1
|
Wilson SA, Tank RKJ, Hobbs JK, Foster SJ, Garner EC. An exhaustive multiple knockout approach to understanding cell wall hydrolase function in Bacillus subtilis. mBio 2023; 14:e0176023. [PMID: 37768080 PMCID: PMC10653849 DOI: 10.1128/mbio.01760-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/03/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE In order to grow, bacterial cells must both create and break down their cell wall. The enzymes that are responsible for these processes are the target of some of our best antibiotics. Our understanding of the proteins that break down the wall- cell wall hydrolases-has been limited by redundancy among the large number of hydrolases many bacteria contain. To solve this problem, we identified 42 cell wall hydrolases in Bacillus subtilis and created a strain lacking 40 of them. We show that cells can survive using only a single cell wall hydrolase; this means that to understand the growth of B. subtilis in standard laboratory conditions, it is only necessary to study a very limited number of proteins, simplifying the problem substantially. We additionally show that the ∆40 strain is a research tool to characterize hydrolases, using it to identify three "helper" hydrolases that act in certain stress conditions.
Collapse
Affiliation(s)
- Sean A. Wilson
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Raveen K. J. Tank
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Jamie K. Hobbs
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Simon J. Foster
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ethan C. Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
2
|
Naamala J, Subramanian S, Msimbira LA, Smith DL. Effect of NaCl stress on exoproteome profiles of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H. Front Microbiol 2023; 14:1206152. [PMID: 37700863 PMCID: PMC10493332 DOI: 10.3389/fmicb.2023.1206152] [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: 04/17/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023] Open
Abstract
Salt stress can affect survival, multiplication and ability of plant growth promoting microorganisms to enhance plant growth. Changes in a microbe's proteome profile is one of the mechanisms employed by PGPM to enhance tolerance of salt stress. This study was focused on understanding changes in the exoproteome profile of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H when exposed to salt stress. The strains were cultured in 100 mL M13 (B. amyloliquefaciens) and 100 mL De man, Rogosa and Sharpe (MRS) (L. helveticus) media, supplemented with 200 and 0 mM NaCl (control), at pH 7.0. The strains were then incubated for 48 h (late exponential growth phase), at 120 rpm and 30 (B. amyloliquefaciens) and 37 (L. helveticus) °C. The microbial cultures were then centrifuged and filtered sterilized, to obtain cell free supernatants whose proteome profiles were studied using LC-MS/MS analysis and quantified using scaffold. Results of the study revealed that treatment with 200 mM NaCl negatively affected the quantity of identified proteins in comparison to the control, for both strains. There was upregulation and downregulation of some proteins, even up to 100%, which resulted in identification of proteins significantly unique between the control or 200 mM NaCl (p ≤ 0.05), for both microbial species. Proteins unique to 200 mM NaCl were mostly those involved in cell wall metabolism, substrate transport, oxidative stress tolerance, gene expression and DNA replication and repair. Some of the identified unique proteins have also been reported to enhance plant growth. In conclusion, based on the results of the work described here, PGPM alter their exoproteome profile when exposed to salt stress, potentially upregulating proteins that enhance their tolerance to this stress.
Collapse
Affiliation(s)
| | | | | | - Donald L. Smith
- Department of Plant Science, McGill University, Montreal, QC, Canada
| |
Collapse
|
3
|
Adams JD, Sander KB, Criddle CS, Arkin AP, Clark DS. Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products. Microb Cell Fact 2023; 22:69. [PMID: 37046248 PMCID: PMC10091555 DOI: 10.1186/s12934-023-02064-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Intracellular biomacromolecules, such as industrial enzymes and biopolymers, represent an important class of bio-derived products obtained from bacterial hosts. A common key step in the downstream separation of these biomolecules is lysis of the bacterial cell wall to effect release of cytoplasmic contents. Cell lysis is typically achieved either through mechanical disruption or reagent-based methods, which introduce issues of energy demand, material needs, high costs, and scaling problems. Osmolysis, a cell lysis method that relies on hypoosmotic downshock upon resuspension of cells in distilled water, has been applied for bioseparation of intracellular products from extreme halophiles and mammalian cells. However, most industrial bacterial strains are non-halotolerant and relatively resistant to hypoosmotic cell lysis. RESULTS To overcome this limitation, we developed two strategies to increase the susceptibility of non-halotolerant hosts to osmolysis using Cupriavidus necator, a strain often used in electromicrobial production, as a prototypical strain. In one strategy, C. necator was evolved to increase its halotolerance from 1.5% to 3.25% (w/v) NaCl through adaptive laboratory evolution, and genes potentially responsible for this phenotypic change were identified by whole genome sequencing. The evolved halotolerant strain experienced an osmolytic efficiency of 47% in distilled water following growth in 3% (w/v) NaCl. In a second strategy, the cells were made susceptible to osmolysis by knocking out the large-conductance mechanosensitive channel (mscL) gene in C. necator. When these strategies were combined by knocking out the mscL gene from the evolved halotolerant strain, greater than 90% osmolytic efficiency was observed upon osmotic downshock. A modified version of this strategy was applied to E. coli BL21 by deleting the mscL and mscS (small-conductance mechanosensitive channel) genes. When grown in medium with 4% NaCl and subsequently resuspended in distilled water, this engineered strain experienced 75% cell lysis, although decreases in cell growth rate due to higher salt concentrations were observed. CONCLUSIONS Our strategy is shown to be a simple and effective way to lyse cells for the purification of intracellular biomacromolecules and may be applicable in many bacteria used for bioproduction.
Collapse
Affiliation(s)
- Jeremy David Adams
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Kyle B Sander
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Craig S Criddle
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
| |
Collapse
|
4
|
Research Progress on the Effect of Autolysis to Bacillus subtilis Fermentation Bioprocess. FERMENTATION 2022. [DOI: 10.3390/fermentation8120685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacillus subtilis is a gram-positive bacterium, a promising microorganism due to its strong extracellular protein secretion ability, non-toxic, and relatively mature industrial fermentation technology. However, cell autolysis during fermentation restricts the industrial application of B. subtilis. With the fast advancement of molecular biology and genetic engineering technology, various advanced procedures and gene editing tools have been used to successfully construct autolysis-resistant B. subtilis chassis cells to manufacture various biological products. This paper first analyses the causes of autolysis in B. subtilis from a mechanistic perspective and outlines various strategies to address autolysis in B. subtilis. Finally, potential strategies for solving the autolysis problem of B. subtilis are foreseen.
Collapse
|
5
|
Wang C, Li S, Zhang Z, Yu Z, Yu L, Tian F, Chen W, Zhai Q. Phocaeicola faecalis sp. nov., a strictly anaerobic bacterial strain adapted to the human gut ecosystem. Antonie van Leeuwenhoek 2021; 114:1225-1235. [PMID: 34129122 DOI: 10.1007/s10482-021-01595-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/16/2021] [Indexed: 01/22/2023]
Abstract
A novel strictly anaerobic, Gram-negative bacterium, designated as strain FXJYN30E22T, was isolated from the feces of a healthy woman in Yining county, Xinjiang province, China. This strain was non-spore-forming, bile-resistant, non-motile and rod-shaped. It was found to belong to a single separate group in the Phocaeicola genus based on its 16 S ribosomal RNA (rRNA) gene sequence. Alignments of 16 S rRNA gene sequences showed only a low sequence identity (≤ 95.5 %) between strain FXJYN30E22T and all other Phocaeicola strains in public data bases. The genome (43.0% GC) of strain FXJYN30E22T was sequenced, and used for phylogenetic analysis which showed that strain FXJYN30E22T was most closely related to the type strain Phocaeicola massiliensis JCM 13223T. The average nucleotide identity (ANI) value and digital DNA-DNA hybridization (dDDH) between FXJYN30E22T and P. massiliensis JCM 13223T were 90.4 and 41.9 %, which were lower than the generally accepted species boundaries (94.0 and 70 %, respectively). The major cellular fatty acids and polar lipids were anteiso-branched C15:0 and phosphatidylethanolamine, respectively. The result of genome annotation and KEGG analysis showed that strain FXJYN30E22T contains a number of genes in polysaccharide and fatty acid synthesis that indicated adaptation to the human gut system. Furthermore, a pbpE (penicillin-binding protein) gene was found in the genome of strain FXJYN30E22T but in no other Phocaeicola species, which suggested this gene might be contribute to the adaptive capacity of strain FXJYN30E22T. Based on our data, strain FXJYN30E22T (= CGMCC1.17870T/KCTC25195T) was classified as a novel Phocaeicola species, and the name Phocaeicola faecalis sp. nov., was proposed.
Collapse
Affiliation(s)
- Chen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Binhu District, Wuxi, 214122, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Sijia Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Binhu District, Wuxi, 214122, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zhendong Zhang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, 441053, China
| | - Zhiming Yu
- Wuxi People's Hospital Affliated to Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Binhu District, Wuxi, 214122, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Binhu District, Wuxi, 214122, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Binhu District, Wuxi, 214122, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Binhu District, Wuxi, 214122, Jiangsu, China. .,School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| |
Collapse
|
6
|
Wood TE, Howard SA, Förster A, Nolan LM, Manoli E, Bullen NP, Yau HCL, Hachani A, Hayward RD, Whitney JC, Vollmer W, Freemont PS, Filloux A. The Pseudomonas aeruginosa T6SS Delivers a Periplasmic Toxin that Disrupts Bacterial Cell Morphology. Cell Rep 2020; 29:187-201.e7. [PMID: 31577948 PMCID: PMC6899460 DOI: 10.1016/j.celrep.2019.08.094] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 07/02/2019] [Accepted: 08/27/2019] [Indexed: 01/10/2023] Open
Abstract
The type VI secretion system (T6SS) is crucial in interbacterial competition and is a virulence determinant of many Gram-negative bacteria. Several T6SS effectors are covalently fused to secreted T6SS structural components such as the VgrG spike for delivery into target cells. In Pseudomonas aeruginosa, the VgrG2b effector was previously proposed to mediate bacterial internalization into eukaryotic cells. In this work, we find that the VgrG2b C-terminal domain (VgrG2bC-ter) elicits toxicity in the bacterial periplasm, counteracted by a cognate immunity protein. We resolve the structure of VgrG2bC-ter and confirm it is a member of the zinc-metallopeptidase family of enzymes. We show that this effector causes membrane blebbing at midcell, which suggests a distinct type of T6SS-mediated growth inhibition through interference with cell division, mimicking the impact of β-lactam antibiotics. Our study introduces a further effector family to the T6SS arsenal and demonstrates that VgrG2b can target both prokaryotic and eukaryotic cells. The structure of the VgrG2b C-terminal domain presents a metallopeptidase fold VgrG2b exerts antibacterial activity in the periplasmic space Toxicity of VgrG2b is counteracted by a cognate periplasmic immunity protein VgrG2bC-ter-intoxicated prey cells bleb at the midcell and lyse
Collapse
Affiliation(s)
- Thomas E Wood
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sophie A Howard
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Andreas Förster
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Laura M Nolan
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Eleni Manoli
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Nathan P Bullen
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Hamish C L Yau
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Abderrahman Hachani
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Richard D Hayward
- Division of Microbiology and Parasitology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Paul S Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| |
Collapse
|
7
|
Rath H, Sappa PK, Hoffmann T, Gesell Salazar M, Reder A, Steil L, Hecker M, Bremer E, Mäder U, Völker U. Impact of high salinity and the compatible solute glycine betaine on gene expression of Bacillus subtilis. Environ Microbiol 2020; 22:3266-3286. [PMID: 32419322 DOI: 10.1111/1462-2920.15087] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 12/15/2022]
Abstract
The Gram-positive bacterium Bacillus subtilis is frequently exposed to hyperosmotic conditions. In addition to the induction of genes involved in the accumulation of compatible solutes, high salinity exerts widespread effects on B. subtilis physiology, including changes in cell wall metabolism, induction of an iron limitation response, reduced motility and suppression of sporulation. We performed a combined whole-transcriptome and proteome analysis of B. subtilis 168 cells continuously cultivated at low or high (1.2 M NaCl) salinity. Our study revealed significant changes in the expression of more than one-fourth of the protein-coding genes and of numerous non-coding RNAs. New aspects in understanding the impact of high salinity on B. subtilis include a sustained low-level induction of the SigB-dependent general stress response and strong repression of biofilm formation under high-salinity conditions. The accumulation of compatible solutes such as glycine betaine aids the cells to cope with water stress by maintaining physiologically adequate levels of turgor and also affects multiple cellular processes through interactions with cellular components. Therefore, we additionally analysed the global effects of glycine betaine on the transcriptome and proteome of B. subtilis and revealed that it influences gene expression not only under high-salinity, but also under standard growth conditions.
Collapse
Affiliation(s)
- Hermann Rath
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Praveen K Sappa
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Alexander Reder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Leif Steil
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Michael Hecker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
| |
Collapse
|
8
|
Fischer C, Ahn YC, Vederas JC. Catalytic mechanism and properties of pyridoxal 5'-phosphate independent racemases: how enzymes alter mismatched acidity and basicity. Nat Prod Rep 2020; 36:1687-1705. [PMID: 30994146 DOI: 10.1039/c9np00017h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: up to March 2019 Amino acid racemases and epimerases are key enzymes that invert the configuration of common amino acids and supply many corresponding d-isomers in living organisms. Some d-amino acids are inherently bioactive, whereas others are building blocks for important biomolecules, for example lipid II, the bacterial cell wall precursor. Peptides containing them have enhanced proteolytic stability and can act as important recognition elements in mammalian systems. Selective inhibition of certain amino acid racemases (e.g. glutamate racemase) is believed to offer a promising target for new antibacterial drugs effective against pathogens resistant to current antibiotics. Many amino acid racemases employ imine formation with pyridoxal phosphate (PLP) as a cofactor to accelerate the abstraction of the alpha proton. However, the group reviewed herein achieves racemization of free amino acids without the use of cofactors or metals, and uses a thiol/thiolate pair for deprotonation and reprotonation. All bacteria and higher plants contain such enzymes, for example diaminopimelate epimerase, which is required for lysine biosynthesis in these organisms. This process cannot be accomplished without an enzyme catalyst as the acidities of a thiol and the substrate α-hydrogen are inherently mismatched by at least 10 orders of magnitude. This review describes the structural and mechanistic studies on PLP-independent racemases and the evolving view of key enzymatic machinery that accomplishes these remarkable transformations.
Collapse
Affiliation(s)
- Conrad Fischer
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2.
| | | | | |
Collapse
|
9
|
Park MJ, Park MS, Ji GE. Improvement of electroporation-mediated transformation efficiency for a Bifidobacterium strain to a reproducibly high level. J Microbiol Methods 2018; 159:112-119. [PMID: 30529116 DOI: 10.1016/j.mimet.2018.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 02/07/2023]
Abstract
Bifidobacteria are representative probiotics which are defined as live microorganisms that confer a health benefit on the host. Because of their safety and healthfulness when applied to humans, bifidobacteria are suitable as genetically engineered bacteria for applications to benefit human physiology and pathology. However, molecular biological studies of bifidobacteria have been limited due to insufficient genetic tools including effective transformation methods. The aim of this study is to improve the electroporation-mediated transformation efficiency of bifidobacteria to a reproducibly high level. The crucial factors that determine electroporation efficiency are the restriction-modification system, together with the cell wall and cell membrane structure of the bacteria. We optimized the bifidobacterial electroporation conditions by focusing on these factors as well as the amount of plasmid DNA used, the electrical parameters and the bacterial growth phase. As a result, the electroporation efficiency of B. bifidum BGN4 drastically and consistently increased from 103 to 105 CFU / μg DNA. The most significant factor for increasing the electroporation efficiency was the cell wall weakening mediated by NaCl, which improved the electroporation frequency by 20 times. Because the optimized electrotransformation conditions reported here should be widely applicable to other Bifidobacterium species, these could promote the extensive genetic manipulation of the various Bifidobacterium species in future studies.
Collapse
Affiliation(s)
- Min Ju Park
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Myeong Soo Park
- Research Center, BIFIDO Co., Ltd, Hongcheon 205-804, Republic of Korea; Department of Hotel Culinary Arts, Yeonsung University, Anyang 430-749, Republic of Korea.
| | - Geun Eog Ji
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Republic of Korea; Research Center, BIFIDO Co., Ltd, Hongcheon 205-804, Republic of Korea.
| |
Collapse
|
10
|
Huang S, Gaucher F, Cauty C, Jardin J, Le Loir Y, Jeantet R, Chen XD, Jan G. Growth in Hyper-Concentrated Sweet Whey Triggers Multi Stress Tolerance and Spray Drying Survival in Lactobacillus casei BL23: From the Molecular Basis to New Perspectives for Sustainable Probiotic Production. Front Microbiol 2018; 9:2548. [PMID: 30405593 PMCID: PMC6204390 DOI: 10.3389/fmicb.2018.02548] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 10/05/2018] [Indexed: 12/14/2022] Open
Abstract
Lactobacillus casei BL23 has a recognized probiotic potential, which includes immune modulation, protection toward induced colitis, toward induced colon cancer and toward dissemination of pathogens. In L. casei, as well as in other probiotics, both probiotic and technological abilities are highly dependent (1) on the substrate used to grow bacteria and (2) on the process used to dry and store this biomass. Production and storage of probiotics, at a reasonable financial and environmental cost, becomes a crucial challenge. Food-grade media must be used, and minimal process is preferred. In this context, we have developed a “2-in-1” medium used both to grow and to dry L. casei BL23, considered a fragile probiotic strain. This medium consists in hyper-concentrated sweet whey (HCSW). L. casei BL23 grows in HCSW up to 30% dry matter, which is 6 times-concentrated sweet whey. Compared to isotonic sweet whey (5% dry matter), these growth conditions enhanced tolerance of L. casei BL23 toward heat, acid and bile salts stress. HCSW also triggered intracellular accumulation of polyphosphate, of glycogen and of trehalose. A gel-free global proteomic differential analysis further evidenced overexpression of proteins involved in pathways known to participate in stress adaptation, including environmental signal transduction, oxidative and metal defense, DNA repair, protein turnover and repair, carbohydrate, phosphate and amino acid metabolism, and in osmoadaptation. Accordingly, HCSW cultures of L. casei BL23 exhibited enhanced survival upon spray drying, a process known to drastically affect bacterial viability. This work opens new perspectives for sustainable production of dried probiotic lactobacilli, using food industry by-products and lowering energy costs.
Collapse
Affiliation(s)
- Song Huang
- Suzhou Key Laboratory of Green Chemical Engineering, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science, Soochow University, Jiangsu, China.,UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Floriane Gaucher
- UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France.,Bioprox, Levallois-Perret, France
| | - Chantal Cauty
- UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Julien Jardin
- UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Yves Le Loir
- UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Romain Jeantet
- Suzhou Key Laboratory of Green Chemical Engineering, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science, Soochow University, Jiangsu, China.,UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Xiao Dong Chen
- Suzhou Key Laboratory of Green Chemical Engineering, School of Chemical and Environmental Engineering, College of Chemistry, Chemical Engineering and Material Science, Soochow University, Jiangsu, China
| | - Gwénaël Jan
- UMR1253 STLO, Agrocampus Ouest, INRA, Rennes, France
| |
Collapse
|
11
|
Targeting the permeability barrier and peptidoglycan recycling pathways to disarm Pseudomonas aeruginosa against the innate immune system. PLoS One 2017; 12:e0181932. [PMID: 28742861 PMCID: PMC5526577 DOI: 10.1371/journal.pone.0181932] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/10/2017] [Indexed: 11/19/2022] Open
Abstract
Antimicrobial resistance is a continuously increasing threat that severely compromises our antibiotic arsenal and causes thousands of deaths due to hospital-acquired infections by pathogens such as Pseudomonas aeruginosa, situation further aggravated by the limited development of new antibiotics. Thus, alternative strategies such as those targeting bacterial resistance mechanisms, virulence or potentiating the activity of our immune system resources are urgently needed. We have recently shown that mutations simultaneously causing the peptidoglycan recycling blockage and the β-lactamase AmpC overexpression impair the virulence of P.aeruginosa. These findings suggested that peptidoglycan metabolism might be a good target not only for fighting antibiotic resistance, but also for the attenuation of virulence and/or potentiation of our innate immune weapons. Here we analyzed the activity of the innate immune elements peptidoglycan recognition proteins (PGRPs) and lysozyme against P. aeruginosa. We show that while lysozyme and PGRPs have a very modest basal effect over P. aeruginosa, their bactericidal activity is dramatically increased in the presence of subinhibitory concentrations of the permeabilizing agent colistin. We also show that the P. aeruginosa lysozyme inhibitors seem to play a very residual protective role even in permeabilizing conditions. In contrast, we demonstrate that, once the permeability barrier is overpassed, the activity of lysozyme and PGRPs is dramatically enhanced when inhibiting key peptidoglycan recycling components (such as the 3 AmpDs, AmpG or NagZ), indicating a decisive protective role for cell-wall recycling and that direct peptidoglycan-binding supports, at least partially, the activity of these enzymes. Finally, we show that recycling blockade when occurring simultaneously with AmpC overexpression determines a further decrease in the resistance against PGRP2 and lysozyme, linked to quantitative changes in the cell-wall. Thus, our results help to delineate new strategies against P. aeruginosa infections, simultaneously targeting β–lactam resistance, cell-wall metabolism and virulence, ultimately enhancing the activity of our innate immune weapons.
Collapse
|
12
|
Hattori M, Torres GA, Tanaka N, Okada S, Endo A, Nakagawa J. Detection and analysis of Lactobacillus paracasei penicillin-binding proteins revealed the presence of cholate-sensitive penicillin-binding protein 3 and an elongated cell shape in a cholate-sensitive strain. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2016; 36:65-72. [PMID: 28439489 PMCID: PMC5395426 DOI: 10.12938/bmfh.16-019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/08/2016] [Indexed: 11/21/2022]
Abstract
Penicillin-binding proteins (PBPs) are responsible for peptidoglycan synthesis. By using biotinylated ampicillin, we detected PBPs of Lactobacillus paracasei strains. Ten PBPs were identified, 7 of which had apparent molecular sizes similar to those of Escherichia coli. In the presence of cholate, strain NRIC 0625 showed an elongated shape, and its putative PBP3 showed cholate-sensitive penicillin-binding activity. Furthermore, this strain was highly sensitive to cefalexin, which is known to inhibit cell division by inactivating PBP3. These results suggest that the septum synthetase PBP3 of lactic acid bacteria can be one of the targets of intestinal bile acid.
Collapse
Affiliation(s)
- Masahiro Hattori
- Graduate School of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri city, Hokkaido 099-2493, Japan
| | - Glaezel Angelique Torres
- Graduate School of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri city, Hokkaido 099-2493, Japan
| | - Naoto Tanaka
- Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Sanae Okada
- Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Akihito Endo
- Graduate School of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri city, Hokkaido 099-2493, Japan
| | - Junichi Nakagawa
- Graduate School of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri city, Hokkaido 099-2493, Japan
| |
Collapse
|
13
|
Nagler K, Krawczyk AO, De Jong A, Madela K, Hoffmann T, Laue M, Kuipers OP, Bremer E, Moeller R. Identification of Differentially Expressed Genes during Bacillus subtilis Spore Outgrowth in High-Salinity Environments Using RNA Sequencing. Front Microbiol 2016; 7:1564. [PMID: 27766092 PMCID: PMC5052260 DOI: 10.3389/fmicb.2016.01564] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/20/2016] [Indexed: 12/02/2022] Open
Abstract
In its natural habitat, the soil bacterium Bacillus subtilis often has to cope with fluctuating osmolality and nutrient availability. Upon nutrient depletion it can form dormant spores, which can revive to form vegetative cells when nutrients become available again. While the effects of salt stress on spore germination have been analyzed previously, detailed knowledge on the salt stress response during the subsequent outgrowth phase is lacking. In this study, we investigated the changes in gene expression during B. subtilis outgrowth in the presence of 1.2 M NaCl using RNA sequencing. In total, 402 different genes were upregulated and 632 genes were downregulated during 90 min of outgrowth in the presence of salt. The salt stress response of outgrowing spores largely resembled the osmospecific response of vegetative cells exposed to sustained high salinity and included strong upregulation of genes involved in osmoprotectant uptake and compatible solute synthesis. The σB-dependent general stress response typically triggered by salt shocks was not induced, whereas the σW regulon appears to play an important role for osmoadaptation of outgrowing spores. Furthermore, high salinity induced many changes in the membrane protein and transporter transcriptome. Overall, salt stress seemed to slow down the complex molecular reorganization processes (“ripening”) of outgrowing spores by exerting detrimental effects on vegetative functions such as amino acid metabolism.
Collapse
Affiliation(s)
- Katja Nagler
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center Cologne, Germany
| | - Antonina O Krawczyk
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Anne De Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Kazimierz Madela
- Advanced Light and Electron Microscopy, Center for Biological Threats and Special Pathogens, Robert Koch Institute Berlin, Germany
| | - Tamara Hoffmann
- Laboratory of Microbiology, Department of Biology, Philipps-University Marburg Marburg, Germany
| | - Michael Laue
- Advanced Light and Electron Microscopy, Center for Biological Threats and Special Pathogens, Robert Koch Institute Berlin, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Erhard Bremer
- Laboratory of Microbiology, Department of Biology, Philipps-University Marburg Marburg, Germany
| | - Ralf Moeller
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center Cologne, Germany
| |
Collapse
|
14
|
Palomino MM, Waehner PM, Fina Martin J, Ojeda P, Malone L, Sánchez Rivas C, Prado Acosta M, Allievi MC, Ruzal SM. Influence of osmotic stress on the profile and gene expression of surface layer proteins in Lactobacillus acidophilus ATCC 4356. Appl Microbiol Biotechnol 2016; 100:8475-84. [PMID: 27376794 DOI: 10.1007/s00253-016-7698-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/12/2016] [Accepted: 06/19/2016] [Indexed: 02/02/2023]
Abstract
In this work, we studied the role of surface layer (S-layer) proteins in the adaptation of Lactobacillus acidophilus ATCC 4356 to the osmotic stress generated by high salt. The amounts of the predominant and the auxiliary S-layer proteins SlpA and SlpX were strongly influenced by the growth phase and high-salt conditions (0.6 M NaCl). Changes in gene expression were also observed as the mRNAs of the slpA and slpX genes increased related to the growth phase and presence of high salt. A growth stage-dependent modification on the S-layer protein profile in response to NaCl was observed: while in control conditions, the auxiliary SlpX protein represented less than 10 % of the total S-layer protein, in high-salt conditions, it increased to almost 40 % in the stationary phase. The increase in S-layer protein synthesis in the stress condition could be a consequence of or a way to counteract the fragility of the cell wall, since a decrease in the cell wall thickness and envelope components (peptidoglycan layer and lipoteichoic acid content) was observed in L. acidophilus when compared to a non-S-layer-producing species such as Lactobacillus casei. Also, the stationary phase and growth in high-salt medium resulted in increased release of S-layer proteins to the supernatant medium. Overall, these findings suggest that pre-growth in high-salt conditions would result in an advantage for the probiotic nature of L. acidophilus ATCC 4356 as the increased amount and release of the S-layer might be appropriate for its antimicrobial capacity.
Collapse
Affiliation(s)
- María Mercedes Palomino
- Laboratorio Bacterias Gram Positivas, sus Fagos y Estrés, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-UBA, IQUIBICEN-CONICET, Ciudad Universitaria, Pabellon II, piso 4, Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina
| | - Pablo M Waehner
- Laboratorio Bacterias Gram Positivas, sus Fagos y Estrés, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-UBA, IQUIBICEN-CONICET, Ciudad Universitaria, Pabellon II, piso 4, Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina
| | - Joaquina Fina Martin
- Laboratorio Bacterias Gram Positivas, sus Fagos y Estrés, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-UBA, IQUIBICEN-CONICET, Ciudad Universitaria, Pabellon II, piso 4, Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina
| | - Paula Ojeda
- Laboratorio Bacterias Gram Positivas, sus Fagos y Estrés, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-UBA, IQUIBICEN-CONICET, Ciudad Universitaria, Pabellon II, piso 4, Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina
| | - Lucía Malone
- Laboratorio Bacterias Gram Positivas, sus Fagos y Estrés, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-UBA, IQUIBICEN-CONICET, Ciudad Universitaria, Pabellon II, piso 4, Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina
| | - Carmen Sánchez Rivas
- Laboratorio Bacterias Gram Positivas, sus Fagos y Estrés, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-UBA, IQUIBICEN-CONICET, Ciudad Universitaria, Pabellon II, piso 4, Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina
| | - Mariano Prado Acosta
- Laboratorio Bacterias Gram Positivas, sus Fagos y Estrés, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-UBA, IQUIBICEN-CONICET, Ciudad Universitaria, Pabellon II, piso 4, Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina
| | - Mariana C Allievi
- Laboratorio Bacterias Gram Positivas, sus Fagos y Estrés, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-UBA, IQUIBICEN-CONICET, Ciudad Universitaria, Pabellon II, piso 4, Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina
| | - Sandra M Ruzal
- Laboratorio Bacterias Gram Positivas, sus Fagos y Estrés, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales-UBA, IQUIBICEN-CONICET, Ciudad Universitaria, Pabellon II, piso 4, Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina.
| |
Collapse
|
15
|
Helmann JD. Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope. Curr Opin Microbiol 2016; 30:122-132. [PMID: 26901131 DOI: 10.1016/j.mib.2016.02.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 01/20/2023]
Abstract
Bacillus subtilis provides a model for investigation of the bacterial cell envelope, the first line of defense against environmental threats. Extracytoplasmic function (ECF) sigma factors activate genes that confer resistance to agents that threaten the integrity of the envelope. Although their individual regulons overlap, σ(W) is most closely associated with membrane-active agents, σ(X) with cationic antimicrobial peptide resistance, and σ(V) with resistance to lysozyme. Here, I highlight the role of the σ(M) regulon, which is strongly induced by conditions that impair peptidoglycan synthesis and includes the core pathways of envelope synthesis and cell division, as well as stress-inducible alternative enzymes. Studies of these cell envelope stress responses provide insights into how bacteria acclimate to the presence of antibiotics.
Collapse
Affiliation(s)
- John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
16
|
Möll A, Dörr T, Alvarez L, Davis BM, Cava F, Waldor MK. A D, D-carboxypeptidase is required for Vibrio cholerae halotolerance. Environ Microbiol 2015; 17:527-40. [PMID: 25631756 DOI: 10.1111/1462-2920.12779] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/06/2015] [Accepted: 01/08/2015] [Indexed: 11/28/2022]
Abstract
The biological roles of low molecular weight penicillin-binding proteins (LMW PBP) have been difficult to discern in Gram-negative organisms. In Escherichia coli, mutants lacking these proteins often have no phenotype, and cells lacking all seven LMW PBPs remain viable. In contrast, we report here that Vibrio cholerae lacking DacA-1, a PBP5 homologue, displays slow growth, aberrant morphology and altered peptidoglycan (PG) homeostasis in Luria-Bertani (LB) medium, as well as a profound plating defect. DacA-1 alone among V. cholerae's LMW PBPs is critical for bacterial growth; mutants lacking the related protein DacA-2 and/or homologues of PBP4 or PBP7 displayed normal growth and morphology. Remarkably, the growth and morphology of the dacA-1 mutant were unimpaired in LB media containing reduced concentrations of NaCl (100 mM or less), and also within suckling mice, a model host for the study of cholera pathogenesis. Peptidoglycan from the dacA-1 mutant contained elevated pentapeptide levels in standard and low salt media, and comparative analyses suggest that DacA-1 is V. cholerae's principal DD-carboxypeptidase. The basis for the dacA-1 mutant's halosensitivity is unknown; nonetheless, the mutant's survival in biochemically uncharacterized environments (such as the suckling mouse intestine) can be used as a reporter of low Na(+) content.
Collapse
Affiliation(s)
- Andrea Möll
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02155, USA; Department of Microbiology and Immunobiology, Harvard Medical School, HHMI, Boston, MA, 02155, USA
| | | | | | | | | | | |
Collapse
|
17
|
Arnaouteli S, Giastas P, Andreou A, Tzanodaskalaki M, Aldridge C, Tzartos SJ, Vollmer W, Eliopoulos E, Bouriotis V. Two Putative Polysaccharide Deacetylases Are Required for Osmotic Stability and Cell Shape Maintenance in Bacillus anthracis. J Biol Chem 2015; 290:13465-78. [PMID: 25825488 PMCID: PMC4505593 DOI: 10.1074/jbc.m115.640029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Indexed: 11/26/2022] Open
Abstract
Membrane-anchored lipoproteins have a broad range of functions and play key roles in several cellular processes in Gram-positive bacteria. BA0330 and BA0331 are the only lipoproteins among the 11 known or putative polysaccharide deacetylases of Bacillus anthracis. We found that both lipoproteins exhibit unique characteristics. BA0330 and BA0331 interact with peptidoglycan, and BA0330 is important for the adaptation of the bacterium to grow in the presence of a high concentration of salt, whereas BA0331 contributes to the maintenance of a uniform cell shape. They appear not to alter the peptidoglycan structure and do not contribute to lysozyme resistance. The high resolution x-ray structure of BA0330 revealed a C-terminal domain with the typical fold of a carbohydrate esterase 4 and an N-terminal domain unique for this family, composed of a two-layered (4 + 3) β-sandwich with structural similarity to fibronectin type 3 domains. Our data suggest that BA0330 and BA0331 have a structural role in stabilizing the cell wall of B. anthracis.
Collapse
Affiliation(s)
- Sofia Arnaouteli
- From the Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece
| | - Petros Giastas
- the Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece
| | - Athina Andreou
- the Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Mary Tzanodaskalaki
- the Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Christine Aldridge
- the Institute for Cell and Molecular Biosciences, Centre for Bacterial Cell Biology, Newcastle University, NE2 4AX Newcastle upon Tyne, United Kingdom, and
| | - Socrates J Tzartos
- the Department of Neurobiology, Hellenic Pasteur Institute, Vasilissis Sofias 127, 11521 Athens, Greece, the Department of Pharmacy, University of Patras, 26504, Patras, Greece
| | - Waldemar Vollmer
- the Institute for Cell and Molecular Biosciences, Centre for Bacterial Cell Biology, Newcastle University, NE2 4AX Newcastle upon Tyne, United Kingdom, and
| | - Elias Eliopoulos
- the Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Vassilis Bouriotis
- From the Department of Biology, Enzyme Biotechnology Group, University of Crete, Vasilika Vouton, 70013 Heraklion, Crete, Greece, the Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece,
| |
Collapse
|
18
|
Yin L, Xue Y, Ma Y. Global Microarray Analysis of Alkaliphilic Halotolerant Bacterium Bacillus sp. N16-5 Salt Stress Adaptation. PLoS One 2015; 10:e0128649. [PMID: 26030352 PMCID: PMC4452262 DOI: 10.1371/journal.pone.0128649] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/29/2015] [Indexed: 11/29/2022] Open
Abstract
The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 is often exposed to salt stress in its natural habitats. In this study, we used one-colour microarrays to investigate adaptive responses of Bacillus sp. N16-5 transcriptome to long-term growth at different salinity levels (0%, 2%, 8%, and 15% NaCl) and to a sudden salt increase from 0% to 8% NaCl. The common strategies used by bacteria to survive and grow at high salt conditions, such as K+ uptake, Na+ efflux, and the accumulation of organic compatible solutes (glycine betaine and ectoine), were observed in Bacillus sp. N16-5. The genes of SigB regulon involved in general stress responses and chaperone-encoding genes were also induced by high salt concentration. Moreover, the genes regulating swarming ability and the composition of the cytoplasmic membrane and cell wall were also differentially expressed. The genes involved in iron uptake were down-regulated, whereas the iron homeostasis regulator Fur was up-regulated, suggesting that Fur may play a role in the salt adaption of Bacillus sp. N16-5. In summary, we present a comprehensive gene expression profiling of alkaliphilic Bacillus sp. N16-5 cells exposed to high salt stress, which would help elucidate the mechanisms underlying alkaliphilic Bacillus spp. survival in and adaptation to salt stress.
Collapse
Affiliation(s)
- Liang Yin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (YM)
| |
Collapse
|
19
|
Song Z, Chen L, Wang J, Lu Y, Jiang W, Zhang W. A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803. Mol Cell Proteomics 2014; 13:3519-32. [PMID: 25239498 DOI: 10.1074/mcp.m113.035675] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To improve ethanol production directly from CO2 in photosynthetic cyanobacterial systems, one key issue that needs to be addressed is the low ethanol tolerance of cyanobacterial cells. Our previous proteomic and transcriptomic analyses found that several regulatory proteins were up-regulated by exogenous ethanol in Synechocystis sp. PCC6803. In this study, through tolerance analysis of the gene disruption mutants of the up-regulated regulatory genes, we uncovered that one transcriptional regulator, Sll0794, was related directly to ethanol tolerance in Synechocystis. Using a quantitative iTRAQ-LC-MS/MS proteomics approach coupled with quantitative real-time reverse transcription-PCR (RT-qPCR), we further determined the possible regulatory network of Sll0794. The proteomic analysis showed that in the Δsll0794 mutant grown under ethanol stress a total of 54 and 87 unique proteins were down- and up-regulated, respectively. In addition, electrophoretic mobility shift assays demonstrated that the Sll0794 transcriptional regulator was able to bind directly to the upstream regions of sll1514, slr1512, and slr1838, which encode a 16.6 kDa small heat shock protein, a putative sodium-dependent bicarbonate transporter and a carbon dioxide concentrating mechanism protein CcmK, respectively. The study provided a proteomic description of the putative ethanol-tolerance network regulated by the sll0794 gene, and revealed new insights on the ethanol-tolerance regulatory mechanism in Synechocystis. As the first regulatory protein discovered related to ethanol tolerance, the gene may serve as a valuable target for transcription machinery engineering to further improve ethanol tolerance in Synechocystis. All MS data have been deposited in the ProteomeXchange with identifier PXD001266 (http://proteomecentral.proteomexchange.org/dataset/PXD001266).
Collapse
Affiliation(s)
- Zhongdi Song
- From the ‡Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China; §Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China; ¶Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China
| | - Lei Chen
- From the ‡Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China; §Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China; ¶Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China;
| | - Jiangxin Wang
- From the ‡Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China; §Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China; ¶Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China
| | - Yinhua Lu
- ‖Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Weihong Jiang
- ‖Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Weiwen Zhang
- From the ‡Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China; §Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China; ¶Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China;
| |
Collapse
|
20
|
Stress responses of the industrial workhorse Bacillus licheniformis to osmotic challenges. PLoS One 2013; 8:e80956. [PMID: 24348917 PMCID: PMC3858371 DOI: 10.1371/journal.pone.0080956] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 11/19/2022] Open
Abstract
The Gram-positive endospore-forming bacterium Bacillus licheniformis can be found widely in nature and it is exploited in industrial processes for the manufacturing of antibiotics, specialty chemicals, and enzymes. Both in its varied natural habitats and in industrial settings, B. licheniformis cells will be exposed to increases in the external osmolarity, conditions that trigger water efflux, impair turgor, cause the cessation of growth, and negatively affect the productivity of cell factories in biotechnological processes. We have taken here both systems-wide and targeted physiological approaches to unravel the core of the osmostress responses of B. licheniformis. Cells were suddenly subjected to an osmotic upshift of considerable magnitude (with 1 M NaCl), and their transcriptional profile was then recorded in a time-resolved fashion on a genome-wide scale. A bioinformatics cluster analysis was used to group the osmotically up-regulated genes into categories that are functionally associated with the synthesis and import of osmostress-relieving compounds (compatible solutes), the SigB-controlled general stress response, and genes whose functional annotation suggests that salt stress triggers secondary oxidative stress responses in B. licheniformis. The data set focusing on the transcriptional profile of B. licheniformis was enriched by proteomics aimed at identifying those proteins that were accumulated by the cells through increased biosynthesis in response to osmotic stress. Furthermore, these global approaches were augmented by a set of experiments that addressed the synthesis of the compatible solutes proline and glycine betaine and assessed the growth-enhancing effects of various osmoprotectants. Combined, our data provide a blueprint of the cellular adjustment processes of B. licheniformis to both sudden and sustained osmotic stress.
Collapse
|
21
|
Palomino MM, Allievi MC, Gründling A, Sanchez-Rivas C, Ruzal SM. Osmotic stress adaptation in Lactobacillus casei BL23 leads to structural changes in the cell wall polymer lipoteichoic acid. Microbiology (Reading) 2013; 159:2416-2426. [DOI: 10.1099/mic.0.070607-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Maria Mercedes Palomino
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, London, UK
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - Mariana C. Allievi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, London, UK
| | - Carmen Sanchez-Rivas
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - Sandra M. Ruzal
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| |
Collapse
|
22
|
Roces C, Wegmann U, Campelo AB, García P, Rodríguez A, Martínez B. Lack of the host membrane protease FtsH hinders release of the Lactococcus lactis bacteriophage TP712. J Gen Virol 2013; 94:2814-2818. [PMID: 24018314 DOI: 10.1099/vir.0.057182-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The temperate bacteriophage TP712 was unable to plaque on Lactococcus lactis ΔftsH lacking the membrane protease FtsH and complementation in trans restored the WT phenotype. Absence of ftsH did not hinder phage adsorption, phage DNA delivery or activation of the lytic cycle. Thin sections revealed that TP712 virions appeared to be correctly assembled inside the ΔftsH host, but were not released. These virions were infective, demonstrating that a functional host FtsH is required by TP712 to proceed effectively with lysis of the host.
Collapse
Affiliation(s)
- Clara Roces
- DairySafe Group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Udo Wegmann
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, United Kingdom
| | - Ana B Campelo
- DairySafe Group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Pilar García
- DairySafe Group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Ana Rodríguez
- DairySafe Group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Beatriz Martínez
- DairySafe Group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| |
Collapse
|
23
|
Durack J, Ross T, Bowman JP. Characterisation of the transcriptomes of genetically diverse Listeria monocytogenes exposed to hyperosmotic and low temperature conditions reveal global stress-adaptation mechanisms. PLoS One 2013; 8:e73603. [PMID: 24023890 PMCID: PMC3762727 DOI: 10.1371/journal.pone.0073603] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 07/29/2013] [Indexed: 12/29/2022] Open
Abstract
The ability of Listeria monocytogenes to adapt to various food and food- processing environments has been attributed to its robustness, persistence and prevalence in the food supply chain. To improve the present understanding of molecular mechanisms involved in hyperosmotic and low-temperature stress adaptation of L. monocytogenes, we undertook transcriptomics analysis on three strains adapted to sub-lethal levels of these stress stimuli and assessed functional gene response. Adaptation to hyperosmotic and cold-temperature stress has revealed many parallels in terms of gene expression profiles in strains possessing different levels of stress tolerance. Gene sets associated with ribosomes and translation, transcription, cell division as well as fatty acid biosynthesis and peptide transport showed activation in cells adapted to either cold or hyperosmotic stress. Repression of genes associated with carbohydrate metabolism and transport as well as flagella was evident in stressed cells, likely linked to activation of CodY regulon and consequential cellular energy conservation.
Collapse
Affiliation(s)
- Juliana Durack
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Tom Ross
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - John P. Bowman
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| |
Collapse
|
24
|
Activity of the osmotically regulated yqiHIK promoter from Bacillus subtilis is controlled at a distance. J Bacteriol 2012; 194:5197-208. [PMID: 22843846 DOI: 10.1128/jb.01041-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The yqiHIK gene cluster from Bacillus subtilis is predicted to encode an extracellular lipoprotein (YqiH), a secreted N-acetylmuramoyl-L-alanine amidase (YqiI), and a cytoplasmic glycerophosphodiester phosphodiesterase (YqiK). Reverse transcriptase PCR (RT-PCR) analysis showed that the yqiHIK genes are transcribed as an operon. Consistent with the in silico prediction, we found that the purified YqiI protein exhibited hydrolytic activity toward peptidoglycan sacculi. Transcription studies with yqiH-treA reporter fusion strains revealed that the expression of yqiHIK is subjected to finely tuned osmotic control, but enhanced expression occurs only in severely osmotically stressed cells. Primer extension analysis pinpointed the osmotically responsive yqiHIK promoter, and site-directed mutagenesis was employed to assess functionally important sequences required for promoter activity and osmotic control. Promoter variants with constitutive activity were isolated. A deletion analysis of the yqiHIK regulatory region showed that a 53-bp AT-rich DNA segment positioned 180 bp upstream of the -35 sequence is critical for the activity and osmotic regulation of the yqiHIK promoter. Hence, the expression of yqiHIK is subjected to genetic control at a distance. Upon the onset of growth of cells of the B. subtilis wild-type strain in high-salinity medium (1.2 M NaCl), we observed gross morphological deformations of cells that were then reversed to a rod-shaped morphology again when the cells had adjusted to the high-salinity environment. The products of the yqiHIK gene cluster were not critical for reestablishing rod-shaped morphology, but the deletion of this operon yielded a B. subtilis mutant impaired in growth in a defined minimal medium and at high salinity.
Collapse
|
25
|
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]
|
26
|
Listeria monocytogenes shows temperature-dependent and -independent responses to salt stress, including responses that induce cross-protection against other stresses. Appl Environ Microbiol 2012; 78:2602-12. [PMID: 22307309 DOI: 10.1128/aem.07658-11] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The food-borne pathogen Listeria monocytogenes experiences osmotic stress in many habitats, including foods and the gastrointestinal tract of the host. During transmission, L. monocytogenes is likely to experience osmotic stress at different temperatures and may adapt to osmotic stress in a temperature-dependent manner. To understand the impact of temperature on the responses this pathogen uses to adapt to osmotic stress, we assessed genome-wide changes in the L. monocytogenes H7858 transcriptome during short-term and long-term adaptation to salt stress at 7°C and 37°C. At both temperatures, the short-term response to salt stress included increased transcript levels of sigB and SigB-regulated genes, as well as mrpABCDEFG, encoding a sodium/proton antiporter. This antiporter was found to play a role in adaptation to salt stress at both temperatures; ΔmrpABCDEFG had a significantly longer lag phase than the parent strain in BHI plus 6% NaCl at 7°C and 37°C. The short-term adaptation to salt stress at 7°C included increased transcript levels of two genes encoding carboxypeptidases that modify peptidoglycan. These carboxypeptidases play a role in the short-term adaptation to salt stress only at 7°C, where the deletion mutants had significantly different lag phases than the parent strain. Changes in the transcriptome at both temperatures suggested that exposure to salt stress could provide cross-protection to other stresses, including peroxide stress. Short-term exposure to salt stress significantly increased H(2)O(2) resistance at both temperatures. These results provide information for the development of knowledge-based intervention methods against this pathogen, as well as provide insight into potential mechanisms of cross-protection.
Collapse
|
27
|
van Melis CCJ, Nierop Groot MN, Tempelaars MH, Moezelaar R, Abee T. Characterization of germination and outgrowth of sorbic acid-stressed Bacillus cereus ATCC 14579 spores: phenotype and transcriptome analysis. Food Microbiol 2010; 28:275-83. [PMID: 21315984 DOI: 10.1016/j.fm.2010.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 04/01/2010] [Accepted: 04/10/2010] [Indexed: 11/15/2022]
Abstract
Sorbic acid (SA) is widely used as a preservative, but the effect of SA on spore germination and outgrowth has gained limited attention up to now. Therefore, the effect of sorbic acid on germination of spores of Bacillus cereus strain ATCC 14579 was analyzed both at phenotype and transcriptome level. Spore germination and outgrowth were assessed at pH 5.5 without and with 0.75, 1.5 and 3.0 mM (final concentrations) undissociated sorbic acid (HSA). This resulted in distinct HSA concentration-dependent phenotypes, varying from reduced germination and outgrowth rates to complete blockage of germination at 3.0 mM HSA. The phenotypes reflecting different stages in the germination process could be confirmed using flow cytometry and could be recognized at transcriptome level by distinct expression profiles. In the absence and presence of 0.75 and 1.5 mM HSA, similar cellular ATP levels were found up to the initial stage of outgrowth, suggesting that HSA-induced inhibition of outgrowth is not caused by depletion of ATP. Transcriptome analysis revealed the presence of a limited number of transcripts in dormant spores, outgrowth related expression, and genes specifically associated with sorbic acid stress, including alterations in cell envelope and multidrug resistance. The potential role of these HSA-stress associated genes in spore outgrowth is discussed.
Collapse
Affiliation(s)
- C C J van Melis
- Top Institute Food and Nutrition, Wageningen, The Netherlands.
| | | | | | | | | |
Collapse
|
28
|
A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation. J Bacteriol 2009; 192:870-82. [PMID: 19948795 DOI: 10.1128/jb.01106-09] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In its natural habitats, Bacillus subtilis is exposed to changing osmolarity, necessitating adaptive stress responses. Transcriptomic and proteomic approaches can provide a picture of the dynamic changes occurring in salt-stressed B. subtilis cultures because these studies provide an unbiased view of cells coping with high salinity. We applied whole-genome microarray technology and metabolic labeling, combined with state-of-the-art proteomic techniques, to provide a global and time-resolved picture of the physiological response of B. subtilis cells exposed to a severe and sudden osmotic upshift. This combined experimental approach provided quantitative data for 3,961 mRNA transcription profiles, 590 expression profiles of proteins detected in the cytosol, and 383 expression profiles of proteins detected in the membrane fraction. Our study uncovered a well-coordinated induction of gene expression subsequent to an osmotic upshift that involves large parts of the SigB, SigW, SigM, and SigX regulons. Additionally osmotic upregulation of a large number of genes that do not belong to these regulons was observed. In total, osmotic upregulation of about 500 B. subtilis genes was detected. Our data provide an unprecedented rich basis for further in-depth investigation of the physiological and genetic responses of B. subtilis to hyperosmotic stress.
Collapse
|