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Yeak KYC, Tempelaars M, Wu JL, Westerveld W, Reder A, Michalik S, Dhople VM, Völker U, Pané-Farré J, Wells-Bennik MHJ, Abee T. SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus. BMC Microbiol 2023; 23:37. [PMID: 36759782 PMCID: PMC9912610 DOI: 10.1186/s12866-023-02783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND The Bacillus cereus Sigma B (SigB) dependent general stress response is activated via the two-component RsbKY system, which involves a phosphate transfer from RsbK to RsbY. It has been hypothesized that the Hpr-like phosphocarrier protein (Bc1009) encoded by bc1009 in the SigB gene cluster may play a role in this transfer, thereby acting as a regulator of SigB activation. Alternatively, Bc1009 may be involved in the activation of a subset of SigB regulon members. RESULTS We first investigated the potential role of bc1009 to act as a SigB regulator but ruled out this possibility as the deletion of bc1009 did not affect the expression of sigB and other SigB gene cluster members. The SigB-dependent functions of Bc1009 were further examined in B. cereus ATCC14579 via comparative proteome profiling (backed up by transcriptomics) of wt, Δbc1009 and ΔsigB deletion mutants under heat stress at 42 °C. This revealed 284 proteins displaying SigB-dependent alterations in protein expression levels in heat-stressed cells, including a subgroup of 138 proteins for which alterations were also Bc1009-dependent. Next to proteins with roles in stress defense, newly identified SigB and Bc1009-dependent proteins have roles in cell motility, signal transduction, transcription, cell wall biogenesis, and amino acid transport and metabolism. Analysis of lethal stress survival at 50 °C after pre-adaptation at 42 °C showed intermediate survival efficacy of Δbc1009 cells, highest survival of wt, and lowest survival of ΔsigB cells, respectively. Additional comparative proteome analysis of non-stressed wt and mutant cells at 30 °C revealed 96 proteins with SigB and Bc1009-dependent differences in levels: 51 were also identified under heat stress, and 45 showed significant differential expression at 30 °C. This includes proteins with roles in carbohydrate/ion transport and metabolism. Overlapping functions at 30 °C and 42 °C included proteins involved in motility, and ΔsigB and Δbc1009 cells showed reduced motility compared to wt cells in swimming assays at both temperatures. CONCLUSION Our results extend the B. cereus SigB regulon to > 300 members, with a novel role of SigB-dependent Bc1009 in the activation of a subregulon of > 180 members, conceivably via interactions with other transcriptional regulatory networks.
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Affiliation(s)
- Kah Yen Claire Yeak
- grid.419921.60000 0004 0588 7915NIZO, Kernhemseweg 2, PO Box 20, 6718 ZB Ede, The Netherlands ,grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Marcel Tempelaars
- grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Jia Lun Wu
- grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Wouter Westerveld
- grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, PO Box 8129, 6700 EV Wageningen, The Netherlands
| | - Alexander Reder
- grid.5603.0Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- grid.5603.0Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Vishnu M. Dhople
- grid.5603.0Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- grid.5603.0Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- grid.10253.350000 0004 1936 9756Center for Synthetic Microbiology (SYNMIKRO) & Department of Chemistry, Philipps-University Marburg, Karl-Von-Frisch-Strasse 14, 35043 Marburg, Germany
| | | | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, PO Box 8129, 6700 EV, Wageningen, The Netherlands.
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Yeak KYC, Boekhorst J, Wels M, Abee T, Wells-Bennik MHJ. Prediction and validation of novel SigB regulon members in Bacillus subtilis and regulon structure comparison to Bacillales members. BMC Microbiol 2023; 23:17. [PMID: 36653740 PMCID: PMC9847131 DOI: 10.1186/s12866-022-02700-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/11/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Sigma factor B (SigB) is the central regulator of the general stress response in Bacillus subtilis and regulates a group of genes in response to various stressors, known as the SigB regulon members. Genes that are directly regulated by SigB contain a promotor binding motif (PBM) with a previously identified consensus sequence. RESULTS In this study, refined SigB PBMs were derived and different spacer compositions and lengths (N12-N17) were taken into account. These were used to identify putative SigB-regulated genes in the B. subtilis genome, revealing 255 genes: 99 had been described in the literature and 156 genes were newly identified, increasing the number of SigB putative regulon members (with and without a SigB PBM) to > 500 in B. subtilis. The 255 genes were assigned to five categories (I-V) based on their similarity to the original SigB consensus sequences. The functionalities of selected representatives per category were assessed using promoter-reporter fusions in wt and ΔsigB mutants upon exposure to heat, ethanol, and salt stress. The activity of the PrsbV (I) positive control was induced upon exposure to all three stressors. PytoQ (II) showed SigB-dependent activity only upon exposure to ethanol, whereas PpucI (II) with a N17 spacer and PylaL (III) with a N16 spacer showed mild induction regardless of heat/ethanol/salt stress. PywzA (III) and PyaaI (IV) displayed ethanol-specific SigB-dependent activities despite a lower-level conserved - 10 binding motif. PgtaB (V) was SigB-induced under ethanol and salt stress while lacking a conserved - 10 binding region. The activities of PygaO and PykaA (III) did not show evident changes under the conditions tested despite having a SigB PBM that highly resembled the consensus. The identified extended SigB regulon candidates in B. subtilis are mainly involved in coping with stress but are also engaged in other cellular processes. Orthologs of SigB regulon candidates with SigB PBMs were identified in other Bacillales genomes, but not all showed a SigB PBM. Additionally, genes involved in the integration of stress signals to activate SigB were predicted in these genomes, indicating that SigB signaling and regulon genes are species-specific. CONCLUSION The entire SigB regulatory network is sophisticated and not yet fully understood even for the well-characterized organism B. subtilis 168. Knowledge and information gained in this study can be used in further SigB studies to uncover a complete picture of the role of SigB in B. subtilis and other species.
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Affiliation(s)
- Kah Yen Claire Yeak
- grid.419921.60000 0004 0588 7915NIZO, Ede, The Netherlands ,grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Jos Boekhorst
- grid.419921.60000 0004 0588 7915NIZO, Ede, The Netherlands ,grid.4818.50000 0001 0791 5666Host Microbe Interactomics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Michiel Wels
- grid.419921.60000 0004 0588 7915NIZO, Ede, The Netherlands ,grid.426040.4Rijk Zwaan Breeding B.V, Fijnaart, The Netherlands
| | - Tjakko Abee
- grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
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Reconstruction and analysis of transcriptome regulatory network of Methanobrevibacter ruminantium M1. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4
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Yang X, Wang Z, Zhang C, Wang L, Pang L, Zhang D, Man C, Jiang Y. Assessment of the production of Bacillus cereus protease and its effect on the quality of ultra-high temperature-sterilized whole milk. J Dairy Sci 2021; 104:6577-6587. [PMID: 33741157 DOI: 10.3168/jds.2020-19818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/30/2021] [Indexed: 01/09/2023]
Abstract
Bacillus cereus is one of the most important spoilage microorganisms in milk. The heat-resistant protease produced is the main factor that causes rotten, bitter off-flavors and age gelation during the shelf-life of milk. In this study, 55 strains of B. cereus were evaluated, of which 25 strains with protease production ability were used to investigate proteolytic activity and protease heat resistance. The results showed that B. cereus C58 had strong protease activity, and its protease also had the highest thermal stability after heat treatment of 70°C (30 min) and 100°C (10 min). The protease was identified as protease HhoA, with a molecular mass of 43.907 kDa. The protease activity of B. cereus C58 in UHT-sterilized whole milk (UHT milk) showed an increase with the growth of bacteria, especially during the logarithmic growth phase. In addition, the UHT milk incubated with protease from B. cereus C58 at 28°C (24 h) and 10°C (6 d) were used to evaluate the effects of protease on the quality of UHT milk, including protein hydrolysis and physical stability. The results showed that the hydrolysis of casein was κ-CN, β-CN, and αS-CN successively, whereas whey protein was not hydrolyzed. The degree of protein hydrolysis, viscosity, and particle size of the UHT milk increased. The changes in protein and fat contents indicated that fat globules floated at 28°C and settled at 10°C, respectively. Meanwhile, confocal laser scanning microscopy images revealed that the protease caused the stability of UHT milk to decrease, thus forming age gelation.
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Affiliation(s)
- Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Zhenghui Wang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Chenxi Zhang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Lihan Wang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Lidong Pang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Dongyan Zhang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China.
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin, 150030, China.
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The Alternative Sigma Factor SigB Is Required for the Pathogenicity of Bacillus thuringiensis. J Bacteriol 2020; 202:JB.00265-20. [PMID: 32817096 DOI: 10.1128/jb.00265-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/11/2020] [Indexed: 11/20/2022] Open
Abstract
To adapt to changing and potentially hostile environments, bacteria can activate the transcription of genes under the control of alternative sigma factors, such as SigB, a master regulator of the general stress response in several Gram-positive species. Bacillus thuringiensis is a Gram-positive spore-forming invertebrate pathogen whose life cycle includes a variety of environments, including plants and the insect hemocoel or gut. Here, we assessed the role of SigB during the infectious cycle of B. thuringiensis in a Galleria mellonella insect model. We used a fluorescent reporter coupled to flow cytometry and showed that SigB was activated in vivo We also showed that the pathogenicity of the ΔsigB mutant was severely affected when inoculated via the oral route, suggesting that SigB is critical for B. thuringiensis adaptation to the gut environment of the insect. We could not detect an effect of the sigB deletion on the survival of the bacteria or on their sporulation efficiency in the cadavers. However, the gene encoding the pleiotropic regulator Spo0A was upregulated in the ΔsigB mutant cells during the infectious process.IMPORTANCE Pathogenic bacteria often need to transition between different ecosystems, and their ability to cope with such variations is critical for their survival. Several Gram-positive species have developed an adaptive response mediated by the general stress response alternative sigma factor SigB. In order to understand the ecophysiological role of this regulator in Bacillus thuringiensis, an entomopathogenic bacterium widely used as a biopesticide, we sought to examine the fate of a ΔsigB mutant during its life cycle in the natural setting of an insect larva. This allowed us, in particular, to show that SigB was activated during infection and that it was required for the pathogenicity of B. thuringiensis via the oral route of infection.
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den Besten HM, Amézquita A, Bover-Cid S, Dagnas S, Ellouze M, Guillou S, Nychas G, O'Mahony C, Pérez-Rodriguez F, Membré JM. Next generation of microbiological risk assessment: Potential of omics data for exposure assessment. Int J Food Microbiol 2018; 287:18-27. [DOI: 10.1016/j.ijfoodmicro.2017.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 09/15/2017] [Accepted: 10/03/2017] [Indexed: 12/30/2022]
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7
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Hollensteiner J, Poehlein A, Spröer C, Bunk B, Sheppard AE, Rosentstiel P, Schulenburg H, Liesegang H. Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246. Stand Genomic Sci 2017; 12:48. [PMID: 28852435 PMCID: PMC5569534 DOI: 10.1186/s40793-017-0259-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/08/2017] [Indexed: 01/22/2023] Open
Abstract
10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of the genus 10.1601/nm.4857. The defining feature of the species is the ability to produce parasporal crystal inclusion bodies, consisting of δ-endotoxins, encoded by cry-genes. Here we present the complete annotated genome sequence of the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one 5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to 150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes, including 36 rRNA genes. The plasmids encode 997 proteins and 4 t-RNA's. Analysis of the genome revealed a large number of mobile elements involved in genome plasticity including 11 plasmids and 16 chromosomal prophages. Three different nematicidal toxin genes were identified and classified according to the Cry toxin naming committee as cry13Aa2, cry13Ba1, and cry13Ab1. Strikingly, these genes are located on the chromosome in close proximity to three separate prophages. Moreover, four putative toxin genes of different toxin classes were identified on the plasmids p120510 (Vip-like toxin), p120416 (Cry-like toxin) and p109822 (two Bin-like toxins). A comparative genome analysis of 10.1601/nm.5000 MYBT18246 with three closely related 10.1601/nm.5000 strains enabled determination of the pan-genome of 10.1601/nm.5000 MYBT18246, revealing a large number of singletons, mostly represented by phage genes, morons and cryptic genes.
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Affiliation(s)
- Jacqueline Hollensteiner
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anna E. Sheppard
- Present address: Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Philip Rosentstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
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8
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Evolutionary processes and environmental factors underlying the genetic diversity and lifestyles of Bacillus cereus group bacteria. Res Microbiol 2017; 168:309-318. [DOI: 10.1016/j.resmic.2016.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 07/03/2016] [Accepted: 07/05/2016] [Indexed: 11/22/2022]
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9
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Jackson LA, Day M, Allen J, Scott E, Dyer DW. Iron-regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth. BMC Genomics 2017; 18:317. [PMID: 28431495 PMCID: PMC5399841 DOI: 10.1186/s12864-017-3684-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/06/2017] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND For most pathogens, iron (Fe) homeostasis is crucial for maintenance within the host and the ability to cause disease. The primary transcriptional regulator that controls intracellular Fe levels is the Fur (ferric uptake regulator) protein, which exerts its action on transcription by binding to a promoter-proximal sequence termed the Fur box. Fur-regulated transcriptional responses are often fine-tuned at the post-transcriptional level through the action of small regulatory RNAs (sRNAs). Consequently, identifying sRNAs contributing to the control of Fe homeostasis is important for understanding the Fur-controlled bacterial Fe-response network. RESULTS In this study, we sequenced size-selected directional libraries representing sRNA samples from Neisseria gonorrhoeae strain FA 1090, and examined the Fe- and temporal regulation of these sRNAs. RNA-seq data for all time points identified a pool of at least 340 potential sRNAs. Differential analysis demonstrated that expression appeared to be regulated by Fe availability for at least fifteen of these sRNAs. Fourteen sRNAs were induced in high Fe conditions, consisting of both cis and trans sRNAs, some of which are predicted to control expression of a known virulence factor, and one SAM riboswitch. An additional putative cis-acting sRNA was repressed by Fe availability. In the pathogenic Neisseria species, one sRNA that contributes to Fe-regulated post-transcriptional control is the Fur-repressible sRNA NrrF. The expression of five Fe-induced sRNAs appeared to be at least partially controlled by NrrF, while the remainder was expressed independently of NrrF. The expression of the 14 Fe-induced sRNAs also exhibited temporal control, as their expression levels increased dramatically as the bacteria entered stationary phase. CONCLUSIONS Here we report the temporal expression of Fe-regulated sRNAs in N. gonorrhoeae FA 1090 with several appearing to be controlled by the Fe-repressible sRNA NrrF. Temporal regulation of these sRNAs suggests a regulatory role in controlling functions necessary for survival, and may be important for phenotypes often associated with altered growth rates, such as biofilm formation or intracellular survival. Future functional studies will be needed to understand how these regulatory sRNAs contribute to gonococcal biology and pathogenesis.
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Affiliation(s)
- Lydgia A. Jackson
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences, 975 NE 10th Street, Oklahoma City, OK 73104 USA
| | - Michael Day
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences, 975 NE 10th Street, Oklahoma City, OK 73104 USA
| | - Jennie Allen
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences, 975 NE 10th Street, Oklahoma City, OK 73104 USA
| | - Edgar Scott
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences, 975 NE 10th Street, Oklahoma City, OK 73104 USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences, 975 NE 10th Street, Oklahoma City, OK 73104 USA
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Burall LS, Simpson AC, Chou L, Laksanalamai P, Datta AR. A novel gene, lstC, of Listeria monocytogenes is implicated in high salt tolerance. Food Microbiol 2015; 48:72-82. [PMID: 25790994 DOI: 10.1016/j.fm.2014.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 12/01/2014] [Accepted: 12/16/2014] [Indexed: 01/08/2023]
Abstract
Listeria monocytogenes, causative agent of human listeriosis, has been isolated from a wide variety of foods including deli meats, soft cheeses, cantaloupes, sprouts and canned mushrooms. Standard control measures for restricting microbial growth such as refrigeration and high salt are often inadequate as L. monocytogenes grows quite well in these environments. In an effort to better understand the genetic and physiological basis by which L. monocytogenes circumvents these controls, a transposon library of L. monocytogenes was screened for changes in their ability to grow in 7% NaCl and/ or at 5 °C. This work identified a transposon insertion upstream of an operon, here named lstABC, that led to a reduction in growth in 7% NaCl. In-frame deletion studies identified lstC which codes for a GNAT-acetyltransferase being responsible for the phenotype. Transcriptomic and RT-PCR analyses identified nine genes that were upregulated in the presence of high salt in the ΔlstC mutant. Further analysis of lstC and the genes affected by ΔlstC is needed to understand LstC's role in salt tolerance.
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Affiliation(s)
- Laurel S Burall
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Alexandra C Simpson
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Luoth Chou
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Pongpan Laksanalamai
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Atin R Datta
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
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Toby IT, Widmer J, Dyer DW. Divergence of protein-coding capacity and regulation in the Bacillus cereus sensu lato group. BMC Bioinformatics 2014; 15 Suppl 11:S8. [PMID: 25350501 PMCID: PMC4251056 DOI: 10.1186/1471-2105-15-s11-s8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The Bacillus cereus sensu lato group contains ubiquitous facultative anaerobic soil-borne Gram-positive spore-forming bacilli. Molecular phylogeny and comparative genome sequencing have suggested that these organisms should be classified as a single species. While clonal in nature, there do not appear to be species-specific clonal lineages, excepting B. anthracis, in spite of the wide array of phenotypes displayed by these organisms. RESULTS We compared the protein-coding content of 201 B. cereus sensu lato genomes to characterize differences and understand the consequences of these differences on biological function. From this larger group we selected a subset consisting of 25 whole genomes for deeper analysis. Cluster analysis of orthologous proteins grouped these genomes into five distinct clades. Each clade could be characterized by unique genes shared among the group, with consequences for the phenotype of each clade. Surprisingly, this population structure recapitulates our recent observations on the divergence of the generalized stress response (SigB) regulons in these organisms. Divergence of the SigB regulon among these organisms is primarily due to the placement of SigB-dependent promoters that bring genes from a common gene pool into/out of the SigB regulon. CONCLUSIONS Collectively, our observations suggest the hypothesis that the evolution of these closely related bacteria is a consequence of two distinct processes. Horizontal gene transfer, gene duplication/divergence and deletion dictate the underlying coding capacity in these genomes. Regulatory divergence overlays this protein coding reservoir and shapes the expression of both the unique and shared coding capacity of these organisms, resulting in phenotypic divergence. Data from other organisms suggests that this is likely a common pattern in prokaryotic evolution.
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Affiliation(s)
- Inimary T Toby
- University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC-1106, Oklahoma City, OK 73104, USA
| | - Jonah Widmer
- University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC-1106, Oklahoma City, OK 73104, USA
| | - David W Dyer
- University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC-1106, Oklahoma City, OK 73104, USA
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Ghosh N, Goel AK, Alam SI. Exoproteome analysis of a novel strain of Bacillus cereus implicated in disease resembling cutaneous anthrax. INFECTION GENETICS AND EVOLUTION 2014; 22:1-11. [PMID: 24412723 DOI: 10.1016/j.meegid.2013.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 11/06/2013] [Accepted: 12/11/2013] [Indexed: 12/15/2022]
Abstract
Bacillus cereus belongs to B. cereus sensu lato group, shared by six other related species including Bacillus anthracis. B. anthracis is the causative agent for serious illness affecting a wide range of animals as well as humans and is a category A Biological and Toxin Warfare (BTW) agent. Recent studies indicate that a Bacillus species other than B. anthracis can cause anthrax-like disease and role of anthrax virulence plasmids (pXO1 and pXO2) on the pathogenicity of B. cereus has been documented. B. cereus strain TF5 was isolated from the tissue fluid of cutaneous anthrax-like skin lesions of a human patient from an anthrax endemic area in India. The strain harboured a PA gene, however, presence of pXO1 or pXO2-like plasmids could not be ascertained using reported primers. Abundant exoproteome of the strain in the early stationary phase was elucidated using a 2-DE MS approach and compared with that from a reference B. cereus strain. Analysis of proteins showing qualitative and quantitative differences between the two strains indicated an altered regulatory mechanism and putative role of S-layer protein and sphingomyelinase in the pathogenesis of strain TF5. Phylogenetic analysis of the S-layer protein indicated close affiliation of the strain with anthracis-like B. cereus strains such as B. cereus var. anthracis strain CI; whereas sphingomyelinase exhibited specific relationship with all the strains of B. anthracis apart from that with anthracis-like B. cereus strains.
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Affiliation(s)
- Neha Ghosh
- Biotechnology Division, Defence Research and Development Establishment, Gwalior 474002, India.
| | - Ajay Kumar Goel
- Biotechnology Division, Defence Research and Development Establishment, Gwalior 474002, India.
| | - Syed Imteyaz Alam
- Biotechnology Division, Defence Research and Development Establishment, Gwalior 474002, India.
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Desriac N, Broussolle V, Postollec F, Mathot AG, Sohier D, Coroller L, Leguerinel I. Bacillus cereus cell response upon exposure to acid environment: toward the identification of potential biomarkers. Front Microbiol 2013; 4:284. [PMID: 24106490 PMCID: PMC3788345 DOI: 10.3389/fmicb.2013.00284] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/03/2013] [Indexed: 01/20/2023] Open
Abstract
Microorganisms are able to adapt to different environments and evolve rapidly, allowing them to cope with their new environments. Such adaptive response and associated protections toward other lethal stresses, is a crucial survival strategy for a wide spectrum of microorganisms, including food spoilage bacteria, pathogens, and organisms used in functional food applications. The growing demand for minimal processed food yields to an increasing use of combination of hurdles or mild preservation factors in the food industry. A commonly used hurdle is low pH which allows the decrease in bacterial growth rate but also the inactivation of pathogens or spoilage microorganisms. Bacillus cereus is a well-known food-borne pathogen leading to economical and safety issues in food industry. Because survival mechanisms implemented will allow bacteria to cope with environmental changes, it is important to provide understanding of B. cereus stress response. Thus this review deals with the adaptive traits of B. cereus cells facing to acid stress conditions. The acid stress response of B. cereus could be divided into four groups (i) general stress response (ii) pH homeostasis, (iii) metabolic modifications and alkali production and (iv) secondary oxidative stress response. This current knowledge may be useful to understand how B. cereus cells may cope to acid environment such as encountered in food products and thus to find some molecular biomarkers of the bacterial behavior. These biomarkers could be furthermore used to develop new microbial behavior prediction tools which can provide insights into underlying molecular physiological states which govern the behavior of microorganisms and thus opening the avenue toward the detection of stress adaptive behavior at an early stage and the control of stress-induced resistance throughout the food chain.
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Affiliation(s)
- Noémie Desriac
- ADRIA Développement, UMT 08.3 PHYSI’Opt, QuimperFrance
- EA3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, UMT 08.3 PHYSI’Opt, IFR148 ScInBioS, Université de BrestQuimper, France
| | - Véronique Broussolle
- UMR408, Sécurité et Qualité des Produits d’Origine Végétale, Institut National de la Recherche AgronomiqueAvignon, France
- UMR408, Sécurité et Qualité des Produits d’Origine Végétale, Université d’Avignon et des Pays de VaucluseAvignon, France
| | | | - Anne-Gabrielle Mathot
- EA3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, UMT 08.3 PHYSI’Opt, IFR148 ScInBioS, Université de BrestQuimper, France
| | | | - Louis Coroller
- EA3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, UMT 08.3 PHYSI’Opt, IFR148 ScInBioS, Université de BrestQuimper, France
| | - Ivan Leguerinel
- EA3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, UMT 08.3 PHYSI’Opt, IFR148 ScInBioS, Université de BrestQuimper, France
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