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Abstract
The DNA-binding protein from starved cells, Dps, is a universally conserved prokaryotic ferritin that, in many species, also binds DNA. Dps homologs have been identified in the vast majority of bacterial species and several archaea. Dps also may play a role in the global regulation of gene expression, likely through chromatin reorganization. Dps has been shown to use both its ferritin and DNA-binding functions to respond to a variety of environmental pressures, including oxidative stress. One mechanism that allows Dps to achieve this is through a global nucleoid restructuring event during stationary phase, resulting in a compact, hexacrystalline nucleoprotein complex called the biocrystal that occludes damaging agents from DNA. Due to its small size, hollow spherical structure, and high stability, Dps is being developed for applications in biotechnology.
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Heme A Synthase Deficiency Affects the Ability of Bacillus cereus to Adapt to a Nutrient-Limited Environment. Int J Mol Sci 2022; 23:ijms23031033. [PMID: 35162964 PMCID: PMC8835132 DOI: 10.3390/ijms23031033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 11/30/2022] Open
Abstract
The branched aerobic respiratory chain in Bacillus cereus comprises three terminal oxidases: cytochromes aa3, caa3, and bd. Cytochrome caa3 requires heme A for activity, which is produced from heme O by heme A synthase (CtaA). In this study, we deleted the ctaA gene in B. cereus AH187 strain, this deletion resulted in loss of cytochrome caa3 activity. Proteomics data indicated that B. cereus grown in glucose-containing medium compensates for the loss of cytochrome caa3 activity by remodeling its respiratory metabolism. This remodeling involves up-regulation of cytochrome aa3 and several proteins involved in redox stress response—to circumvent sub-optimal respiratory metabolism. CtaA deletion changed the surface-composition of B. cereus, affecting its motility, autoaggregation phenotype, and the kinetics of biofilm formation. Strikingly, proteome remodeling made the ctaA mutant more resistant to cold and exogenous oxidative stresses compared to its parent strain. Consequently, we hypothesized that ctaA inactivation could improve B. cereus fitness in a nutrient-limited environment.
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Zaide G, Elia U, Cohen-Gihon I, Israeli M, Rotem S, Israeli O, Ehrlich S, Cohen H, Lazar S, Beth-Din A, Shafferman A, Zvi A, Cohen O, Chitlaru T. Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains. Microorganisms 2020; 8:microorganisms8121896. [PMID: 33265965 PMCID: PMC7760947 DOI: 10.3390/microorganisms8121896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of Bacillus anthracis. Virulence attenuation of htrA-disrupted Bacillus anthracis strains was attributed to susceptibility of ΔhtrA strains to stress insults, as evidenced by affected growth under various stress conditions. Here, we report a comparative RNA-seq transcriptomic study generating a database of differentially expressed genes in the B. anthracishtrA-disrupted and wild type parental strains under oxidative stress. The study demonstrates that, apart from protease and chaperone activities, HtrA exerts a regulatory role influencing expression of more than 1000 genes under stress. Functional analysis of groups or individual genes exhibiting strain-specific modulation, evidenced (i) massive downregulation in the ΔhtrA and upregulation in the WT strains of various transcriptional regulators, (ii) downregulation of translation processes in the WT strain, and (iii) downregulation of metal ion binding functions and upregulation of sporulation-associated functions in the ΔhtrA strain. These modulated functions are extensively discussed. Fifteen genes uniquely upregulated in the wild type strain were further interrogated for their modulation in response to other stress regimens. Overexpression of one of these genes, encoding for MazG (a nucleoside triphosphate pyrophosphohydrolase involved in various stress responses in other bacteria), in the ΔhtrA strain resulted in partial alleviation of the H2O2-sensitive phenotype.
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Naditz AL, Dzieciol M, Wagner M, Schmitz-Esser S. Plasmids contribute to food processing environment-associated stress survival in three Listeria monocytogenes ST121, ST8, and ST5 strains. Int J Food Microbiol 2019; 299:39-46. [PMID: 30953994 DOI: 10.1016/j.ijfoodmicro.2019.03.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/04/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022]
Abstract
Listeria monocytogenes is a food-borne pathogen responsible for the disease listeriosis and is commonly isolated from food and food production facilities. Many L. monocytogenes strains contain plasmids, though the contributions of plasmids to survival in food production environments are unknown. Three L. monocytogenes ST5, ST8, and ST121 strains containing plasmids, which harbor putative stress response genes, were cured of their plasmids. Wildtype (WT) and plasmid-cured strains were exposed to disinfectant, oxidative, heat, acid, or salt stress. After stress exposure, cells were plated for colony forming unit (CFU) counts to determine survivors. L. monocytogenes WT strains exposed to 0.01% (vol/vol) H2O2, 1% (vol/vol) lactic acid, and 15% (wt/vol) NaCl, pH 5 showed significantly higher counts of survivors compared to the plasmid-cured strains. The number of survivors for the ST5 WT strain exposed to 10 μg/mL benzalkonium chloride (BC) was significantly higher than in the plasmid-cured strain. The ST8 and ST5 strains were exposed to elevated temperature (50° and 55 °C respectively); only the ST5 WT strain had significantly higher numbers of survivors than the plasmid-cured strains. Our data revealed that L. monocytogenes ST5, ST8, and ST121 plasmids contribute to tolerance against elevated temperature, salinity, acidic environments, oxidative stress and disinfectants.
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Affiliation(s)
- Annabel L Naditz
- Department of Animal Science, Iowa State University, Ames, IA, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, USA
| | - Monika Dzieciol
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- Institute for Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria; Austrian Competence Center for Feed and Food Quality, Safety and Innovation (FFoQSI), Technopark C, 3430 Tulln, Austria
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, IA, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, USA.
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Tirumalai MR, Stepanov VG, Wünsche A, Montazari S, Gonzalez RO, Venkateswaran K, Fox GE. Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates. BMC Microbiol 2018; 18:57. [PMID: 29884123 PMCID: PMC5994023 DOI: 10.1186/s12866-018-1191-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022] Open
Abstract
Background Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis. Results The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. Conclusions It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group. Electronic supplementary material The online version of this article (10.1186/s12866-018-1191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Madhan R Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Andrea Wünsche
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Racquel O Gonzalez
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Kasturi Venkateswaran
- Biotechnology & Planetary Protection Group, NASA Jet Propulsion Laboratories, California Institute of Technology, Pasadena, CA, 91109, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.
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Mott T, Shoe J, Hunter M, Woodson A, Fritts K, Klimko C, Quirk A, Welkos S, Cote C. Comparison of sampling methods to recover germinatedBacillus anthracisandBacillus thuringiensisendospores from surface coupons. J Appl Microbiol 2017; 122:1219-1232. [DOI: 10.1111/jam.13418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/03/2017] [Accepted: 02/04/2017] [Indexed: 11/26/2022]
Affiliation(s)
- T.M. Mott
- Bacteriology Division; United States Army Medical Research Institute of Infectious Disease (USAMRIID); Frederick MD USA
| | - J.L. Shoe
- Bacteriology Division; United States Army Medical Research Institute of Infectious Disease (USAMRIID); Frederick MD USA
| | - M. Hunter
- Bacteriology Division; United States Army Medical Research Institute of Infectious Disease (USAMRIID); Frederick MD USA
| | - A.M. Woodson
- Bacteriology Division; United States Army Medical Research Institute of Infectious Disease (USAMRIID); Frederick MD USA
| | - K.A. Fritts
- Bacteriology Division; United States Army Medical Research Institute of Infectious Disease (USAMRIID); Frederick MD USA
| | - C.P. Klimko
- Bacteriology Division; United States Army Medical Research Institute of Infectious Disease (USAMRIID); Frederick MD USA
| | - A.V. Quirk
- Bacteriology Division; United States Army Medical Research Institute of Infectious Disease (USAMRIID); Frederick MD USA
| | - S.L. Welkos
- Bacteriology Division; United States Army Medical Research Institute of Infectious Disease (USAMRIID); Frederick MD USA
| | - C.K. Cote
- Bacteriology Division; United States Army Medical Research Institute of Infectious Disease (USAMRIID); Frederick MD USA
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He D, Marles-Wright J. Ferritin family proteins and their use in bionanotechnology. N Biotechnol 2015; 32:651-7. [PMID: 25573765 PMCID: PMC4571993 DOI: 10.1016/j.nbt.2014.12.006] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/05/2014] [Accepted: 12/16/2014] [Indexed: 01/20/2023]
Abstract
We discuss bionanotechnology applications of ferritin family proteins. Ferritin family proteins are able to mineralise a range of metal ions. The ferritin and DPS cages can be used in semi-conductor patterning. We explore a commercial application of ferritin as a phosphate removal system for water purification. We examine how the superparamagnetic properties of iron-loaded ferritin can be used in medical imaging.
Ferritin family proteins are found in all kingdoms of life and act to store iron within a protein cage and to protect the cell from oxidative damage caused by the Fenton reaction. The structural and biochemical features of the ferritins have been widely exploited in bionanotechnology applications: from the production of metal nanoparticles; as templates for semi-conductor production; and as scaffolds for vaccine design and drug delivery. In this review we first discuss the structural properties of the main ferritin family proteins, and describe how their organisation specifies their functions. Second, we describe materials science applications of ferritins that rely on their ability to sequester metal within their cavities. Finally, we explore the use of ferritin as a container for drug delivery and as a scaffold for the production of vaccines.
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Affiliation(s)
- Didi He
- Institute of Structural and Molecular Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
| | - Jon Marles-Wright
- Institute of Structural and Molecular Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, United Kingdom.
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Omotade TO, Bernhards RC, Klimko CP, Matthews ME, Hill AJ, Hunter MS, Webster WM, Bozue JA, Welkos SL, Cote CK. The impact of inducing germination of Bacillus anthracis and Bacillus thuringiensis spores on potential secondary decontamination strategies. J Appl Microbiol 2014; 117:1614-33. [PMID: 25196092 DOI: 10.1111/jam.12644] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/03/2014] [Accepted: 09/03/2014] [Indexed: 12/22/2022]
Abstract
AIMS Decontamination and remediation of a site contaminated by the accidental or intentional release of fully virulent Bacillus anthracis spores are difficult, costly and potentially damaging to the environment. Development of novel decontamination strategies that have minimal environmental impacts remains a high priority. Although ungerminated spores are amongst the most resilient organisms known, once exposed to germinants, the germinating spores, in some cases, become susceptible to antimicrobial environments. We evaluated the concept that once germinated, B. anthracis spores would be less hazardous and significantly easier to remediate than ungerminated dormant spores. METHODS AND RESULTS Through in vitro germination and sensitivity assays, we demonstrated that upon germination, B. anthracis Ames spores and Bacillus thuringiensis Al Hakam spores (serving as a surrogate for B. anthracis) become susceptible to environmental stressors. The majority of these germinated B. anthracis and B. thuringiensis spores were nonviable after exposure to a defined minimal germination-inducing solution for prolonged periods of time. Additionally, we examined the impact of potential secondary disinfectant strategies including bleach, hydrogen peroxide, formaldehyde and artificial UV-A, UV-B and UV-C radiation, employed after a 60-min germination-induction step. Each secondary disinfectant employs a unique mechanism of killing; as a result, germination-induction strategies are better suited for some secondary disinfectants than others. CONCLUSIONS These results provide evidence that the deployment of an optimal combination strategy of germination-induction/secondary disinfection may be a promising aspect of wide-area decontamination following a B. anthracis contamination event. SIGNIFICANCE AND IMPACT OF THE STUDY By inducing spores to germinate, our data confirm that the resulting cells exhibit sensitivities that can be leveraged when paired with certain decontamination measures. This increased susceptibility could be exploited to devise more efficient and safe decontamination measures and may obviate the need for more stringent methods that are currently in place.
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Affiliation(s)
- T O Omotade
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD, USA
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Kim SK, Park MK, Kim SH, Oh KG, Jung KH, Hong CH, Yoon JW, Chai YG. Identification of stringent response-related and potential serological proteins released from Bacillus anthracis overexpressing the RelA/SpoT homolog, Rsh Bant. Curr Microbiol 2014; 69:436-44. [PMID: 24838666 DOI: 10.1007/s00284-014-0606-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/20/2014] [Indexed: 11/28/2022]
Abstract
RelA and SpoT synthesize ppGpp, a key effector molecule that facilitates the adaptation of bacteria to nutrient starvation and other stresses, known as the stringent response. To investigate the role of Rsh Bant , a putative RelA/SpoT homolog (encoded by BAS4302) in Bacillus anthracis, we examined the alteration of the secretome profiles after the overexpression of a functional His-Rsh Bant protein in the B. anthracis strain Sterne at the stationary growth phase. In the ppGpp-deficient E. coli mutant strain CF1693, overexpression of Rsh Bant restored a ppGpp-dependent growth defect on minimal glucose media. The secretome profiles obtained using a two-dimensional electrophoresis (2-DE) analysis were altered by overexpression of Rsh Bant in B. anthracis. Among the 66 protein spots differentially expressed >1.5-fold, the 29 proteins were abundant for further identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Functional categorization of those proteins implicated their involvement in various biological activities. Taken together, our results imply that overexpression of a functional His-Rsh Bant can lead to the increased levels of intracellular ppGpp in B. anthracis, resulting in the significant changes in its secretome profiling. The stringent response-controlled proteins identified are likely useful as potential targets for serodiagnostic applications.
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Affiliation(s)
- Se Kye Kim
- Department of Molecular and Life Sciences, Hanyang University, 1271, Ansan, 426-791, Gyeonggi-do, Republic of Korea
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Handtke S, Schroeter R, Jürgen B, Methling K, Schlüter R, Albrecht D, van Hijum SAFT, Bongaerts J, Maurer KH, Lalk M, Schweder T, Hecker M, Voigt B. Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress. PLoS One 2014; 9:e85625. [PMID: 24465625 PMCID: PMC3896406 DOI: 10.1371/journal.pone.0085625] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/05/2013] [Indexed: 12/16/2022] Open
Abstract
Bacillus pumilus is characterized by a higher oxidative stress resistance than other comparable industrially relevant Bacilli such as B. subtilis or B. licheniformis. In this study the response of B. pumilus to oxidative stress was investigated during a treatment with high concentrations of hydrogen peroxide at the proteome, transcriptome and metabolome level. Genes/proteins belonging to regulons, which are known to have important functions in the oxidative stress response of other organisms, were found to be upregulated, such as the Fur, Spx, SOS or CtsR regulon. Strikingly, parts of the fundamental PerR regulon responding to peroxide stress in B. subtilis are not encoded in the B. pumilus genome. Thus, B. pumilus misses the catalase KatA, the DNA-protection protein MrgA or the alkyl hydroperoxide reductase AhpCF. Data of this study suggests that the catalase KatX2 takes over the function of the missing KatA in the oxidative stress response of B. pumilus. The genome-wide expression analysis revealed an induction of bacillithiol (Cys-GlcN-malate, BSH) relevant genes. An analysis of the intracellular metabolites detected high intracellular levels of this protective metabolite, which indicates the importance of bacillithiol in the peroxide stress resistance of B. pumilus.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Rebecca Schroeter
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Britta Jürgen
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Rabea Schlüter
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Dirk Albrecht
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Sacha A. F. T. van Hijum
- Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; and Division Processing and Safety, NIZO Food Research B.V., Ede, The Netherlands
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Jülich, Germany
| | | | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Birgit Voigt
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
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Shu JC, Soo PC, Chen JC, Hsu SH, Chen LC, Chen CY, Liang SH, Buu LM, Chen CC. Differential regulation and activity against oxidative stress of Dps proteins in Bacillus cereus. Int J Med Microbiol 2013; 303:662-73. [DOI: 10.1016/j.ijmm.2013.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Ekman M, Sandh G, Nenninger A, Oliveira P, Stensjö K. Cellular and functional specificity among ferritin-like proteins in the multicellular cyanobacterium Nostoc punctiforme. Environ Microbiol 2013; 16:829-44. [PMID: 23992552 DOI: 10.1111/1462-2920.12233] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/28/2013] [Indexed: 01/26/2023]
Abstract
Ferritin-like proteins constitute a remarkably heterogeneous protein family, including ferritins, bacterioferritins and Dps proteins. The genome of the filamentous heterocyst-forming cyanobacterium Nostoc punctiforme encodes five ferritin-like proteins. In the present paper, we report a multidimensional characterization of these proteins. Our phylogenetic and bioinformatics analyses suggest both structural and physiological differences among the ferritin-like proteins. The expression of these five genes responded differently to hydrogen peroxide treatment, with a significantly higher rise in transcript level for Npun_F3730 as compared with the other four genes. A specific role for Npun_F3730 in the cells tolerance against hydrogen peroxide was also supported by the inactivation of Npun_F3730, Npun_R5701 and Npun_R6212; among these, only the ΔNpun_F3730 strain showed an increased sensitivity to hydrogen peroxide compared with wild type. Analysis of promoter-GFP reporter fusions of the ferritin-like genes indicated that Npun_F3730 and Npun_R5701 were expressed in all cell types of a diazotrophic culture, while Npun_F6212 was expressed specifically in heterocysts. Our study provides the first comprehensive analysis combining functional differentiation and cellular specificity within this important group of proteins in a multicellular cyanobacterium.
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Affiliation(s)
- Martin Ekman
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
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13
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Barendt S, Lee H, Birch C, Nakano MM, Jones M, Zuber P. Transcriptomic and phenotypic analysis of paralogous spx gene function in Bacillus anthracis Sterne. Microbiologyopen 2013; 2:695-714. [PMID: 23873705 PMCID: PMC3831629 DOI: 10.1002/mbo3.109] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 06/05/2013] [Accepted: 06/17/2013] [Indexed: 11/15/2022] Open
Abstract
Spx of Bacillus subtilis is a redox-sensitive protein, which, under disulfide stress, interacts with RNA polymerase to activate genes required for maintaining thiol homeostasis. Spx orthologs are highly conserved among low %GC Gram-positive bacteria, and often exist in multiple paralogous forms. In this study, we used B. anthracis Sterne, which harbors two paralogous spx genes, spxA1 and spxA2, to examine the phenotypes of spx null mutations and to identify the genes regulated by each Spx paralog. Cells devoid of spxA1 were sensitive to diamide and hydrogen peroxide, while the spxA1 spoxA2 double mutant was hypersensitive to the thiol-specific oxidant, diamide. Bacillus anthracis Sterne strains expressing spxA1DD or spxA2DD alleles encoding protease-resistant products were used in microarray and quantitative real-time polymerase chain reaction (RT-qPCR) analyses in order to uncover genes under SpxA1, SpxA2, or SpxA1/SpxA2 control. Comparison of transcriptomes identified many genes that were upregulated when either SpxA1DD or SpxA2DD was produced, but several genes were uncovered whose transcript levels increased in only one of the two SpxADD-expression strains, suggesting that each Spx paralog governs a unique regulon. Among genes that were upregulated were those encoding orthologs of proteins that are specifically involved in maintaining intracellular thiol homeostasis or alleviating oxidative stress. Some of these genes have important roles in B. anthracis pathogenesis, and a large number of upregulated hypothetical genes have no homology outside of the B. cereus/thuringiensis group. Microarray and RT-qPCR analyses also unveiled a regulatory link that exists between the two spx paralogous genes. The data indicate that spxA1 and spxA2 are transcriptional regulators involved in relieving disulfide stress but also control a set of genes whose products function in other cellular processes. Bacillus anthracis harbors two paralogs of the global transcriptional regulator of stress response, SpxA. SpxA1 and SpxA2 contribute to disulfide stress tolerance, but only SpxA1 functions in resistance to peroxide. Transcriptome analysis uncovered potential SpxA1 and SpxA2 regulon members, which include genes activated by both paralogs. However, paralog-specific gene activation was also observed. Genes encoding glutamate racemase, CoA disulfide reductase, and products functioning in bacillithiol biosynthesis, are among the genes activated by the SpxA paralogs.
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Affiliation(s)
- Skye Barendt
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University, Beaverton, Oregon
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14
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Campylobacter jejuni Dps protein binds DNA in the presence of iron or hydrogen peroxide. J Bacteriol 2013; 195:1970-8. [PMID: 23435977 DOI: 10.1128/jb.00059-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Iron is an essential cofactor for many enzymes; however, this metal can lead to the formation of reactive oxygen species. Ferritin proteins bind and oxidize Fe(2+) to Fe(3+), storing this metal in a nonreactive form. In some organisms, a particular subfamily of ferritins, namely, Dps proteins, have the ability to bind DNA. Here we show that the Campylobacter jejuni Dps has DNA binding activity that is uniquely activated by Fe(2+) or H2O2 at below neutral pH. The Dps-DNA binding activity correlated with the ability of Dps to self-aggregate. The Dps-DNA interaction was inhibited by NaCl and Mg(2+), suggesting the formation of ionic interactions between Dps and DNA. Alkylation of cysteines affected DNA binding in the presence of H2O2 but not in the presence of Fe(2+). Replacement of all cysteines in C. jejuni Dps with serines did not affect DNA binding, excluding the participation of cysteine in H2O2 sensing. Dps was able to protect DNA in vitro from enzymatic cleavage and damage by hydroxyl radicals. A C. jejuni dps mutant was less resistant to H2O2 in vivo. The concerted activation of Dps-DNA binding in response to low pH, H2O2, and Fe(2+) may protect C. jejuni DNA during host colonization.
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Comparative genomic and functional analysis of Lactobacillus casei and Lactobacillus rhamnosus strains marketed as probiotics. Appl Environ Microbiol 2013; 79:1923-33. [PMID: 23315726 DOI: 10.1128/aem.03467-12] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Four Lactobacillus strains were isolated from marketed probiotic products, including L. rhamnosus strains from Vifit (Friesland Campina) and Idoform (Ferrosan) and L. casei strains from Actimel (Danone) and Yakult (Yakult Honsa Co.). Their genomes and phenotypes were characterized and compared in detail with L. casei strain BL23 and L. rhamnosus strain GG. Phenotypic analysis of the new isolates indicated differences in carbohydrate utilization between L. casei and L. rhamnosus strains, which could be linked to their genotypes. The two isolated L. rhamnosus strains had genomes that were virtually identical to that of L. rhamnosus GG, testifying to their genomic stability and integrity in food products. The L. casei strains showed much greater genomic heterogeneity. Remarkably, all strains contained an intact spaCBA pilus gene cluster. However, only the L. rhamnosus strains produced mucus-binding SpaCBA pili under the conditions tested. Transcription initiation mapping demonstrated that the insertion of an iso-IS30 element upstream of the pilus gene cluster in L. rhamnosus strains but absent in L. casei strains had constituted a functional promoter driving pilus gene expression. All L. rhamnosus strains triggered an NF-κB response via Toll-like receptor 2 (TLR2) in a reporter cell line, whereas the L. casei strains did not or did so to a much lesser extent. This study demonstrates that the two L. rhamnosus strains isolated from probiotic products are virtually identical to L. rhamnosus GG and further highlights the differences between these and L. casei strains widely marketed as probiotics, in terms of genome content, mucus-binding and metabolic capacities, and host signaling capabilities.
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Huillet E, Tempelaars MH, André-Leroux G, Wanapaisan P, Bridoux L, Makhzami S, Panbangred W, Martin-Verstraete I, Abee T, Lereclus D. PlcRa, a new quorum-sensing regulator from Bacillus cereus, plays a role in oxidative stress responses and cysteine metabolism in stationary phase. PLoS One 2012; 7:e51047. [PMID: 23239999 PMCID: PMC3519770 DOI: 10.1371/journal.pone.0051047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/29/2012] [Indexed: 12/31/2022] Open
Abstract
We characterized a new quorum-sensing regulator, PlcRa, which is present in various members of the B. cereus group and identified a signaling heptapeptide for PlcRa activity: PapRa7. We demonstrated that PlcRa is a 3D structural paralog of PlcR using sequence analysis and homology modeling. A comparison of the transcriptomes at the onset of stationary phase of a ΔplcRa mutant and the wild-type B. cereus ATCC 14579 strain showed that 68 genes were upregulated and 49 genes were downregulated in the ΔplcRa mutant strain (>3-fold change). Genes involved in the cysteine metabolism (putative CymR regulon) were downregulated in the ΔplcRa mutant strain. We focused on the gene with the largest difference in expression level between the two conditions, which encoded -AbrB2- a new regulator of the AbrB family. We demonstrated that purified PlcRa bound specifically to the abrB2 promoter in the presence of synthetic PapRa7, in an electrophoretic mobility shift assay. We further showed that the AbrB2 regulator controlled the expression of the yrrT operon involved in methionine to cysteine conversion. We found that the ΔplcRa mutant strain was more sensitive to hydrogen peroxide- and disulfide-induced stresses than the wild type. When cystine was added to the culture of the ΔplcRa mutant, challenged with hydrogen peroxide, growth inhibition was abolished. In conclusion, we identified a new RNPP transcriptional regulator in B. cereus that activated the oxidative stress response and cysteine metabolism in transition state cells.
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Affiliation(s)
- Eugénie Huillet
- INRA, UMR1319 Micalis, Génétique microbienne et Environnement, Guyancourt, France
- * E-mail: (EH); (DL)
| | - Marcel H. Tempelaars
- Wageningen University, Laboratory of Food Microbiology, Wageningen, The Netherlands
| | | | - Pagakrong Wanapaisan
- INRA, UMR1319 Micalis, Génétique microbienne et Environnement, Guyancourt, France
- Mahidol University, Department of Biotechnology, Faculty of Science, Bangkok, Thailand
| | - Ludovic Bridoux
- INRA, UMR1319 Micalis, Génétique microbienne et Environnement, Guyancourt, France
| | | | - Watanalai Panbangred
- Mahidol University, Department of Biotechnology, Faculty of Science, Bangkok, Thailand
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Laboratoire de Pathogénèse des Bactéries Anaérobies, Paris, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Tjakko Abee
- Wageningen University, Laboratory of Food Microbiology, Wageningen, The Netherlands
| | - Didier Lereclus
- INRA, UMR1319 Micalis, Génétique microbienne et Environnement, Guyancourt, France
- * E-mail: (EH); (DL)
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Abstract
Dps proteins are the structural relatives of bacterioferritins and ferritins ubiquitously present in the bacterial and archaeal kingdoms. The ball-shaped enzymes play important roles in the detoxification of ROS (reactive oxygen species), in iron scavenging to prevent Fenton reactions and in the mechanical protection of DNA. Detoxification of ROS and iron chaperoning represent the most archetypical functions of dodecameric Dps enzymes. Recent crystallographic studies of these dodecameric complexes have unravelled species-dependent mechanisms of iron uptake into the hollow spheres. Subsequent functions in iron oxidation at ferroxidase centres are highly conserved among bacteria. Final nucleation of iron as iron oxide nanoparticles has been demonstrated to originate at acidic residues located on the inner surface. Some Dps enzymes are also implicated in newly observed catalytic functions related to the formation of molecules playing roles in bacterium–host cell communication. Most recently, Dps complexes are attracting attention in semiconductor science as biomimetic tools for the technical production of the smallest metal-based quantum nanodots used in nanotechnological approaches, such as memory storage or solar cell development.
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Tu WY, Pohl S, Summpunn P, Hering S, Kerstan S, Harwood CR. Comparative analysis of the responses of related pathogenic and environmental bacteria to oxidative stress. Microbiology (Reading) 2012; 158:636-647. [DOI: 10.1099/mic.0.057000-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Wang Yung Tu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Susanne Pohl
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Pijug Summpunn
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Silvio Hering
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sandra Kerstan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Colin R. Harwood
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
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Abstract
Although successful iron acquisition by pathogens within a host is a prerequisite for the establishment of infection, surprisingly little is known about the intracellular distribution of iron within bacterial pathogens. We have used a combination of anaerobic native liquid chromatography, inductively coupled plasma mass spectrometry, principal-component analysis, and peptide mass fingerprinting to investigate the cytosolic iron distribution in the pathogen Bacillus anthracis. Our studies identified three of the major iron pools as being associated with the electron transfer protein ferredoxin, the miniferritin Dps2, and the superoxide dismutase (SOD) enzymes SodA1 and SodA2. Although both SOD isozymes were predicted to utilize manganese cofactors, quantification of the metal ions associated with SodA1 and SodA2 in cell extracts established that SodA1 is associated with both manganese and iron, whereas SodA2 is bound exclusively to iron in vivo. These data were confirmed by in vitro assays using recombinant protein preparations, showing that SodA2 is active with an iron cofactor, while SodA1 is cambialistic, i.e., active with manganese or iron. Furthermore, we observe that B. anthracis cells exposed to superoxide stress increase their total iron content more than 2-fold over 60 min, while the manganese and zinc contents are unaffected. Notably, the acquired iron is not localized to the three identified cytosolic iron pools.
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