeria monocytogenes CtsR regulon, is involved in virulence but not in general stress tolerance. J Bacteriol 2004; 186:1165-74. [PMID: 14762012 PMCID: PMC344206 DOI: 10.1128/jb.186.4.1165-1174.2004] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clp-HSP100 ATPases are a widespread family of ubiquitous proteins that occur in both prokaryotes and eukaryotes and play important roles in the folding of newly synthesized proteins and refolding of aggregated proteins. They have also been shown to participate in the virulence of several pathogens, including Listeria monocytogenes. Here, we describe a member of the Clp-HSP100 family of L. monocytogenes that harbors all the characteristics of the ClpB subclass, which is absent in the closely related gram-positive model organism, Bacillus subtilis. Transcriptional analysis of clpB revealed a heat shock-inducible sigma(A)-type promoter. Potential binding sites for the CtsR regulator of stress response were identified in the promoter region. In vivo and in vitro approaches were used to show that expression of clpB is repressed by CtsR, a finding indicating that clpB is a novel member of the L. monocytogenes CtsR regulon. We showed that ClpB is involved in the pathogenicity of L. monocytogenes since the DeltaclpB mutant is significantly affected by virulence in a murine model of infection; we also demonstrate that this effect is apparently not due to a defect in general stress resistance. Indeed, ClpB is not involved in tolerance to heat, salt, detergent, puromycin, or cold stress, even though its synthesis is inducible by heat shock. However, ClpB was shown to play a role in induced thermotolerance, allowing increased resistance of L. monocytogenes to lethal temperatures. This work gives the first example of a clpB gene directly controlled by CtsR and describes the first role for a ClpB protein in induced thermotolerance and virulence in a gram-positive organism.
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Affiliation(s)
- Arnaud Chastanet
- Unité de Biochimie Microbienne, Institut Pasteur, CNRS URA 2172, 75724 Paris Cedex 15, France
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37
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Tanaka T, Fukui T, Atomi H, Imanaka T. Characterization of an exo-beta-D-glucosaminidase involved in a novel chitinolytic pathway from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol 2003; 185:5175-81. [PMID: 12923090 PMCID: PMC181003 DOI: 10.1128/jb.185.17.5175-5181.2003] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously clarified that the chitinase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 produces diacetylchitobiose (GlcNAc(2)) as an end product from chitin. Here we sought to identify enzymes in T. kodakaraensis that were involved in the further degradation of GlcNAc(2). Through a search of the T. kodakaraensis genome, one candidate gene identified as a putative beta-glycosyl hydrolase was found in the near vicinity of the chitinase gene. The primary structure of the candidate protein was homologous to the beta-galactosidases in family 35 of glycosyl hydrolases at the N-terminal region, whereas the central region was homologous to beta-galactosidases in family 42. The purified protein from recombinant Escherichia coli clearly showed an exo-beta-D-glucosaminidase (GlcNase) activity but not beta-galactosidase activity. This GlcNase (GlmA(Tk)), a homodimer of 90-kDa subunits, exhibited highest activity toward reduced chitobiose at pH 6.0 and 80 degrees C and specifically cleaved the nonreducing terminal glycosidic bond of chitooligosaccharides. The GlcNase activity was also detected in T. kodakaraensis cells, and the expression of GlmA(Tk) was induced by GlcNAc(2) and chitin, strongly suggesting that GlmA(Tk) is involved in chitin catabolism in T. kodakaraensis. These results suggest that T. kodakaraensis, unlike other organisms, possesses a novel chitinolytic pathway where GlcNAc(2) from chitin is first deacetylated and successively hydrolyzed to glucosamine. This is the first report that reveals the primary structure of GlcNase not only from an archaeon but also from any organism.
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Affiliation(s)
- Takeshi Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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38
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Tanaka K, Kobayashi K, Ogasawara N. The Bacillus subtilis YufLM two-component system regulates the expression of the malate transporters MaeN (YufR) and YflS, and is essential for utilization of malate in minimal medium. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2317-2329. [PMID: 12949159 DOI: 10.1099/mic.0.26257-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Gram-positive bacterium Bacillus subtilis has a complete set of enzymes for the tricarboxylic acid (TCA) cycle and can grow aerobically using most of the TCA cycle intermediates (malate, fumarate, succinate and citrate) as a sole carbon source. The B. subtilis genome sequence contains three paralogous two-component regulatory systems, CitST, DctSR and YufLM. CitST and DctSR activate the expression of a transporter of the Mg(2+)-citrate complex (CitM) and a fumarate and succinate transporter (DctP), respectively. These findings prompted an investigation of whether the YufL sensor and its cognate regulator, YufM, play a role in malate uptake. This paper reports that the YufM regulator shows in vitro binding to the promoter region of two malate transporter genes, maeN and yflS, and is responsible for inducing their expression in vivo. It was also found that inactivation of the yufM or maeN genes resulted in bacteria that could not grow in a minimal salts medium containing malate as a sole carbon source, indicating that the induction of the MaeN transporter by the YufM regulator is essential for the utilization of malate as a carbon source. Inactivation of the yufL gene resulted in the constitutive expression of MaeN. This expression was suppressed by reintroduction of the kinase domain of YufL, indicating that the YufL sensor is required for proper signal detection and signalling specificity. The authors propose that a phosphatase activity of YufL plays an important role in the YufLM two-component regulatory system. The studies reported here have revealed that members of a set of paralogous two-component regulatory systems in B. subtilis, CitST, DctSR and YufLM, are involved in a related function--uptake (and metabolism) of the TCA cycle intermediates--but with distinct substrate specificities.
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Affiliation(s)
- Kousei Tanaka
- Department of Bioinformatics and Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0101, Japan
| | - Kazuo Kobayashi
- Department of Bioinformatics and Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0101, Japan
| | - Naotake Ogasawara
- Department of Bioinformatics and Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0101, Japan
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39
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Wiegert T, Schumann W. Analysis of a DNA-binding motif of the Bacillus subtilis HrcA repressor protein. FEMS Microbiol Lett 2003; 223:101-6. [PMID: 12799007 DOI: 10.1016/s0378-1097(03)00350-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The hrcA gene of Bacillus subtilis encodes a transcriptional repressor protein which negatively controls the heat shock operons dnaK and groESL. Alignment of the HrcA protein with repressor proteins from the NCBI database revealed that it exhibits a striking homology near its N-terminal part with proteins of the DeoR family. This region contains a helix-turn-helix motif and has been shown to be involved in DNA binding. To investigate whether this is also true for the HrcA protein, three critical amino acid residues were changed within or adjacent to the recognition helix. While single amino acid replacements barely influenced the binding activity, alteration of two consecutive amino acid residues within the recognition helix completely abolished the binding activity. When this mutant hrcA allele was expressed together with the wild-type allele within the same cell, it conferred a dominant-negative phenotype to the cells underlining that these amino acid residues are crucial for specific DNA binding and that HrcA binds to DNA in an oligomeric form.
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Affiliation(s)
- Thomas Wiegert
- Institute of Genetics, University of Bayreuth, D-95440, Bayreuth, Germany.
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40
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Davies KM, Lewis PJ. Localization of rRNA synthesis in Bacillus subtilis: characterization of loci involved in transcription focus formation. J Bacteriol 2003; 185:2346-53. [PMID: 12644506 PMCID: PMC151511 DOI: 10.1128/jb.185.7.2346-2353.2003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2002] [Accepted: 01/14/2003] [Indexed: 11/20/2022] Open
Abstract
In Bacillus subtilis, RNA polymerase becomes concentrated into regions of the nucleoid called transcription foci. With green fluorescent protein-tagged RNA polymerase, these structures are only observed at higher growth rates and have been shown to represent the sites of rRNA synthesis. There are 10 rRNA (rrn) operons distributed around nearly half of the chromosome. In this study we analyzed the rrn composition of transcription foci with fluorescently tagged loci and showed that they comprise the origin-proximal operon rrnO but not the more dispersed rrnE or rrnD. This suggests that transcription foci comprise only the seven origin-proximal operons rrnO, rrnA, rrnJ, rrnW, rrnI, rrnH, and rrnG. These results have important implications for our understanding of microbial chromosome structure.
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Affiliation(s)
- Karen M Davies
- School of Environmental and Life Sciences, Biological Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia
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41
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Chastanet A, Fert J, Msadek T. Comparative genomics reveal novel heat shock regulatory mechanisms in Staphylococcus aureus and other Gram-positive bacteria. Mol Microbiol 2003; 47:1061-73. [PMID: 12581359 DOI: 10.1046/j.1365-2958.2003.03355.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Multiple regulatory mechanisms for coping with stress co-exist in low G+C Gram-positive bacteria. Among these, the HrcA and CtsR repressors control distinct regulons in the model organism, Bacillus subtilis. We recently identified an orthologue of the CtsR regulator of stress response in the major pathogen, Staphylococcus aureus. Sequence analysis of the S. aureus genome revealed the presence of potential CtsR operator sites not only upstream from genes encoding subunits of the Clp ATP-dependent protease, as in B. subtilis, but also, unexpectedly, within the promoter regions of the dnaK and groESL operons known to be specifically controlled by HrcA. The tandem arrangement of the CtsR and HrcA operators suggests a novel mode of dual heat shock regulation by these two repressors. The S. aureus ctsR and hrcA genes were cloned under the control of the PxylA xylose-inducible promoter and used to demonstrate dual regulation of the dnaK and groESL operons by both CtsR and HrcA, using B. subtilis as a heterologous host. Direct binding by both repressors was shown in vitro by gel mobility shift and DNase I footprinting experiments using purified S. aureus CtsR and HrcA proteins. DeltactsR, DeltahrcA and DeltactsRDeltahrcA mutants of S. aureus were constructed, indicating that the two repressors are not redundant but, instead, act together synergistically to maintain low basal levels of expression of the dnaK and groESL operons in the absence of stress. This novel regulatory mode appears to be specific to Staphylococci.
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Affiliation(s)
- Arnaud Chastanet
- Unité de Biochimie Microbienne, CNRS URA 2172, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
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42
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Chastanet A, Msadek T. ClpP of Streptococcus salivarius is a novel member of the dually regulated class of stress response genes in gram-positive bacteria. J Bacteriol 2003; 185:683-7. [PMID: 12511518 PMCID: PMC145324 DOI: 10.1128/jb.185.2.683-687.2003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleotide sequence analysis of the Streptococcus salivarius clpP locus revealed potential binding sites for both the CtsR and HrcA repressors. Dual regulation by HrcA and CtsR was demonstrated by using Bacillus subtilis as a heterologous host, and CtsR was shown to bind directly to the clpP promoter sequence. This is the first example of a clpP gene under the control of HrcA.
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Affiliation(s)
- Arnaud Chastanet
- Unité de Biochimie Microbienne, Institut Pasteur, URA 2172 du Centre National de la Recherche Scientifique, 75724 Paris Cedex 15, France
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43
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Pessela BCC, Mateo C, Carrascosa AV, Vian A, García JL, Rivas G, Alfonso C, Guisan JM, Fernández-Lafuente R. One-step purification, covalent immobilization, and additional stabilization of a thermophilic poly-His-tagged beta-galactosidase from Thermus sp. strain T2 by using novel heterofunctional chelate-epoxy Sepabeads. Biomacromolecules 2003; 4:107-13. [PMID: 12523854 DOI: 10.1021/bm020086j] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using the poly-His-tagged-beta-galactosidase from Thermus sp. strain T2 overexpressed in Escherichia coli (MC1116) as a model enzyme, we have developed a strategy to purify and immobilize proteins in a single step, combining the excellent properties of epoxy groups for enzyme immobilization with the good performance of immobilized metal-chelate affinity chromatography for protein purification. The aforementioned enzyme could not be immobilized onto standard epoxy supports with good yields, and after purification and storage, it exhibited a strong trend to yield very large aggregates as shown by ultracentrifugation experiments. That preparation could not be immobilized in any support, very likely because the pores of the solid became clogged by the large aggregates. These novel epoxy-metal chelate heterofunctional supports contain a low concentration of Co(2+) chelated in IDA groups and a high density of epoxy groups. This enabled the selective adsorption of poly-His-tagged enzymes, and as this adsorption step is necessary for the covalent immobilization procedure, the selective covalent immobilization of the target enzyme could take place. This strategy allowed similar maximum loadings of the target enzyme using either pure or crude preparations of the enzyme. The enzyme derivative presented a very high activity at 70 degrees C (over 1000 IU in the hydrolysis of lactose) and very high stability and stabilization when compared to its soluble counterpart (activity remained unaltered after several days of incubation at 50 degrees C). In fact, this preparation was much more stable than when the same enzyme was immobilized onto standard epoxy Sepabeads.
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Affiliation(s)
- Benevides C C Pessela
- Departamento de Biocatálisis, Instituto de Catálisis, CSIC, Campus Universidad Autónoma, 28049 Madrid, Spain
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44
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Reischl S, Wiegert T, Schumann W. Isolation and analysis of mutant alleles of the Bacillus subtilis HrcA repressor with reduced dependency on GroE function. J Biol Chem 2002; 277:32659-67. [PMID: 12082092 DOI: 10.1074/jbc.m201372200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hrcA gene of Bacillus subtilis codes for a transcriptional repressor protein that negatively regulates expression of the heptacistronic dnaK and the bicistronic groE operon by binding to an operator-element called CIRCE. Recently, we have published data suggesting that the activity of HrcA is modulated by the GroE chaperonin system. Biochemical analyses of the HrcA protein have been hampered so far by its strong tendency to aggregate. Here, a genetic method was used to isolate mutant forms of HrcA with increased activity under conditions of decreased GroE function. One of these mutant forms (HrcA114) containing five amino acid replacements exhibited enhanced solubility when overexpressed. HrcA114 purified under native conditions produced two retarded CIRCE-containing DNA fragments in band shift experiments. The amount of the larger fragment increased after addition of GroEL, GroES, and ATP but decreased when ATP was replaced by the nonhydrolyzable ATP analog ATPgammaS. DNase I footprinting experiments exhibited full protection of the CIRCE element and neighboring nucleotides in an asymmetric way. An in vitro binding assay using affinity chromatography showed direct and specific interaction between HrcA114 and GroEL. All these experimental data are in full agreement with our previously published model that HrcA needs the GroE chaperonin system for activation.
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Affiliation(s)
- Silke Reischl
- Institute of Genetics, University of Bayreuth, Universitaetsstrasse 30, Bayreuth D-95440, Germany
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45
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Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, Wakagi T. Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose. J Mol Biol 2002; 322:79-91. [PMID: 12215416 DOI: 10.1016/s0022-2836(02)00746-5] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The beta-galactosidase from an extreme thermophile, Thermus thermophilus A4 (A4-beta-Gal), is thermostable and belongs to the glycoside hydrolase family 42 (GH-42). As the first known structures of a GH-42 enzyme, we determined the crystal structures of free and galactose-bound A4-beta-Gal at 1.6A and 2.2A resolution, respectively. A4-beta-Gal forms a homotrimeric structure resembling a flowerpot. Each monomer has an active site located inside a large central tunnel. The N-terminal domain of A4-beta-Gal has a TIM barrel fold, as predicted from hydrophobic cluster analysis. The putative catalytic residues of A4-beta-Gal (Glu141 and Glu312) superimpose well with the catalytic residues of Escherichia coli beta-galactosidase. The environment around the catalytic nucleophile (Glu312) is similar to that in the case of E.coli beta-galactosidase, but the recognition mechanism for a substrate is different. Trp182 of the next subunit of the trimer constitutes a part of the active-site pocket, indicating that the trimeric structure is essential for the enzyme activity. Structural comparison with other glycoside hydrolases revealed that many features of the 4/7 superfamily are conserved in the A4-beta-Gal structure. On the basis of the results of 1H NMR spectroscopy, A4-beta-Gal was determined to be a "retaining" enzyme. Interestingly, the active site was similar with those of retaining enzymes, but the overall fold of the TIM barrel domain was very similar to that of an inverting enzyme, beta-amylase.
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46
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Chastanet A, Prudhomme M, Claverys JP, Msadek T. Regulation of Streptococcus pneumoniae clp genes and their role in competence development and stress survival. J Bacteriol 2001; 183:7295-307. [PMID: 11717289 PMCID: PMC95579 DOI: 10.1128/jb.183.24.7295-7307.2001] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In vitro mariner transposon mutagenesis of Streptococcus pneumoniae chromosomal DNA was used to isolate regulatory mutants affecting expression of the comCDE operon, encoding the peptide quorum-sensing two-component signal transduction system controlling competence development. A transposon insertion leading to increased comC expression was found to lie directly upstream from the S. pneumoniae clpP gene, encoding the proteolytic subunit of the Clp ATP-dependent protease, whose expression in Bacillus subtilis is controlled by the CtsR repressor. In order to examine clp gene regulation in S. pneumoniae, a detailed analysis of the complete genome sequence was performed, indicating that there are five likely CtsR-binding sites located upstream from the clpE, clpP, and clpL genes and the ctsR-clpC and groESL operons. The S. pneumoniae ctsR gene was cloned under the control of an inducible promoter and used to demonstrate regulation of the S. pneumoniae clpP and clpE genes and the clpC and groESL operons by using B. subtilis as a heterologous host. The CtsR protein of S. pneumoniae was purified and shown to bind specifically to the clpP, clpC, clpE, and groESL regulatory regions. S. pneumoniae Delta ctsR, Delta clpP, Delta clpC, and Delta clpE mutants were constructed by gene deletion/replacement. ClpP was shown to act as a negative regulator, preventing competence gene expression under inappropriate conditions. Phenotypic analyses also indicated that ClpP and ClpE are both required for thermotolerance. Contrary to a previous report, we found that ClpC does not play a major role in competence development, autolysis, pneumolysin production, or growth at high temperature of S. pneumoniae.
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Affiliation(s)
- A Chastanet
- Unité de Biochimie Microbienne, Institut Pasteur, URA 2172 du Centre National de la Recherche Scientifique, 75724 Paris Cedex 15, France
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47
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Hung MN, Xia Z, Hu NT, Lee BH. Molecular and biochemical analysis of two beta-galactosidases from Bifidobacterium infantis HL96. Appl Environ Microbiol 2001; 67:4256-63. [PMID: 11526031 PMCID: PMC93155 DOI: 10.1128/aem.67.9.4256-4263.2001] [Citation(s) in RCA: 59] [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
Two genes encoding beta-galactosidase isoenzymes, beta-galI and beta-galIII, from Bifidobacterium infantis HL96 were revealed on 3.6- and 2.4-kb DNA fragments, respectively, by nucleotide sequence analysis of the two fragments. beta-galI (3,069 bp) encodes a 1,022-amino-acid (aa) polypeptide with a predicted molecular mass of 113 kDa. A putative ribosome binding site and a promoter sequence were recognized at the 5' flanking region of beta-galI. Further upstream a partial sequence of an open reading frame revealed a putative lactose permease gene transcribing divergently from beta-galI. The beta-galIII gene (2,076 bp) encodes a 691-aa polypeptide with a calculated molecular mass of 76 kDa. A rho-independent transcription terminator-like sequence was found 25 bp downstream of the termination codon. The amino acid sequences of beta-GalI and beta-GalIII are homologous to those found in the LacZ and the LacG families, respectively. The acid-base, nucleophilic, and substrate recognition sites conserved in the LacZ family were found in beta-GalI, and a possible acid-base site proposed for the LacG family was located in beta-GalIII, which featured a glutamate at residue 160. The coding regions of the beta-galI and beta-galIII genes were each cloned downstream of a T7 promoter for overexpression in Escherichia coli. The molecular masses of the overexpressed proteins, as estimated by polyacrylamide gel electrophoresis on sodium dodecyl sulfate-polyacrylamide gels, agree with their predicted molecular weights. beta-GalI and beta-GalIII were specific for beta-D-anomer-linked galactoside substrates. Both are more active in response to ONPG (o-nitrophenyl-beta-D-galactopyranoside) than in response to lactose, particularly beta-GalIII. The galacto-oligosaccharide yield in the reaction catalyzed by beta-GalI at 37 degrees C in 20% (wt/vol) lactose solution was 130 mg/ml, which is more than six times higher than the maximum yield obtained with beta-GalIII. The structure of the major trisaccharide produced by beta-GalI catalysis was characterized as O-beta-D-galactopyranosyl-(1-3)-O-beta-D-galactopyranosyl-(1-4)-D-glucopyranose (3'-galactosyl-lactose).
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Affiliation(s)
- M N Hung
- Department of Food Science and Agricultural Chemistry, McGill University, Ste-Anne-de-Bellevue, Quebec H9X 3V9, Canada
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48
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Härtl B, Wehrl W, Wiegert T, Homuth G, Schumann W. Development of a new integration site within the Bacillus subtilis chromosome and construction of compatible expression cassettes. J Bacteriol 2001; 183:2696-9. [PMID: 11274134 PMCID: PMC95191 DOI: 10.1128/jb.183.8.2696-2699.2001] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2000] [Accepted: 01/08/2001] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis lacA gene, coding for beta-galactosidase, has been explored as a new site able to accept DNA sequences from nonreplicating delivery vectors. Two such delivery expression vectors have been constructed and shown to be useful in obtaining regulated expression from the chromosomal location. In another experiment, it was shown that the integration of a regulatory gene at the lacA locus was able to control the expression of a transcriptional fusion at the amyE locus. These experiments demonstrate that both integration sites can be used simultaneously to obtain regulated expression of desired genes.
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Affiliation(s)
- B Härtl
- Institute of Genetics, University of Bayreuth, D-95440 Bayreuth, Germany
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49
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Abstract
The gram-positive bacterium Bacillus subtilisis capable of using numerous carbohydrates as single sources of carbon and energy. In this review, we discuss the mechanisms of carbon catabolism and its regulation. Like many other bacteria, B. subtilis uses glucose as the most preferred source of carbon and energy. Expression of genes involved in catabolism of many other substrates depends on their presence (induction) and the absence of carbon sources that can be well metabolized (catabolite repression). Induction is achieved by different mechanisms, with antitermination apparently more common in B. subtilis than in other bacteria. Catabolite repression is regulated in a completely different way than in enteric bacteria. The components mediating carbon catabolite repression in B. subtilis are also found in many other gram-positive bacteria of low GC content.
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Affiliation(s)
- J Stülke
- Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie, Biochemie und Genetik der Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Reischl S, Thake S, Homuth G, Schumann W. Transcriptional analysis of three Bacillus subtilis genes coding for proteins with the alpha-crystallin domain characteristic of small heat shock proteins. FEMS Microbiol Lett 2001; 194:99-103. [PMID: 11150673 DOI: 10.1111/j.1574-6968.2001.tb09453.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In silico analysis of the complete Bacillus subtilis genome revealed the presence of three genes whose deduced amino acid sequences exhibit an alpha-crystallin domain characteristic for the family of small heat shock proteins: cotM (which has already been identified [Henriques et al. (1997) J. Bacteriol 179, 1887-1897]), yocM, and cotP (formerly ydfT). Analysis of the expression of all three genes by slot-blot experiments and by transcriptional fusions revealed that none of them was heat-inducible. Transcription of cotP was induced late during sporulation by the sporulation-specific sigma factor sigma(K) and negatively controlled by the GerE repressor. No expression of the yocM gene was found under all standard laboratory conditions tested. Both a cotP knockout mutant as well as a cotM cotP double knockout turned out to be viable and form spores and exhibited no germination defect.
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Affiliation(s)
- S Reischl
- Institute of Genetics, University of Bayreuth, D-95440, Germany
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