1
|
Trunet C, Vischer N, Coroller L, Brul S. Germination and outgrowth of Bacillus mycoides KBAB4 spores are impacted by environmental pH, quantitatively analyzed at single cell level with sporetracker. Food Microbiol 2024; 121:104509. [PMID: 38637073 DOI: 10.1016/j.fm.2024.104509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/06/2024] [Accepted: 02/24/2024] [Indexed: 04/20/2024]
Abstract
Quantifying spore germination and outgrowth heterogeneity is challenging. Single cell level analysis should provide supplementary knowledge regarding the impact of unfavorable conditions on germination and outgrowth dynamics. This work aimed to quantify the impact of pH on spore germination and outgrowth, investigating the behavior of individual spore crops, produced under optimal and suboptimal conditions. Bacillus mycoides (formerly B. weihenstephanensis) KBAB4 spores, produced at pH 7.4 and at pH 5.5 were incubated at different pH values, from pH 5.2 to 7.4. The spores were monitored by microscopy live imaging, in controlled conditions, at 30 °C. The images were analyzed using SporeTracker, to determine the state of single cells. The impact of pH on germination and outgrowth times and rates was estimated and the correlation between these parameters was quantified. The correlation between germination and outgrowth times was significantly higher at low pH. These results suggest that an environmental pressure highlights the heterogeneity of spore germination and outgrowth within a spore population. Results were consistent with previous observations at population level, now confirmed and extended to single cell level. Therefore, single cell level analyses can be used to quantify the heterogeneity of spore populations, which is of interest in order to control the development of spore-forming bacteria, responsible for food safety issues.
Collapse
Affiliation(s)
- C Trunet
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29000, Quimper, France.
| | - N Vischer
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - L Coroller
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29000, Quimper, France
| | - S Brul
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| |
Collapse
|
2
|
Qi W, Jonker MJ, de Leeuw W, Brul S, ter Kuile BH. Role of RelA-synthesized (p)ppGpp and ROS-induced mutagenesis in de novo acquisition of antibiotic resistance in E. coli. iScience 2024; 27:109579. [PMID: 38617560 PMCID: PMC11015494 DOI: 10.1016/j.isci.2024.109579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024] Open
Abstract
The stringent response of bacteria to starvation and stress also fulfills a role in addressing the threat of antibiotics. Within this stringent response, (p)ppGpp, synthesized by RelA or SpoT, functions as a global alarmone. However, the effect of this (p)ppGpp on resistance development is poorly understood. Here, we show that knockout of relA or rpoS curtails resistance development against bactericidal antibiotics. The emergence of mutated genes associated with starvation and (p)ppGpp, among others, indicates the activation of stringent responses. The growth rate is decreased in ΔrelA-resistant strains due to the reduced ability to synthesize (p)ppGpp and the persistence of deacylated tRNA impeding protein synthesis. Sluggish cellular activity causes decreased production of reactive oxygen species (ROS), thereby reducing oxidative damage, leading to weakened DNA mismatch repair, potentially reducing the generation of mutations. These findings offer new targets for mitigating antibiotic resistance development, potentially achieved through inhibiting (p)ppGpp or ROS synthesis.
Collapse
Affiliation(s)
- Wenxi Qi
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Martijs J. Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Wim de Leeuw
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Benno H. ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
3
|
Huang Y, Swarge BN, Roseboom W, Bleeker JD, Brul S, Setlow P, Kramer G. Integrative Metabolomics and Proteomics Allow the Global Intracellular Characterization of Bacillus subtilis Cells and Spores. J Proteome Res 2024; 23:596-608. [PMID: 38190553 PMCID: PMC10845140 DOI: 10.1021/acs.jproteome.3c00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024]
Abstract
Reliable and comprehensive multi-omics analysis is essential for researchers to understand and explore complex biological systems more completely. Bacillus subtilis (B. subtilis) is a model organism for Gram-positive spore-forming bacteria, and in-depth insight into the physiology and molecular basis of spore formation and germination in this organism requires advanced multilayer molecular data sets generated from the same sample. In this study, we evaluated two monophasic methods for polar and nonpolar compound extraction (acetonitrile/methanol/water; isopropanol/water, and 60% ethanol) and two biphasic methods (chloroform/methanol/water, and methyl tert-butyl ether/methanol/water) on coefficients of variation of analytes, identified metabolite composition, and the quality of proteomics profiles. The 60% EtOH protocol proved to be the easiest in sample processing and was more amenable to automation. Collectively, we annotated 505 and 484 metabolites and identified 1665 and 1562 proteins in B. subtilis vegetative cells and spores, respectively. We also show differences between vegetative cells and spores from a multi-omics perspective and demonstrate that an integrative multi-omics analysis can be implemented from one sample using the 60% EtOH protocol. The results obtained by the 60% EtOH protocol provide comprehensive insight into differences in the metabolic and protein makeup of B. subtilis vegetative cells and spores.
Collapse
Affiliation(s)
- Yixuan Huang
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Molecular
Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bhagyashree N. Swarge
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Molecular
Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Winfried Roseboom
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jurre D. Bleeker
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Molecular
Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Peter Setlow
- Department
of Molecular Biology and Biophysics, UConn
Health, Farmington, Connecticut 06030-3305, United States
| | - Gertjan Kramer
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| |
Collapse
|
4
|
Liu S, Huang Y, Jensen S, Laman P, Kramer G, Zaat SAJ, Brul S. Molecular physiological characterization of the dynamics of persister formation in Staphylococcus aureus. Antimicrob Agents Chemother 2024; 68:e0085023. [PMID: 38051079 PMCID: PMC10777834 DOI: 10.1128/aac.00850-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023] Open
Abstract
Bacteria possess the ability to enter a growth-arrested state known as persistence in order to survive antibiotic exposure. Clinically, persisters are regarded as the main causative agents for chronic and recurrent infectious diseases. To combat this antibiotic-tolerant population, a better understanding of the molecular physiology of persisters is required. In this study, we collected samples at different stages of the biphasic kill curve to reveal the dynamics of the cellular molecular changes that occur in the process of persister formation. After exposure to antibiotics with different modes of action, namely, vancomycin and enrofloxacin, similar persister levels were obtained. Both shared and distinct stress responses were enriched for the respective persister populations. However, the dynamics of the presence of proteins linked to the persister phenotype throughout the biphasic kill curve and the molecular profiles in a stable persistent population did show large differences, depending on the antibiotic used. This suggests that persisters at the molecular level are highly stress specific, emphasizing the importance of characterizing persisters generated under different stress conditions. Additionally, although generated persisters exhibited cross-tolerance toward tested antibiotics, combined therapies were demonstrated to be a promising approach to reduce persister levels. In conclusion, this investigation sheds light on the stress-specific nature of persisters, highlighting the necessity of tailored treatment approaches and the potential of combined therapy.
Collapse
Affiliation(s)
- Shiqi Liu
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Yixuan Huang
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Sean Jensen
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Paul Laman
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| | - Sebastian A. J. Zaat
- Department of Medical Microbiology and Infection Prevention, Amsterdam institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute for Life Sciences, Amsterdam, the Netherlands
| |
Collapse
|
5
|
Qi W, Jonker MJ, de Leeuw W, Brul S, ter Kuile BH. Reactive oxygen species accelerate de novo acquisition of antibiotic resistance in E. coli. iScience 2023; 26:108373. [PMID: 38025768 PMCID: PMC10679899 DOI: 10.1016/j.isci.2023.108373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/06/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Reactive oxygen species (ROS) produced as a secondary effect of bactericidal antibiotics are hypothesized to play a role in killing bacteria. If correct, ROS may play a role in development of de novo resistance. Here we report that single-gene knockout strains with reduced ROS scavenging exhibited enhanced ROS accumulation and more rapid acquisition of resistance when exposed to sublethal levels of bactericidal antibiotics. Consistent with this observation, the ROS scavenger thiourea in the medium decelerated resistance development. Thiourea downregulated the transcriptional level of error-prone DNA polymerase and DNA glycosylase MutM, which counters the incorporation and accumulation of 8-hydroxy-2'-deoxyguanosine (8-HOdG) in the genome. The level of 8-HOdG significantly increased following incubation with bactericidal antibiotics but decreased after treatment with the ROS scavenger thiourea. These observations suggest that in E. coli sublethal levels of ROS stimulate de novo development of resistance, providing a mechanistic basis for hormetic responses induced by antibiotics.
Collapse
Affiliation(s)
- Wenxi Qi
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Martijs J. Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Wim de Leeuw
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Benno H. ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
6
|
Chen T, Brul S, Hugenholtz J. Exploring the potential of Bacillus subtilis as cell factory for food ingredients and special chemicals. Microb Cell Fact 2023; 22:200. [PMID: 37777723 PMCID: PMC10542680 DOI: 10.1186/s12934-023-02208-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND Bacillus subtilis has been established as model microorganism for fundamental research in the laboratory on protein production/secretion and sporulation and as model bacterium for controlling spoilage in the food industry. It has also been used for production of (commercial) enzymes and several secondary metabolites such as vitamins. However, this doesn't fully reflect the potential of B. subtilis as a cell-factory. Here, various strains of B. subtilis, including food-grade, spore-deficient strains and industrially used strains, were compared for their growth and metabolic potential. Industry-relevant parameters were analyzed for all strains under various aeration regimes, under anaerobic conditions, in various nutritious and nutrient-limited cultivation media, with and without organic nitrogen sources, and with and without sugar. RESULTS Practical experiments were conducted to compare industrial relevant properties like growth rates, intracellular components and extracellular metabolite profile of different B. subtilis strains. Based on growth flexibility in different media, we found that some strains like NCIB3610 and DSM1092 are adapted to inorganic or organic nitrogen source utilization, which is highly relevant when considering a biorefinery approach using various cheap and abundant waste/sidestreams. Secondly, spore-deficient strains such as 3NA, 168 S and PY79S, showed advantages in microbial protein and acetolactate pathway expression, which is associated with applications in food industry for protein supplement and diacetyl production. Lastly, WB800 and PY79S exhibited potential for fermentative production of dipicolinic acid, 2,3-butanediol and lactic acid that could serve as precursors for biopolymers. CONCLUSION This study demonstrates the broad potential for more extensive industrial use of Bacillus subtilis in the (bio-based) chemical industry for use of sidestreams, in the personal care industry, in the food industry for food additive production, and in the bio-sustainable industry for biofuel and bio-degradable plastic precursors production. In addition, selecting different B. subtilis strains for specific purposes makes full use of the diversity of this species and increases the potential of B. subtilis in its contribution to the bio-based economy.
Collapse
Affiliation(s)
- Taichi Chen
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands.
| | - Jeroen Hugenholtz
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands.
- NoPalm Ingredients BV, Nieuwe Kanaal 7a, Wageningen, 6709 PA, The Netherlands.
| |
Collapse
|
7
|
van Leeuwen PT, Brul S, Zhang J, Wortel MT. Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications. FEMS Microbiol Rev 2023; 47:7080139. [PMID: 36931888 PMCID: PMC10062696 DOI: 10.1093/femsre/fuad012] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023] Open
Abstract
The human gut harbors native microbial communities, forming a highly complex ecosystem. Synthetic microbial communities (SynComs) of the human gut are an assembly of microorganisms isolated from human mucosa or fecal samples. In recent decades, the ever-expanding culturing capacity and affordable sequencing, together with advanced computational modeling, started a ''golden age'' for harnessing the beneficial potential of SynComs to fight gastrointestinal disorders, such as infections and chronic inflammatory bowel diseases. As simplified and completely defined microbiota, SynComs offer a promising reductionist approach to understanding the multi-species and multi-kingdom interactions in the microbe-host-immune axis. However, there are still many challenges to overcome before we can precisely construct SynComs of designed function and efficacy that allow the translation of scientific findings to patients' treatments. Here we discussed the strategies used to design, assemble, and test a SynCom, and address the significant challenges, which are of microbiological, engineering, and translational nature, that stand in the way of using SynComs as live bacterial therapeutics.
Collapse
Affiliation(s)
- Pim T van Leeuwen
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jianbo Zhang
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Meike T Wortel
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| |
Collapse
|
8
|
Korza G, DePratti S, Fairchild D, Wicander J, Kanaan J, Shames H, Nichols FC, Cowan A, Brul S, Setlow P. Expression of the 2Duf protein in wild-type Bacillus subtilis spores stabilizes inner membrane proteins and increases spore resistance to wet heat and hydrogen peroxide. J Appl Microbiol 2023; 134:lxad040. [PMID: 36841229 PMCID: PMC10035073 DOI: 10.1093/jambio/lxad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/09/2023] [Accepted: 02/24/2023] [Indexed: 02/27/2023]
Abstract
AIMS This work aimed to characterize spore inner membrane (IM) properties and the mechanism of spore killing by wet heat and H2O2 with spores overexpressing the 2Duf protein, which is naturally encoded from a transposon found only in some Bacillus strains with much higher spore resistance than wild-type spores. METHODS AND RESULTS Killing of Bacillus subtilis spores by wet heat or hydrogen peroxide (H2O2) was slower when 2Duf was present, and Ca-dipicolinic acid release was slower than killing. Viabilities on rich plates of wet heat- or H2O2 -treated spores +/- 2Duf were lower when NaCl was added, but higher with glucose. Addition of glucose but not Casamino acids addition increased treated spores' viability on minimal medium plates. Spores with 2Duf required higher heat activation for germination, and their germination was more wet-heat resistant than that of wild-type spores, processes that involve IM proteins. IM permeability and lipid mobility were lower in spores with 2Duf, although IM phospholipid composition was similar in spores +/- 2Duf. CONCLUSIONS These results and previous work suggests that wet heat and H2O2 kill spores by damaging an IM enzyme or enzymes involved in oxidative phosphorylation.
Collapse
Affiliation(s)
- George Korza
- Department of Molecular Biology and Biophysics, Farmington, CT 06030-3305, USA
| | - Sarah DePratti
- Department of Molecular Biology and Biophysics, Farmington, CT 06030-3305, USA
| | - Daniel Fairchild
- Department of Molecular Biology and Biophysics, Farmington, CT 06030-3305, USA
| | - James Wicander
- Department of Molecular Biology and Biophysics, Farmington, CT 06030-3305, USA
| | - Julia Kanaan
- Department of Molecular Biology and Biophysics, Farmington, CT 06030-3305, USA
| | - Hannah Shames
- Department of Molecular Biology and Biophysics, Farmington, CT 06030-3305, USA
| | - Frank C Nichols
- Division of Periodontology, UConn Health, Farmington, CT 06030-3305, USA
| | - Ann Cowan
- Department of Molecular Biology and Biophysics, Farmington, CT 06030-3305, USA
| | - Stanley Brul
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Science, University of Amsterdam, 1098XH Amsterdam, UK
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, Farmington, CT 06030-3305, USA
| |
Collapse
|
9
|
Yu B, Kanaan J, Shames H, Wicander J, Aryal M, Li Y, Korza G, Brul S, Kramer G, Li YQ, Nichols FC, Hao B, Setlow P. Identification and characterization of new proteins crucial for bacterial spore resistance and germination. Front Microbiol 2023; 14:1161604. [PMID: 37113233 PMCID: PMC10126465 DOI: 10.3389/fmicb.2023.1161604] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
2Duf, named after the presence of a transmembrane (TM) Duf421 domain and a small Duf1657 domain in its sequence, is likely located in the inner membrane (IM) of spores in some Bacillus species carrying a transposon with an operon termed spoVA 2mob. These spores are known for their extreme resistance to wet heat, and 2Duf is believed to be the primary contributor to this trait. In this study, we found that the absence of YetF or YdfS, both Duf421 domain-containing proteins and found only in wild-type (wt) B. subtilis spores with YetF more abundant, leads to decreased resistance to wet heat and agents that can damage spore core components. The IM phospholipid compositions and core water and calcium-dipicolinic acid levels of YetF-deficient spores are similar to those of wt spores, but the deficiency could be restored by ectopic insertion of yetF, and overexpression of YetF increased wt spore resistance to wet heat. In addition, yetF and ydfS spores have decreased germination rates as individuals and populations with germinant receptor-dependent germinants and increased sensitivity to wet heat during germination, potentially due to damage to IM proteins. These data are consistent with a model in which YetF, YdfS and their homologs modify IM structure to reduce IM permeability and stabilize IM proteins against wet heat damage. Multiple yetF homologs are also present in other spore forming Bacilli and Clostridia, and even some asporogenous Firmicutes, but fewer in asporogenous species. The crystal structure of a YetF tetramer lacking the TM helices has been reported and features two distinct globular subdomains in each monomer. Sequence alignment and structure prediction suggest this fold is likely shared by other Duf421-containing proteins, including 2Duf. We have also identified naturally occurring 2duf homologs in some Bacilli and Clostridia species and in wt Bacillus cereus spores, but not in wt B. subtilis. Notably, the genomic organization around the 2duf gene in most of these species is similar to that in spoVA 2mob, suggesting that one of these species was the source of the genes on this operon in the extremely wet heat resistant spore formers.
Collapse
Affiliation(s)
- Benjamin Yu
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Julia Kanaan
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Hannah Shames
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - James Wicander
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Makunda Aryal
- Department of Physics, East Carolina University, Greenville, NC, United States
| | - Yunfeng Li
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - George Korza
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life Science, University of Amsterdam, Amsterdam, Netherlands
| | - Yong-qing Li
- Department of Physics, East Carolina University, Greenville, NC, United States
| | - Frank C. Nichols
- Division of Periodontology, UConn Health, Farmington, CT, United States
| | - Bing Hao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- Bing Hao,
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- *Correspondence: Peter Setlow,
| |
Collapse
|
10
|
Benito-Vaquerizo S, Nouse N, Schaap PJ, Hugenholtz J, Brul S, López-Contreras AM, Martins dos Santos VAP, Suarez-Diez M. Model-driven approach for the production of butyrate from CO 2/H 2 by a novel co-culture of C. autoethanogenum and C. beijerinckii. Front Microbiol 2022; 13:1064013. [PMID: 36620068 PMCID: PMC9815533 DOI: 10.3389/fmicb.2022.1064013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
One-carbon (C1) compounds are promising feedstocks for the sustainable production of commodity chemicals. CO2 is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted into valuable products while reducing its atmospheric levels. Acetogens are microorganisms that can grow on CO2/H2 gas mixtures and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with other microbial species that can further process such products, can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone-butanol-ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of an acetogen and a solventogen in a consortium provides a potential platform to produce valuable chemicals from CO2. In this study, metabolic modeling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO2/H2 mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation of Clostridium beijerinckii on these substrates in batch serum bottles and subsequently in pH-controlled bioreactors. Community modeling also suggested that a novel microbial consortium consisting of the acetogen Clostridium autoethanogenum, and the solventogen C. beijerinckii would be feasible and stable. On the basis of this prediction, a co-culture was experimentally established. C. autoethanogenum grew on CO2/H2 producing acetate and traces of ethanol. Acetate was in turn, consumed by C. beijerinckii together with lactate, producing butyrate. These results show that community modeling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable resources.
Collapse
Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Niels Nouse
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,UNLOCK Large Scale Infrastructure for Microbial Communities, Wageningen University and Research and Delft University of Technology, Wageningen, Netherlands
| | - Jeroen Hugenholtz
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Ana M. López-Contreras
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, Netherlands
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,*Correspondence: Maria Suarez-Diez ✉
| |
Collapse
|
11
|
Darphorn TS, Brul S, Ter Kuile BH. Genetic editing of multi-resistance plasmids in Escherichia coli isolated from meat during transfer. Plasmid 2022; 122:102640. [PMID: 35870604 DOI: 10.1016/j.plasmid.2022.102640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022]
Abstract
Resistance plasmids mediate the rapid spread of antimicrobial resistance, which poses a threat to veterinary and human healthcare. This study addresses the question whether resistance plasmids from Escherichia coli isolated from foodstuffs always transfer unchanged to recipient E. coli cells, or that genetic editing can occur. Strains containing between one and five different plasmids were co-incubated with a standard recipient strain. Plasmids isolated from transconjugant strains were sequenced using short and long read technologies and compared to the original plasmids from the donor strains. After one hour of co-incubation only a single plasmid was transferred from donor to recipient strains. If the donor possessed several plasmids, longer co-incubation resulted in multiple plasmids being transferred. Transferred plasmids showed mutations, mostly in mobile genetic elements, in the conjugative transfer gene pilV and in genes involved in plasmid maintenance. In one transconjugant, a resistance cluster encoding tetracycline resistance was acquired by the IncI1 plasmid from the IncX1 plasmid that was also present in the donor strain, but that was not transferred. A single plasmid transferred twelve times back and forth between E. coli strains resulted in a fully conserved plasmid with no mutations, apart from repetitive rearrangements of pilV from and back to its original conformation in the donor strain. The overall outcome suggests that some genetic mutations and rearrangements can occur during plasmid transfer. The possibility of such mutations should be taken into consideration in epidemiological research aimed at attribution of resistance to specific sources.
Collapse
Affiliation(s)
- Tania S Darphorn
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Benno H Ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands; Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, the Netherlands.
| |
Collapse
|
12
|
Darphorn TS, Koenders-van Sintanneland BB, Grootemaat AE, van der Wel NN, Brul S, ter Kuile BH. Transfer dynamics of multi-resistance plasmids in Escherichia coli isolated from meat. PLoS One 2022; 17:e0270205. [PMID: 35797379 PMCID: PMC9262221 DOI: 10.1371/journal.pone.0270205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/06/2022] [Indexed: 12/31/2022] Open
Abstract
Resistance plasmids are crucial for the transfer of antimicrobial resistance and thus form a matter of concern for veterinary and human healthcare. To study plasmid transfer, foodborne Escherichia coli isolates harboring one to five known plasmids were co-incubated with a general recipient strain. Plasmid transfer rates under standardized conditions varied by a factor of almost 106, depending on the recipient/donor strain combination. After 1 hour transconjugants never accounted for more than 3% of the total number of cells. Transconjugants were formed from 14 donors within 1 hour of co-incubation, but in the case of 3 donors 24 hours were needed. Transfer rates were also measured during longer co-incubation, between different species and during repeated back and forth transfer. Longer co-incubation resulted in the transfer of more types of resistance. Maximum growth rates of donor strains varied by a factor of 3. Donor strains often had higher growth rates than the corresponding transconjugants, which grew at the same rate as or slightly faster than the recipient. Hence, possessing one or more plasmids does not seem to burden the harboring strain metabolically. Transfer was species specific and repeated transfer of one plasmid did not result in different transfer rates over time. Transmission Electron microcopy was used to analyze the morphology of the connection between co-incubated strains. Connection by more pili between the cells resulted in better aggregate formation and corresponded with higher transfer rates.
Collapse
Affiliation(s)
- Tania S. Darphorn
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Belinda B. Koenders-van Sintanneland
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Anita E. Grootemaat
- Department of Cell Biology and Histology, Electron Microscopy Centre Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
| | - Nicole N. van der Wel
- Department of Cell Biology and Histology, Electron Microscopy Centre Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Benno H. ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, The Netherlands
| |
Collapse
|
13
|
Pasman R, Krom BP, Zaat SAJ, Brul S. The Role of the Oral Immune System in Oropharyngeal Candidiasis-Facilitated Invasion and Dissemination of Staphylococcus aureus. Front Oral Health 2022; 3:851786. [PMID: 35464779 PMCID: PMC9021398 DOI: 10.3389/froh.2022.851786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Candida albicans and Staphylococcus aureus account for most invasive fungal and bacterial bloodstream infections (BSIs), respectively. However, the initial point of invasion responsible for S. aureus BSIs is often unclear. Recently, C. albicans has been proposed to mediate S. aureus invasion of immunocompromised hosts during co-colonization of oral mucosal surfaces. The status of the oral immune system crucially contributes to this process in two distinct ways: firstly, by allowing invasive C. albicans growth during dysfunction of extra-epithelial immunity, and secondly following invasion by some remaining function of intra-epithelial immunity. Immunocompromised individuals at risk of developing invasive oral C. albicans infections could, therefore, also be at risk of contracting concordant S. aureus BSIs. Considering the crucial contribution of both oral immune function and dysfunction, the aim of this review is to provide an overview of relevant aspects of intra and extra-epithelial oral immunity and discuss predominant immune deficiencies expected to facilitate C. albicans induced S. aureus BSIs.
Collapse
Affiliation(s)
- Raymond Pasman
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Bastiaan P. Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Sebastian A. J. Zaat
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Stanley Brul
| |
Collapse
|
14
|
Wen J, Vischer NOE, de Vos AL, Manders EMM, Setlow P, Brul S. Organization and dynamics of the SpoVAEa protein and its surrounding inner membrane lipids, upon germination of Bacillus subtilis spores. Sci Rep 2022; 12:4944. [PMID: 35322191 PMCID: PMC8943000 DOI: 10.1038/s41598-022-09147-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
The SpoVA proteins make up a channel in the inner membrane (IM) of Bacillus subtilis spores. This channel responds to signals from activated germinant receptors (GRs), and allows release of Ca2+-DPA from the spore core during germination. In the current work, we studied the location and dynamics of SpoVAEa in dormant spores. Notably, the SpoVAEa-SGFP2 proteins were present in a single spot in spores, similar to the IM complex formed by all GRs termed the germinosome. However, while the GRs' spot remains in one location, the SpoVAEa-SGFP2 spot in the IM moved randomly with high frequency. It seems possible that this movement may be a means of communicating germination signals from the germinosome to the IM SpoVA channel, thus stimulating CaDPA release in germination. The dynamics of the SpoVAEa-SGFP2 and its surrounding IM region as stained by fluorescent dyes were also tracked during spore germination, as the dormant spore IM appeared to have an immobile germination related functional microdomain. This microdomain disappeared around the time of appearance of a germinated spore, and the loss of fluorescence of the IM with fluorescent dyes, as well as the appearance of peak SpoVAEa-SGFP2 fluorescent intensity occurred in parallel. These observed events were highly related to spores' rapid phase darkening, which is considered as due to rapid Ca2+DPA release. We also tested the response of SpoVAEa and the IM to thermal treatments at 40-80 °C. Heat treatment triggered an increase of green autofluorescence, which is speculated to be due to coat protein denaturation, and 80 °C treatments induce the appearance of phase-grey-like spores. These spores presumably have a similar intracellular physical state as the phase grey spores detected in the germination but lack the functional proteins for further germination events.
Collapse
Affiliation(s)
- Juan Wen
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Norbert O E Vischer
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Arend L de Vos
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Erik M M Manders
- Confocal.Nl B.V., Science Park 106, 1098 XG, Amsterdam, The Netherlands
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT, 06030-3305, USA
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
| |
Collapse
|
15
|
Liu S, Brul S, Zaat SAJ. Isolation of Persister Cells of Bacillus subtilis and Determination of Their Susceptibility to Antimicrobial Peptides. Int J Mol Sci 2021; 22:10059. [PMID: 34576222 PMCID: PMC8470456 DOI: 10.3390/ijms221810059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/15/2022] Open
Abstract
Persister cells are growth-arrested subpopulations that can survive possible fatal environments and revert to wild types after stress removal. Clinically, persistent pathogens play a key role in antibiotic therapy failure, as well as chronic, recurrent, and antibiotic-resilient infections. In general, molecular and physiological research on persister cells formation and compounds against persister cells are much desired. In this study, we firstly demonstrated that the spore forming Gram-positive model organism Bacillus subtilis can be used to generate persister cells during exposure to antimicrobial compounds. Interestingly, instead of exhibiting a unified antibiotic tolerance profile, different number of persister cells and spores were quantified in various stress conditions. qPCR results also indicated that differential stress responses are related to persister formation in various environmental conditions. We propose, for the first time to the best of our knowledge, an effective method to isolate B. subtilis persister cells from a population using fluorescence-activated cell sorting (FACS), which makes analyzing persister populations feasible. Finally, we show that alpha-helical cationic antimicrobial peptides SAAP-148 and TC-19, derived from human cathelicidin LL-37 and human thrombocidin-1, respectively, have high efficiency against both B. subtilis vegetative cells and persisters, causing membrane permeability and fluidity alteration. In addition, we confirm that in contrast to persister cells, dormant B. subtilis spores are not susceptible to the antimicrobial peptides.
Collapse
Affiliation(s)
- Shiqi Liu
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Sebastian A. J. Zaat
- Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, Department of Medical Microbiology, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| |
Collapse
|
16
|
Koopman N, Katsavelis D, Hove AST, Brul S, de Jonge WJ, Seppen J. The Multifaceted Role of Serotonin in Intestinal Homeostasis. Int J Mol Sci 2021; 22:9487. [PMID: 34502396 PMCID: PMC8431144 DOI: 10.3390/ijms22179487] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
The monoamine serotonin, 5-hydroxytryptamine (5-HT), is a remarkable molecule with conserved production in prokaryotes and eukaryotes and a wide range of functions. In the gastrointestinal tract, enterochromaffin cells are the most important source for 5-HT production. Some intestinal bacterial species are also able to produce 5-HT. Besides its role as a neurotransmitter, 5-HT acts on immune cells to regulate their activation. Several lines of evidence indicate that intestinal 5-HT signaling is altered in patients with inflammatory bowel disease. In this review, we discuss the current knowledge on the production, secretion, and signaling of 5-HT in the intestine. We present an inventory of intestinal immune and epithelial cells that respond to 5-HT and describe the effects of these signaling processes on intestinal homeostasis. Further, we detail the mechanisms by which 5-HT could affect inflammatory bowel disease course and describe the effects of interventions that target intestinal 5-HT signaling.
Collapse
Affiliation(s)
- Nienke Koopman
- Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098XH Amsterdam, The Netherlands; (N.K.); (D.K.); (S.B.)
| | - Drosos Katsavelis
- Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098XH Amsterdam, The Netherlands; (N.K.); (D.K.); (S.B.)
| | - Anne S. ten Hove
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Location AMC, 1105BK Amsterdam, The Netherlands; (A.S.t.H.); (W.J.d.J.)
| | - Stanley Brul
- Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098XH Amsterdam, The Netherlands; (N.K.); (D.K.); (S.B.)
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Location AMC, 1105BK Amsterdam, The Netherlands; (A.S.t.H.); (W.J.d.J.)
| | - Jurgen Seppen
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Location AMC, 1105BK Amsterdam, The Netherlands; (A.S.t.H.); (W.J.d.J.)
| |
Collapse
|
17
|
Tu Z, Dekker HL, Roseboom W, Swarge BN, Setlow P, Brul S, Kramer G. High Resolution Analysis of Proteome Dynamics during Bacillus subtilis Sporulation. Int J Mol Sci 2021; 22:ijms22179345. [PMID: 34502250 PMCID: PMC8431406 DOI: 10.3390/ijms22179345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/19/2021] [Accepted: 08/24/2021] [Indexed: 12/27/2022] Open
Abstract
Bacillus subtilis vegetative cells switch to sporulation upon nutrient limitation. To investigate the proteome dynamics during sporulation, high-resolution time-lapse proteomics was performed in a cell population that was induced to sporulate synchronously. Here, we are the first to comprehensively investigate the changeover of sporulation regulatory proteins, coat proteins, and other proteins involved in sporulation and spore biogenesis. Protein co-expression analysis revealed four co-expressed modules (termed blue, brown, green, and yellow). Modules brown and green are upregulated during sporulation and contain proteins associated with sporulation. Module blue is negatively correlated with modules brown and green, containing ribosomal and metabolic proteins. Finally, module yellow shows co-expression with the three other modules. Notably, several proteins not belonging to any of the known transcription regulons were identified as co-expressed with modules brown and green, and might also play roles during sporulation. Finally, levels of some coat proteins, for example morphogenetic coat proteins, decreased late in sporulation.
Collapse
Affiliation(s)
- Zhiwei Tu
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (H.L.D.); (W.R.); (B.N.S.)
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Henk L. Dekker
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (H.L.D.); (W.R.); (B.N.S.)
| | - Winfried Roseboom
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (H.L.D.); (W.R.); (B.N.S.)
| | - Bhagyashree N. Swarge
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (H.L.D.); (W.R.); (B.N.S.)
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06030-3305, USA;
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Correspondence: (S.B.); (G.K.); Tel.: +31-20-525-7079/6970 (S.B.); +31-20-525-5457 (G.K.)
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (H.L.D.); (W.R.); (B.N.S.)
- Correspondence: (S.B.); (G.K.); Tel.: +31-20-525-7079/6970 (S.B.); +31-20-525-5457 (G.K.)
| |
Collapse
|
18
|
Darphorn TS, Hu Y, Koenders-van Sintanneland BB, Brul S, ter Kuile BH. Multiplication of ampC upon Exposure to a Beta-Lactam Antibiotic Results in a Transferable Transposon in Escherichia coli. Int J Mol Sci 2021; 22:ijms22179230. [PMID: 34502136 PMCID: PMC8430887 DOI: 10.3390/ijms22179230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
Plasmids play a crucial role in spreading antimicrobial resistance genes. Plasmids have many ways to incorporate various genes. By inducing amoxicillin resistance in Escherichia coli, followed by horizontal gene transfer experiments and sequencing, we show that the chromosomal beta-lactamase gene ampC is multiplied and results in an 8–13 kb contig. This contig is comparable to a transposon, showing similarities to variable regions found in environmental plasmids, and can be transferred between E. coli cells. As in eight out of nine replicate strains an almost completely identical transposon was isolated, we conclude that this process is under strict control by the cell. The single transposon that differed was shortened at both ends, but otherwise identical. The outcome of this study indicates that as a result of exposure to beta-lactam antibiotics, E. coli can form a transposon containing ampC that can subsequently be integrated into plasmids or genomes. This observation offers an explanation for the large diversity of genes in plasmids found in nature and proposes mechanisms by which the dynamics of plasmids are maintained.
Collapse
Affiliation(s)
- Tania S. Darphorn
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (T.S.D.); (Y.H.); (B.B.K.-v.S.); (S.B.)
| | - Yuanqing Hu
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (T.S.D.); (Y.H.); (B.B.K.-v.S.); (S.B.)
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
| | - Belinda B. Koenders-van Sintanneland
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (T.S.D.); (Y.H.); (B.B.K.-v.S.); (S.B.)
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (T.S.D.); (Y.H.); (B.B.K.-v.S.); (S.B.)
| | - Benno H. ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (T.S.D.); (Y.H.); (B.B.K.-v.S.); (S.B.)
- The Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Catharijnesingel 59, 3511 GG Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-6-46596684
| |
Collapse
|
19
|
Tu Z, Setlow P, Brul S, Kramer G. Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate. Microorganisms 2021; 9:667. [PMID: 33807113 PMCID: PMC8005191 DOI: 10.3390/microorganisms9030667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 02/07/2023] Open
Abstract
Bacterial endospores (spores) are among the most resistant living forms on earth. Spores of Bacillus subtilis A163 show extremely high resistance to wet heat compared to spores of laboratory strains. In this study, we found that spores of B. subtilis A163 were indeed very wet heat resistant and released dipicolinic acid (DPA) very slowly during heat treatment. We also determined the proteome of vegetative cells and spores of B. subtilis A163 and the differences in these proteomes from those of the laboratory strain PY79, spores of which are much less heat resistant. This proteomic characterization identified 2011 proteins in spores and 1901 proteins in vegetative cells of B. subtilis A163. Surprisingly, spore morphogenic protein SpoVM had no homologs in B. subtilis A163. Comparing protein expression between these two strains uncovered 108 proteins that were differentially present in spores and 93 proteins differentially present in cells. In addition, five of the seven proteins on an operon in strain A163, which is thought to be primarily responsible for this strain's spores high heat resistance, were also identified. These findings reveal proteomic differences of the two strains exhibiting different resistance to heat and form a basis for further mechanistic analysis of the high heat resistance of B. subtilis A163 spores.
Collapse
Affiliation(s)
- Zhiwei Tu
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06030-3303, USA;
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| |
Collapse
|
20
|
Ursem R, Swarge B, Abhyankar WR, Buncherd H, de Koning LJ, Setlow P, Brul S, Kramer G. Identification of Native Cross-Links in Bacillus subtilis Spore Coat Proteins. J Proteome Res 2021; 20:1809-1816. [PMID: 33596081 PMCID: PMC7944565 DOI: 10.1021/acs.jproteome.1c00025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The resistance properties of the bacterial spores are partially due to spore surface proteins, ∼30% of which are said to form an insoluble protein fraction. Previous research has also identified a group of spore coat proteins affected by spore maturation, which exhibit an increased level of interprotein cross-linking. However, the proteins and the types of cross-links involved, previously proposed based on indirect evidence, have yet to be confirmed experimentally. To obtain more insight into the structural basis of the proteinaceous component of the spore coat, we attempted to identify coat cross-links and the proteins involved using new peptide fractionation and bioinformatic methods. Young (day 1) and matured (day 5) Bacillus subtilis spores of wild-type and transglutaminase mutant strains were digested with formic acid and trypsin, and cross-linked peptides were enriched using strong cation exchange chromatography. The enriched cross-linked peptide fractions were subjected to Fourier-transform ion cyclotron resonance tandem mass spectrometry, and the high-quality fragmentation data obtained were analyzed using two specialized software tools, pLink2 and XiSearch, to identify cross-links. This analysis identified specific disulfide bonds between coat proteins CotE-CotE and CotJA-CotJC, obtained evidence of disulfide bonds in the spore crust proteins CotX, CotY, and CotZ, and identified dityrosine and ε-(γ)-glutamyl-lysine cross-linked coat proteins. The findings in this Letter are the first direct biochemical data on protein cross-linking in the spore coat and the first direct evidence of the cross-linked building blocks of the highly ordered and resistant structure called the spore coat.
Collapse
Affiliation(s)
| | | | | | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Songkhla 90110, Thailand
| | | | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut 06030-3305, United States
| | | | | |
Collapse
|
21
|
Weglarz-Tomczak E, Tomczak JM, Talma M, Burda-Grabowska M, Giurg M, Brul S. Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2. Sci Rep 2021; 11:3640. [PMID: 33574416 PMCID: PMC7878891 DOI: 10.1038/s41598-021-83229-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
An efficient treatment against a COVID-19 disease, caused by the novel coronavirus SARS-CoV-2 (CoV2), remains a challenge. The papain-like protease (PLpro) from the human coronavirus is a protease that plays a critical role in virus replication. Moreover, CoV2 uses this enzyme to modulate the host’s immune system to its own benefit. Therefore, it represents a highly promising target for the development of antiviral drugs. We used Approximate Bayesian Computation tools, molecular modelling and enzyme activity studies to identify highly active inhibitors of the PLpro. We discovered organoselenium compounds, ebselen and its structural analogues, as a novel approach for inhibiting the activity of PLproCoV2. Furthermore, we identified, for the first time, inhibitors of PLproCoV2 showing potency in the nanomolar range. Moreover, we found a difference between PLpro from SARS and CoV2 that can be correlated with the diverse dynamics of their replication, and, putatively to disease progression.
Collapse
Affiliation(s)
- Ewelina Weglarz-Tomczak
- Molecular Biology and Microbial Food Safety Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands.
| | - Jakub M Tomczak
- Computational Intelligence Group, Department of Computer Science, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Michał Talma
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wrocław, Poland
| | - Małgorzata Burda-Grabowska
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wrocław, Poland.,Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wrocław, Poland
| | - Mirosław Giurg
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wrocław, Poland
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
22
|
Weglarz-Tomczak E, Rijlaarsdam DJ, Tomczak JM, Brul S. GEM-Based Metabolic Profiling for Human Bone Osteosarcoma under Different Glucose and Glutamine Availability. Int J Mol Sci 2021; 22:1470. [PMID: 33540580 PMCID: PMC7867237 DOI: 10.3390/ijms22031470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 12/31/2022] Open
Abstract
Cancer cell metabolism is dependent on cell-intrinsic factors, such as genetics, and cell-extrinsic factors, such nutrient availability. In this context, understanding how these two aspects interact and how diet influences cellular metabolism is important for developing personalized treatment. In order to achieve this goal, genome-scale metabolic models (GEMs) are used; however, genetics and nutrient availability are rarely considered together. Here, we propose integrated metabolic profiling, a framework that allows enriching GEMs with metabolic gene expression data and information about nutrients. First, the RNA-seq is converted into Reaction Activity Score (RAS) to further scale reaction bounds. Second, nutrient availability is converted to Maximal Uptake Rate (MUR) to modify exchange reactions in a GEM. We applied our framework to the human osteosarcoma cell line (U2OS). Osteosarcoma is a common and primary malignant form of bone cancer with poor prognosis, and, as indicated in our study, a glutamine-dependent type of cancer.
Collapse
Affiliation(s)
- Ewelina Weglarz-Tomczak
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands; (D.J.R.); (S.B.)
| | - Demi J. Rijlaarsdam
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands; (D.J.R.); (S.B.)
| | - Jakub M. Tomczak
- Department of Computer Science, Vrije Universiteit Amsterdam, De Boelelaan 1111, 1081 HV Amsterdam, The Netherlands;
| | - Stanley Brul
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands; (D.J.R.); (S.B.)
| |
Collapse
|
23
|
Weglarz-Tomczak E, Tomczak JM, Brul S. M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models. Bioinformatics 2021; 37:2785-2786. [PMID: 33523116 PMCID: PMC8428599 DOI: 10.1093/bioinformatics/btab060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/31/2020] [Accepted: 01/26/2021] [Indexed: 11/16/2022] Open
Abstract
Motivation The gut microbiota is the human body’s largest population of microorganisms that interact with human intestinal cells. They use ingested nutrients for fundamental biological processes and have important impacts on human physiology, immunity and metabolome in the gastrointestinal tract. Results Here, we present M2R, a Python add-on to cobrapy that allows incorporating information about the gut microbiota metabolism models to human genome-scale metabolic models (GEMs) like RECON3D. The idea behind the software is to modify the lower bounds of the exchange reactions in the model using aggregated in- and out-fluxes from selected microbes. M2R enables users to quickly and easily modify the pool of the metabolites that enter and leave the GEM, which is particularly important for those looking into an analysis of the metabolic interaction between the gut microbiota and human cells and its dysregulation. Availability and implementation M2R is freely available under an MIT License at https://github.com/e-weglarz-tomczak/m2r. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Ewelina Weglarz-Tomczak
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, the Netherlands
| | - Jakub M Tomczak
- Department of Computer Science, Faculty of Science, Vrije Universiteit Amsterdam, the Netherlands
| | - Stanley Brul
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, the Netherlands
| |
Collapse
|
24
|
Darphorn TS, Bel K, Koenders-van Sint Anneland BB, Brul S, Ter Kuile BH. Antibiotic resistance plasmid composition and architecture in Escherichia coli isolates from meat. Sci Rep 2021; 11:2136. [PMID: 33483623 PMCID: PMC7822866 DOI: 10.1038/s41598-021-81683-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/08/2021] [Indexed: 01/30/2023] Open
Abstract
Resistance plasmids play a crucial role in the transfer of antimicrobial resistance from the veterinary sector to human healthcare. In this study plasmids from foodborne Escherichia coli isolates with a known (ES)BL or tetracycline resistance were sequenced entirely with short- and long-read technologies to obtain insight into their composition and to identify driving factors for spreading. Resistant foodborne E. coli isolates often contained several plasmids coding for resistance to various antimicrobials. Most plasmids were large and contained multiple resistance genes in addition to the selected resistance gene. The majority of plasmids belonged to the IncI, IncF and IncX incompatibility groups. Conserved and variable regions could be distinguished in each of the plasmid groups. Clusters containing resistance genes were located in the variable regions. Tetracycline and (extended spectrum) beta-lactamase resistance genes were each situated in separate clusters, but sulphonamide, macrolide and aminoglycoside formed one cluster and lincosamide and aminoglycoside another. In most plasmids, addiction systems were found to maintain presence in the cell.
Collapse
Affiliation(s)
- Tania S. Darphorn
- grid.7177.60000000084992262Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Keshia Bel
- grid.7177.60000000084992262Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Wageningen Food Safety Research, Wageningen University and Research, Postbus 230, 6700 AE Wageningen, The Netherlands
| | - Belinda B. Koenders-van Sint Anneland
- grid.7177.60000000084992262Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- grid.7177.60000000084992262Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Benno H. Ter Kuile
- grid.7177.60000000084992262Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands ,grid.435742.30000 0001 0726 7822Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, The Netherlands
| |
Collapse
|
25
|
Liu S, Brul S, Zaat SAJ. Bacterial Persister-Cells and Spores in the Food Chain: Their Potential Inactivation by Antimicrobial Peptides (AMPs). Int J Mol Sci 2020; 21:E8967. [PMID: 33260797 PMCID: PMC7731242 DOI: 10.3390/ijms21238967] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022] Open
Abstract
The occurrence of bacterial pathogens in the food chain has caused a severe impact on public health and welfare in both developing and developed countries. Moreover, the existence of antimicrobial-tolerant persisting morphotypes of these pathogens including both persister-cells as well as bacterial spores contributes to difficulty in elimination and in recurrent infection. Therefore, comprehensive understanding of the behavior of these persisting bacterial forms in their environmental niche and upon infection of humans is necessary. Since traditional antimicrobials fail to kill persisters and spores due to their (extremely) low metabolic activities, antimicrobial peptides (AMPs) have been intensively investigated as one of the most promising strategies against these persisting bacterial forms, showing high efficacy of inactivation. In addition, AMP-based foodborne pathogen detection and prevention of infection has made significant progress. This review focuses on recent research on common bacterial pathogens in the food chain, their persisting morphotypes, and on AMP-based solutions. Challenges in research and application of AMPs are described.
Collapse
Affiliation(s)
- Shiqi Liu
- Swammerdam Institute for Life Sciences, Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Stanley Brul
- Swammerdam Institute for Life Sciences, Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Sebastian A. J. Zaat
- Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| |
Collapse
|
26
|
Tu Z, R. Abhyankar W, N. Swarge B, van der Wel N, Kramer G, Brul S, J. de Koning L. Artificial Sporulation Induction (ASI) by kinA Overexpression Affects the Proteomes and Properties of Bacillus subtilis Spores. Int J Mol Sci 2020; 21:ijms21124315. [PMID: 32560401 PMCID: PMC7352945 DOI: 10.3390/ijms21124315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/07/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
To facilitate more accurate spore proteomic analysis, the current study focuses on inducing homogeneous sporulation by overexpressing kinA and assesses the effect of synchronized sporulation initiation on spore resistance, structures, the germination behavior at single-spore level and the proteome. The results indicate that, in our set up, the sporulation by overexpressing kinA can generate a spore yield of 70% within 8 h. The procedure increases spore wet heat resistance and thickness of the spore coat and cortex layers, whilst delaying the time to spore phase-darkening and burst after addition of germinant. The proteome analysis reveals that the upregulated proteins in the kinA induced spores, compared to spores without kinA induction, as well as the 'wildtype' spores, are mostly involved in spore formation. The downregulated proteins mostly belong to the categories of coping with stress, carbon and nitrogen metabolism, as well as the regulation of sporulation. Thus, while kinA overexpression enhances synchronicity in sporulation initiation, it also has profound effects on the central equilibrium of spore formation and spore germination, through modulation of the spore molecular composition and stress resistance physiology.
Collapse
Affiliation(s)
- Zhiwei Tu
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (W.R.A.); (B.N.S.)
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (G.K.); (L.J.d.K.)
| | - Wishwas R. Abhyankar
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (W.R.A.); (B.N.S.)
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (G.K.); (L.J.d.K.)
| | - Bhagyashree N. Swarge
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (W.R.A.); (B.N.S.)
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (G.K.); (L.J.d.K.)
| | - Nicole van der Wel
- Department of Medical Biology, Electron Microscopy Centre Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, 1100 DD Amsterdam, The Netherlands;
| | - Gertjan Kramer
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (G.K.); (L.J.d.K.)
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (Z.T.); (W.R.A.); (B.N.S.)
- Correspondence: ; Tel.: +31-20-525-7079 (ext. 6970)
| | - Leo J. de Koning
- Laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; (G.K.); (L.J.d.K.)
| |
Collapse
|
27
|
Lucena RM, Dolz-Edo L, Brul S, de Morais MA, Smits G. Extreme Low Cytosolic pH Is a Signal for Cell Survival in Acid Stressed Yeast. Genes (Basel) 2020; 11:genes11060656. [PMID: 32560106 PMCID: PMC7349538 DOI: 10.3390/genes11060656] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/18/2022] Open
Abstract
Yeast biomass is recycled in the process of bioethanol production using treatment with dilute sulphuric acid to control the bacterial population. This treatment can lead to loss of cell viability, with consequences on the fermentation yield. Thus, the aim of this study was to define the functional cellular responses to inorganic acid stress. Saccharomyces cerevisiae strains with mutation in several signalling pathways, as well as cells expressing pH-sensitive GFP derivative ratiometric pHluorin, were tested for cell survival and cytosolic pH (pHc) variation during exposure to low external pH (pHex). Mutants in calcium signalling and proton extrusion were transiently sensitive to low pHex, while the CWI slt2Δ mutant lost viability. Rescue of this mutant was observed when cells were exposed to extreme low pHex or glucose starvation and was dependent on the induced reduction of pHc. Therefore, a lowered pHc leads to a complete growth arrest, which protects the cells from lethal stress and keeps cells alive. Cytosolic pH is thus a signal that directs the growth stress-tolerance trade-off in yeast. A regulatory model was proposed to explain this mechanism, indicating the impairment of glucan synthesis as the primary cause of low pHex sensitivity.
Collapse
Affiliation(s)
- Rodrigo Mendonça Lucena
- Department of Genetics, Biosciences Centre, Federal University of Pernambuco, Recife 50670-901, Brazil;
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
| | - Laura Dolz-Edo
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
| | - Marcos Antonio de Morais
- Department of Genetics, Biosciences Centre, Federal University of Pernambuco, Recife 50670-901, Brazil;
- Correspondence: (G.S.); (M.A.d.M.J.)
| | - Gertien Smits
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
- Correspondence: (G.S.); (M.A.d.M.J.)
| |
Collapse
|
28
|
Abhyankar WR, Zheng L, Brul S, de Koster CG, de Koning LJ. Vegetative Cell and Spore Proteomes of Clostridioides difficile Show Finite Differences and Reveal Potential Protein Markers. J Proteome Res 2019; 18:3967-3976. [PMID: 31557040 PMCID: PMC6832669 DOI: 10.1021/acs.jproteome.9b00413] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Clostridioides difficile-associated infection
(CDI) is a health-care-associated infection caused, as the name suggests,
by obligate anaerobic pathogen C. difficile and
thus mainly transmitted via highly resistant endospores from one person
to the other. In vivo, the spores need to germinate into cells prior
to establishing an infection. Bile acids and glycine, both available
in sufficient amounts inside the human host intestinal tract, serve
as efficient germinants for the spores. It is therefore, for better
understanding of C. difficile virulence, crucial
to study both the cell and spore states with respect to their genetic,
metabolic, and proteomic composition. In the present study, mass spectrometric
relative protein quantification, based on the 14N/15N peptide isotopic ratios, has led to quantification of over
700 proteins from combined spore and cell samples. The analysis has
revealed that the proteome turnover between a vegetative cell and
a spore for this organism is moderate. Additionally, specific cell
and spore surface proteins, vegetative cell proteins CD1228, CD3301
and spore proteins CD2487, CD2434, and CD0684 are identified as potential
protein markers for C. difficile infection.
Collapse
Affiliation(s)
- Wishwas R Abhyankar
- Department of Molecular Biology and Microbial Food Safety , Swammerdam Institute for Life Sciences, University of Amsterdam Faculty of Science , Science Park 904 , 1098 XH Amsterdam , The Netherlands.,Department of Mass Spectrometry of Bio-Macromolecules , Swammerdam Institute for Life Sciences, University of Amsterdam Faculty of Science , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - Linli Zheng
- Department of Molecular Biology and Microbial Food Safety , Swammerdam Institute for Life Sciences, University of Amsterdam Faculty of Science , Science Park 904 , 1098 XH Amsterdam , The Netherlands.,Department of Mass Spectrometry of Bio-Macromolecules , Swammerdam Institute for Life Sciences, University of Amsterdam Faculty of Science , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety , Swammerdam Institute for Life Sciences, University of Amsterdam Faculty of Science , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - Chris G de Koster
- Department of Mass Spectrometry of Bio-Macromolecules , Swammerdam Institute for Life Sciences, University of Amsterdam Faculty of Science , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| | - Leo J de Koning
- Department of Mass Spectrometry of Bio-Macromolecules , Swammerdam Institute for Life Sciences, University of Amsterdam Faculty of Science , Science Park 904 , 1098 XH Amsterdam , The Netherlands
| |
Collapse
|
29
|
Dolz‐Edo L, van der Deen M, Brul S, Smits GJ. Caloric restriction controls stationary phase survival through Protein Kinase A (PKA) and cytosolic pH. Aging Cell 2019; 18:e12921. [PMID: 30790427 PMCID: PMC6516148 DOI: 10.1111/acel.12921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 12/30/2018] [Accepted: 01/23/2019] [Indexed: 11/28/2022] Open
Abstract
Calorie restriction is the only physiological intervention that extends lifespan throughout all kingdoms of life. In the budding yeast Saccharomyces cerevisiae, cytosolic pH (pHc) controls growth and responds to nutrient availability, decreasing upon glucose depletion. We investigated the interactions between glucose availability, pHc and the central nutrient signalling cAMP‐Protein Kinase A (PKA) pathway. Glucose abundance during the growth phase enhanced acidification upon glucose depletion, via modulation of PKA activity. This actively controlled reduction in starvation pHc correlated with reduced stationary phase survival. Whereas changes in PKA activity affected both acidification and survival, targeted manipulation of starvation pHc showed that cytosolic acidification was downstream of PKA and the causal agent of the reduced chronological lifespan. Thus, caloric restriction controls stationary phase survival through PKA and cytosolic pH.
Collapse
Affiliation(s)
- Laura Dolz‐Edo
- Department of Molecular Biology and Microbial Food Safety Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam The Netherlands
| | - Margaretha van der Deen
- Department of Molecular Biology and Microbial Food Safety Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam The Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam The Netherlands
| | - Gertien Jacoba Smits
- Department of Molecular Biology and Microbial Food Safety Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam The Netherlands
| |
Collapse
|
30
|
Abstract
The small size of spores and the relatively low abundance of germination proteins, cause difficulties in their microscopic analyses using epifluorescence microscopy. Super-resolution three-dimensional Structured Illumination Microscopy (3D-SIM) is a promising tool to overcome this hurdle and reveal the molecular details of the process of germination of Bacillus subtilis (B. subtilis) spores. Here, we describe the use of a modified SIMcheck (ImageJ)-assistant 3D imaging process and fluorescent reporter proteins for SIM microscopy of B. subtilis spores' germinosomes, cluster(s) of germination proteins. We also present a (standard)3D-SIM imaging procedure for FM4-64 staining of B. subtilis spore membranes. By using these procedures, we obtained unsurpassed resolution for germinosome localization and show that >80% of B. subtilis KGB80 dormant spores obtained after sporulation on defined minimal MOPS medium have one or two GerD-GFP and GerKB-mCherry foci. Bright foci were also observed in FM4-64 stained spores' 3D-SIM images suggesting that inner membrane lipid domains of different fluidity likely exist. Further studies that use double labeling procedures with membrane dyes and germinosome reporter proteins to assess co-localization and thus get an optimal overview of the organization of Bacillus germination proteins in the inner spore membrane are possible.
Collapse
Affiliation(s)
- Juan Wen
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam
| | - Raymond Pasman
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam
| | - Erik M M Manders
- Van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam; Confocal.nl BV
| | - Peter Setlow
- Dept. of Molecular Biology and Biophysics, UConn Health
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam;
| |
Collapse
|
31
|
Hoeksema M, Jonker MJ, Brul S, Ter Kuile BH. Effects of a previously selected antibiotic resistance on mutations acquired during development of a second resistance in Escherichia coli. BMC Genomics 2019; 20:284. [PMID: 30975082 PMCID: PMC6458618 DOI: 10.1186/s12864-019-5648-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/27/2019] [Indexed: 12/19/2022] Open
Abstract
Background The effect of mutations conferring antibiotic resistance can depend on the genetic background. To determine if a previously de novo acquired antibiotic resistance influences the adaptation to a second antibiotic, antibiotic resistance was selected for by exposure to stepwise increasing sublethal levels of amoxicillin, enrofloxacin, kanamycin, or tetracycline. E. coli populations adapted to either a single or two antibiotics sequentially were characterized using whole genome population sequencing and MIC measurements. Results In a wild-type background, adaptation to any of the antibiotics resulted in the appearance of well-known mutations, as well as a number of mutated genes not known to be associated with antibiotic resistance. Development of a second resistance in a strain with an earlier acquired resistance to a different antibiotic did not always result in the appearance of all mutations associated with resistance in a wild-type background. In general, a more varied set of mutations was acquired during secondary adaptation. The ability of E. coli to maintain the first resistance during this process depended on the combination of antibiotics used. The maintenance of mutations associated with resistance to the first antibiotic did not always predict the residual MIC for that compound. Conclusions In general, the data presented here indicate that adaptation to each antibiotic is unique and independent. The mutational trajectories available in already resistant cells appear more varied than in wild-type cells, indicating that the genetic background of E. coli influences resistance development. The observed mutations cannot always fully explain the resistance pattern observed, indicating a crucial role for adaptation on the gene expression level in de novo acquisition of antibiotic resistance.
Collapse
Affiliation(s)
- Marloes Hoeksema
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijs J Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Benno H Ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands. .,Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, The Netherlands.
| |
Collapse
|
32
|
Hoeksema M, Jonker MJ, Bel K, Brul S, Ter Kuile BH. Genome rearrangements in Escherichia coli during de novo acquisition of resistance to a single antibiotic or two antibiotics successively. BMC Genomics 2018; 19:973. [PMID: 30591014 PMCID: PMC6307192 DOI: 10.1186/s12864-018-5353-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/07/2018] [Indexed: 11/25/2022] Open
Abstract
Background The ability of bacteria to acquire resistance to antibiotics relies to a large extent on their capacity for genome modification. Prokaryotic genomes are highly plastic and can utilize horizontal gene transfer, point mutations, and gene deletions or amplifications to realize genome expansion and rearrangements. The contribution of point mutations to de novo acquisition of antibiotic resistance is well-established. In this study, the internal genome rearrangement of Escherichia coli during to de novo acquisition of antibiotic resistance was investigated using whole-genome sequencing. Results Cells were made resistant to one of the four antibiotics and subsequently to one of the three remaining. This way the initial genetic rearrangements could be documented together with the effects of an altered genetic background on subsequent development of resistance. A DNA fragment including ampC was amplified by a factor sometimes exceeding 100 as a result of exposure to amoxicillin. Excision of prophage e14 was observed in many samples with a double exposure history, but not in cells exposed to a single antibiotic, indicating that the activation of the SOS stress response alone, normally the trigger for excision, was not sufficient to cause excision of prophage e14. Partial deletion of clpS and clpA occurred in strains exposed to enrofloxacin and tetracycline. Other deletions were observed in some strains, but not in replicates with the exact same exposure history. Various insertion sequence transpositions correlated with exposure to specific antibiotics. Conclusions Many of the genome rearrangements have not been reported before to occur during resistance development. The observed correlation between genome rearrangements and specific antibiotic pressure, as well as their presence in independent replicates indicates that these events do not occur randomly. Taken together, the observed genome rearrangements illustrate the plasticity of the E. coli genome when exposed to antibiotic stress. Electronic supplementary material The online version of this article (10.1186/s12864-018-5353-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Marloes Hoeksema
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijs J Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Keshia Bel
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Benno H Ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands. .,Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, The Netherlands.
| |
Collapse
|
33
|
Omardien S, Drijfhout JW, Vaz FM, Wenzel M, Hamoen LW, Zaat SA, Brul S. Bactericidal activity of amphipathic cationic antimicrobial peptides involves altering the membrane fluidity when interacting with the phospholipid bilayer. Biochimica et Biophysica Acta (BBA) - Biomembranes 2018; 1860:2404-2415. [DOI: 10.1016/j.bbamem.2018.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022]
|
34
|
Omardien S, Drijfhout JW, Zaat SA, Brul S. Cationic Amphipathic Antimicrobial Peptides Perturb the Inner Membrane of Germinated Spores Thus Inhibiting Their Outgrowth. Front Microbiol 2018; 9:2277. [PMID: 30319583 PMCID: PMC6168669 DOI: 10.3389/fmicb.2018.02277] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/06/2018] [Indexed: 11/13/2022] Open
Abstract
The mode of action of four cationic amphipathic antimicrobial peptides (AMPs) was evaluated against the non-pathogenic, Gram-positive, spore-forming bacterium, Bacillus subtilis. The AMPs were TC19, TC84, BP2, and the lantibiotic Nisin A. TC19 and TC84 were derived from the human thrombocidin-1. Bactericidal peptide 2 (BP2) was derived from the human bactericidal permeability increasing protein (BPI). We employed structured illumination microscopy (SIM), fluorescence microscopy, Alexa 488-labeled TC84, B. subtilis mutants producing proteins fused to the green fluorescent protein (GFP) and single-cell live imaging to determine the effects of the peptides against spores. TC19, TC84, BP2, and Nisin A showed to be bactericidal against germinated spores by perturbing the inner membrane, thus preventing outgrowth to vegetative cells. Single cell live imaging showed that the AMPs do not affect the germination process, but the burst time and subsequent generation time of vegetative cells. Alexa 488-labeled TC84 suggested that the TC84 might be binding to the dormant spore-coat. Therefore, dormant spores were also pre-coated with the AMPs and cultured on AMP-free culture medium during single-cell live imaging. Pre-coating of the spores with TC19, TC84, and BP2 had no effect on the germination process, and variably affected the burst time and generation time. However, the percentage of spores that burst and grew out into vegetative cells was drastically lower when pre-coated with Nisin A, suggesting a novel application potential of this lantibiotic peptide against spores. Our findings contribute to the understanding of AMPs and show the potential of AMPs as eventual therapeutic agents against spore-forming bacteria.
Collapse
Affiliation(s)
- Soraya Omardien
- Swammerdam Institute for Life Sciences, Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | | | - Sebastian A Zaat
- Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Stanley Brul
- Swammerdam Institute for Life Sciences, Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
35
|
Swarge BN, Roseboom W, Zheng L, Abhyankar WR, Brul S, de Koster CG, de Koning LJ. "One-Pot" Sample Processing Method for Proteome-Wide Analysis of Microbial Cells and Spores. Proteomics Clin Appl 2018; 12:e1700169. [PMID: 29484825 PMCID: PMC6174930 DOI: 10.1002/prca.201700169] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/22/2018] [Indexed: 11/15/2022]
Abstract
PURPOSE Bacterial endospores, the transmissible forms of pathogenic bacilli and clostridia, are heterogeneous multilayered structures composed of proteins. These proteins protect the spores against a variety of stresses, thus helping spore survival, and assist in germination, by interacting with the environment to form vegetative cells. Owing to the complexity, insolubility, and dynamic nature of spore proteins, it has been difficult to obtain their comprehensive protein profiles. EXPERIMENTAL DESIGN The intact spores of Bacillus subtilis, Bacillus cereus, and Peptoclostridium difficile and their vegetative counterparts were disrupted by bead beating in 6 m urea under reductive conditions. The heterogeneous mixture was then double digested with LysC and trypsin. Next, the peptide mixture was pre-fractionated with zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) followed by reverse-phase LC-FT-MS analysis of the fractions. RESULTS "One-pot" method is a simple, robust method that yields identification of >1000 proteins with high confidence, across all spore layers from B. subtilis, B. cereus, and P. difficile. CONCLUSIONS AND MEDICAL RELEVANCE This method can be employed for proteome-wide analysis of non-spore-forming as well as spore-forming pathogens. Analysis of spore protein profile will help to understand the sporulation and germination processes and to distinguish immunogenic protein markers.
Collapse
Affiliation(s)
- Bhagyashree Nandakishor Swarge
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Winfried Roseboom
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
| | - Linli Zheng
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Wishwas R Abhyankar
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institutes of Life Sciences, University of Amsterdam, The Netherlands
| | - Chris G de Koster
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
| | - Leo J de Koning
- Department of Mass Spectrometry of Bio macromolecules, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
36
|
Stelder SK, Benito de Moya C, Hoefsloot HCJ, de Koning LJ, Brul S, de Koster CG. Correction to “Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach”. J Proteome Res 2018; 17:2562. [PMID: 29856629 PMCID: PMC6150726 DOI: 10.1021/acs.jproteome.8b00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
37
|
Omardien S, Ter Beek A, Vischer N, Montijn R, Schuren F, Brul S. Evaluating novel synthetic compounds active against Bacillus subtilis and Bacillus cereus spores using Live imaging with SporeTrackerX. Sci Rep 2018; 8:9128. [PMID: 29904100 PMCID: PMC6002552 DOI: 10.1038/s41598-018-27529-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/05/2018] [Indexed: 11/12/2022] Open
Abstract
An empirical approach was taken to screen a novel synthetic compound library designed to be active against Gram-positive bacteria. We obtained five compounds that were active against spores from the model organism Bacillus subtilis and the food-borne pathogen Bacillus cereus during our population based experiments. Using single cell live imaging we were able to observe effects of the compounds on spore germination and outgrowth. Difference in sensitivity to the compounds could be observed between B. subtilis and B. cereus using live imaging, with minor difference in the minimal inhibitory and bactericidal concentrations of the compounds against the spores. The compounds all delayed the bursting time of germinated spores and affected the generation time of vegetative cells at sub-inhibitory concentrations. At inhibitory concentrations spore outgrowth was prevented. One compound showed an unexpected potential for preventing spore germination at inhibitory concentrations, which merits further investigation. Our study shows the valuable role single cell live imaging can play in the final selection process of antimicrobial compounds.
Collapse
Affiliation(s)
- Soraya Omardien
- Swammerdam Institute for Life Sciences, Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Alexander Ter Beek
- Swammerdam Institute for Life Sciences, Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Norbert Vischer
- Swammerdam Institute for Life Sciences, Department of Bacterial Cell Biology and Physiology, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Roy Montijn
- Microbiology and Systems Biology Group, TNO, Utrechtseweg 48, 3704HE, Zeist, The Netherlands
| | - Frank Schuren
- Microbiology and Systems Biology Group, TNO, Utrechtseweg 48, 3704HE, Zeist, The Netherlands
| | - Stanley Brul
- Swammerdam Institute for Life Sciences, Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
| |
Collapse
|
38
|
Abhyankar WR, Wen J, Swarge BN, Tu Z, de Boer R, Smelt JPPM, de Koning LJ, Manders E, de Koster CG, Brul S. Proteomics and microscopy tools for the study of antimicrobial resistance and germination mechanisms of bacterial spores. Food Microbiol 2018; 81:89-96. [PMID: 30910091 DOI: 10.1016/j.fm.2018.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/21/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
Abstract
Bacterial spores are ubiquitous in nature and can withstand both chemical and physical stresses. Spores can survive food preservation processes and upon outgrowth cause food spoilage as well as safety risks. The heterogeneous germination and outgrowth behavior of isogenic spore populations exacerbates this risk. A major unknown factor of spores is likely to be the inherently heterogeneous spore protein composition. The proteomics methods discussed here help in broadening the knowledge about spore structure and identification of putative target proteins from spores of different spore formers. Approaches to synchronize Bacillus subtilis spore formation, and to analyze spore proteins as well as the physiology of spore germination and outgrowth are also discussed. Live-imaging and fluorescence microscopy techniques discussed here allow analysis, at single cell level, of the 'germinosome', the process of spore germination itself, spore outgrowth and the spore intracellular pH dynamics. For the latter, a recently published improved pHluorin (IpHluorin) under control of the ptsG promoter is applicable. While the data obtained from such tools offers novel insight in the mechanisms of bacterial spore awakening, it may also be used to probe candidate antimicrobial compounds for inhibitory effects on spore germination and strengthen microbial risk assessment.
Collapse
Affiliation(s)
- W R Abhyankar
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - J Wen
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - B N Swarge
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Z Tu
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - R de Boer
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - J P P M Smelt
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - L J de Koning
- Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - E Manders
- Van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - C G de Koster
- Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - S Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| |
Collapse
|
39
|
Stelder SK, Benito de Moya C, Hoefsloot HCJ, de Koning LJ, Brul S, de Koster CG. Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach. J Proteome Res 2018; 17:903-917. [PMID: 29260567 PMCID: PMC5799878 DOI: 10.1021/acs.jproteome.7b00732] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Spores of Bacillus cereus pose a threat to food
safety due to their high resistance to the heat or acid treatments
commonly used to make food microbiologically safe. Spores may survive
these treatments and later resume growth either on foodstuffs or,
after ingestion, upon entering the gut they are capable of producing
toxins, which cause either vomiting or diarrhea. The outer layers
of the spore, the spore coat and exosporium, consist primarily of
proteins that may serve as potential biomarkers for detection. The
major morphogenetic protein CotE is important for correct assembly
and attachment of the outermost layer, the exosporium, and by extension
retention of many proteins. However, characterization of the proteins
affected by deletion of CotE has been limited to electrophoretic patterns.
Here we report the effect of CotE deletion on the insoluble fraction
of the spore proteome through liquid chromatography–Fourier
transform tandem mass spectrometry (LC–FTMS/MS) analysis. A total of 560 proteins have been identified in both mutant
and wild-type spore coat isolates. A further 163 proteins were identified
exclusively in wild-type spore isolates indicating that they are dependent
on CotE for their association with the spore. Several of these are
newly confirmed as associated with the exosporium, namely BC_2569
(BclF), BC_3345, BC_2427, BC_2878, BC_0666, BC_2984, BC_3481, and
BC_2570. A total of 153 proteins were only identified in ΔCotE
spore isolates. This was observed for proteins that are known or likely
to be interacting with or are encased by CotE. Crucial spore proteins
were quantified using a QconCAT reference standard, the first time
this was used in a biochemically heterogeneous system. This allowed
us to determine the absolute abundance of 21 proteins, which spanned
across three orders of magnitude and together covered 5.66% ±
0.51 of the total spore weight. Applying the QconCAT methodology to
the ΔCotE mutant allowed us to quantify 4.13% ± 0.14 of
the spore total weight and revealed a reduction in abundance for most
known exosporium associated proteins upon CotE deletion. In contrast,
several proteins, either known or likely to be interacting with or
encased by CotE (i.e., GerQ), were more abundant. The results obtained
provide deeper insight into the layered spore structure such as which
proteins are exposed on the outside of the spore. This information
is important for developing detection methods for targeting spores
in a food safety setting. Furthermore, protein stoichiometry and determination
of the abundance of germination mediating enzymes provides useful
information for germination and outgrowth model development.
Collapse
Affiliation(s)
- Sacha K Stelder
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Celia Benito de Moya
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Huub C J Hoefsloot
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Leo J de Koning
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Chris G de Koster
- Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| |
Collapse
|
40
|
Smith RL, Tan JME, Jonker MJ, Jongejan A, Buissink T, Veldhuijzen S, van Kampen AHC, Brul S, van der Spek H. Beyond the polymerase-γ theory: Production of ROS as a mode of NRTI-induced mitochondrial toxicity. PLoS One 2017; 12:e0187424. [PMID: 29095935 PMCID: PMC5667870 DOI: 10.1371/journal.pone.0187424] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/19/2017] [Indexed: 12/17/2022] Open
Abstract
Use of some HIV-1 nucleoside reverse transcriptase inhibitors (NRTI) is associated with severe adverse events. However, the exact mechanisms behind their toxicity has not been fully understood. Mitochondrial dysfunction after chronic exposure to specific NRTIs has predominantly been assigned to mitochondrial polymerase-γ inhibition by NRTIs. However, an increasing amount of data suggests that this is not the sole mechanism. Many NRTI induced adverse events have been linked to the incurrence of oxidative stress, although the causality of events leading to reactive oxygen species (ROS) production and their role in toxicity is unclear. In this study we show that short-term effects of first generation NRTIs, which are rarely discussed in the literature, include inhibition of oxygen consumption, decreased ATP levels and increased ROS production. Collectively these events affect fitness and longevity of C. elegans through mitohormetic signalling events. Furthermore, we demonstrate that these effects can be normalized by addition of the anti-oxidant N-acetylcysteine (NAC), which suggests that ROS likely influence the onset and severity of adverse events upon drug exposure.
Collapse
Affiliation(s)
- Reuben L. Smith
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Amsterdam, The Netherlands
| | - Josephine M. E. Tan
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Amsterdam, The Netherlands
| | - Martijs J. Jonker
- RNA Biology & Applied Bioinformatics, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Thomas Buissink
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Amsterdam, The Netherlands
| | - Steve Veldhuijzen
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Amsterdam, The Netherlands
| | - Antoine H. C. van Kampen
- Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center (AMC), Amsterdam, The Netherlands
- Biosystems data analysis, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Amsterdam, The Netherlands
| | - Stanley Brul
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Amsterdam, The Netherlands
| | - Hans van der Spek
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
41
|
Feng Y, Bakker RT, van Hest RM, Hodiamont CJ, Brul S, Schultsz C, ter Kuile BH. Optimization of therapy against Pseudomonas aeruginosa with ceftazidime and meropenem using chemostats as model for infections. FEMS Microbiol Lett 2017; 364:3906681. [DOI: 10.1093/femsle/fnx142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/28/2017] [Indexed: 12/24/2022] Open
Abstract
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can cause life-threatening infections in patients admitted to intensive care units. Resistance rapidly develops against two drugs of choice: ceftazidime and meropenem. Several therapeutic protocols were compared for reduction in viable cells and limiting development of resistance. Chemostat cultures were exposed to antibiotic concentrations measured in the blood of patients at low (5th percentile), medium (50th percentile) or high (95th percentile) levels in several therapy protocols to simulate therapy. Cultures exposed to ceftazidime recovered after 1 day at low, 2 days at medium and 3 days at high concentrations and developed corresponding levels of resistance. Patterns were very similar for meropenem except that recovery was delayed. Fluctuating levels and intermittent treatment achieved similar reduction of cell numbers at lower resistance costs. Treatment alternating ceftazidime and meropenem reduced cell numbers more than monotherapy, while strongly limiting resistance. Combination therapy was even more effective in both respects. Therapeutic goals are best reached with least risk of resistance when ceftazidime and meropenem are used in combination or alternating, at the highest concentrations the patient can endure. Monotherapy should also apply the highest concentration that is safe for the shortest time that achieves treatment objectives.
Collapse
Affiliation(s)
- Yanfang Feng
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Roosmarijn T Bakker
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Reinier M van Hest
- Department of Hospital Pharmacy & Clinical Pharmacology, Academic Medical Center, Amsterdam 1105AZ, the Netherlands
| | - Caspar J Hodiamont
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105AZ, the Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Constance Schultsz
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105AZ, the Netherlands
- Department of Global Health-Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam 1105AZ, the Netherlands
| | - Benno H ter Kuile
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
- Office for Risk Assessment and Research Coordination Netherlands Food and Consumer Product Safety Authority, Utrecht 3511GG, the Netherlands
| |
Collapse
|
42
|
van Beilen J, Blohmke CJ, Folkerts H, de Boer R, Zakrzewska A, Kulik W, Vaz FM, Brul S, Ter Beek A. RodZ and PgsA Play Intertwined Roles in Membrane Homeostasis of Bacillus subtilis and Resistance to Weak Organic Acid Stress. Front Microbiol 2016; 7:1633. [PMID: 27818647 PMCID: PMC5073135 DOI: 10.3389/fmicb.2016.01633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/30/2016] [Indexed: 11/16/2022] Open
Abstract
Weak organic acids like sorbic and acetic acid are widely used to prevent growth of spoilage organisms such as Bacilli. To identify genes involved in weak acid stress tolerance we screened a transposon mutant library of Bacillus subtilis for sorbic acid sensitivity. Mutants of the rodZ (ymfM) gene were found to be hypersensitive to the lipophilic weak organic acid. RodZ is involved in determining the cell's rod-shape and believed to interact with the bacterial actin-like MreB cytoskeleton. Since rodZ lies upstream in the genome of the essential gene pgsA (phosphatidylglycerol phosphate synthase) we hypothesized that expression of the latter might also be affected in rodZ mutants and hence contribute to the phenotype observed. We show that both genes are co-transcribed and that both the rodZ::mini-Tn10 mutant and a conditional pgsA mutant, under conditions of minimal pgsA expression, were sensitive to sorbic and acetic acid. Both strains displayed a severely altered membrane composition. Compared to the wild-type strain, phosphatidylglycerol and cardiolipin levels were lowered and the average acyl chain length was elongated. Induction of rodZ expression from a plasmid in our transposon mutant led to no recovery of weak acid susceptibility comparable to wild-type levels. However, pgsA overexpression in the same mutant partly restored sorbic acid susceptibility and fully restored acetic acid sensitivity. A construct containing both rodZ and pgsA as on the genome led to some restored growth as well. We propose that RodZ and PgsA play intertwined roles in membrane homeostasis and tolerance to weak organic acid stress.
Collapse
Affiliation(s)
- Johan van Beilen
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Christoph J. Blohmke
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Hendrik Folkerts
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Richard de Boer
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Anna Zakrzewska
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Wim Kulik
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of AmsterdamAmsterdam, Netherlands
| | - Fred M. Vaz
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of AmsterdamAmsterdam, Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Alexander Ter Beek
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| |
Collapse
|
43
|
Omardien S, Brul S, Zaat SAJ. Antimicrobial Activity of Cationic Antimicrobial Peptides against Gram-Positives: Current Progress Made in Understanding the Mode of Action and the Response of Bacteria. Front Cell Dev Biol 2016; 4:111. [PMID: 27790614 PMCID: PMC5063857 DOI: 10.3389/fcell.2016.00111] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 09/21/2016] [Indexed: 01/11/2023] Open
Abstract
Antimicrobial peptides (AMPs) have been proposed as a novel class of antimicrobials that could aid the fight against antibiotic resistant bacteria. The mode of action of AMPs as acting on the bacterial cytoplasmic membrane has often been presented as an enigma and there are doubts whether the membrane is the sole target of AMPs. Progress has been made in clarifying the possible targets of these peptides, which is reported in this review with as focus gram-positive vegetative cells and spores. Numerical estimates are discussed to evaluate the possibility that targets, other than the membrane, could play a role in susceptibility to AMPs. Concerns about possible resistance that bacteria might develop to AMPs are addressed. Proteomics, transcriptomics, and other molecular techniques are reviewed in the context of explaining the response of bacteria to the presence of AMPs and to predict what resistance strategies might be. Emergent mechanisms are cell envelope stress responses as well as enzymes able to degrade and/or specifically bind (and thus inactivate) AMPs. Further studies are needed to address the broadness of the AMP resistance and stress responses observed.
Collapse
Affiliation(s)
- Soraya Omardien
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam, Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam, Netherlands
| | - Sebastian A J Zaat
- Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam Amsterdam, Netherlands
| |
Collapse
|
44
|
Abhyankar WR, Kamphorst K, Swarge BN, van Veen H, van der Wel NN, Brul S, de Koster CG, de Koning LJ. The Influence of Sporulation Conditions on the Spore Coat Protein Composition of Bacillus subtilis Spores. Front Microbiol 2016; 7:1636. [PMID: 27790212 PMCID: PMC5061772 DOI: 10.3389/fmicb.2016.01636] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/30/2016] [Indexed: 11/20/2022] Open
Abstract
Spores are of high interest to the food and health sectors because of their extreme resistance to harsh conditions, especially against heat. Earlier research has shown that spores prepared on solid agar plates have a higher heat resistance than those prepared under a liquid medium condition. It has also been shown that the more mature a spore is, the higher is its heat resistance most likely mediated, at least in part, by the progressive cross-linking of coat proteins. The current study for the first time assesses, at the proteomic level, the effect of two commonly used sporulation conditions on spore protein presence. 14N spores prepared on solid Schaeffer’s-glucose (SG) agar plates and 15N metabolically labeled spores prepared in shake flasks containing 3-(N-morpholino) propane sulfonic acid (MOPS) buffered defined liquid medium differ in their coat protein composition as revealed by LC-FT-MS/MS analyses. The former condition mimics the industrial settings while the latter conditions mimic the routine laboratory environment wherein spores are developed. As seen previously in many studies, the spores prepared on the solid agar plates show a higher thermal resistance than the spores prepared under liquid culture conditions. The 14N:15N isotopic ratio of the 1:1 mixture of the spore suspensions exposes that most of the identified inner coat and crust proteins are significantly more abundant while most of the outer coat proteins are significantly less abundant for the spores prepared on solid SG agar plates relative to the spores prepared in the liquid MOPS buffered defined medium. Sporulation condition-specific differences and variation in isotopic ratios between the tryptic peptides of expected cross-linked proteins suggest that the coat protein cross-linking may also be condition specific. Since the core dipicolinic acid content is found to be similar in both the spore populations, it appears that the difference in wet heat resistance is connected to the differences in the coat protein composition and assembly. Corroborating the proteomic analyses, electron microscopy analyses show a significantly thinner outer coat layer of the spores cultured on the solid agar medium.
Collapse
Affiliation(s)
- Wishwas R Abhyankar
- Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands; Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Kiki Kamphorst
- Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam, Netherlands
| | - Bhagyashree N Swarge
- Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands; Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Henk van Veen
- Department of Cell Biology and Histology, Electron Microscopy Centre Amsterdam, Academic Medical Center Amsterdam, Netherlands
| | - Nicole N van der Wel
- Department of Cell Biology and Histology, Electron Microscopy Centre Amsterdam, Academic Medical Center Amsterdam, Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam, Netherlands
| | - Chris G de Koster
- Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam, Netherlands
| | - Leo J de Koning
- Department of Mass Spectrometry of Bio-macromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam, Netherlands
| |
Collapse
|
45
|
Ter Kuile BH, Kraupner N, Brul S. The risk of low concentrations of antibiotics in agriculture for resistance in human health care. FEMS Microbiol Lett 2016; 363:fnw210. [PMID: 27609231 DOI: 10.1093/femsle/fnw210] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
The contribution of antibiotic resistance originally selected for in the agricultural sector to resistance in human pathogens is not known exactly, but is unlikely to be negligible. It is estimated that 50% to 80% of all antibiotics used are applied in agriculture and the remainder for treating infections in humans. Since dosing regimens are less controlled in agriculture than in human health care, veterinary and environmental microbes are often exposed to sublethal levels of antibiotics. Exposure to sublethal drug concentrations must be considered a risk factor for de novo resistance, transfer of antimicrobial resistant (AMR) genes, and selection for already existing resistance. Resistant zoonotic agents and commensal strains carrying AMR genes reach the human population by a variety of routes, foodstuffs being only one of these. Based on the present knowledge, short treatments with the highest dose that does not cause unacceptable side-effects may be optimal for achieving therapeutic goals while minimizing development of resistance. Novel approaches such as combination or alternating therapy are promising, but need to be explored further before they can be implemented in daily practice.
Collapse
Affiliation(s)
- Benno H Ter Kuile
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute of Life Sciences, 1098 XH, Amsterdam, the Netherlands Office for Risk Assessment and Research, Netherlands Food and Consumer Product Safety Authority, Catharijnesingel 59, 3511 GG Utrecht, the Netherlands
| | - Nadine Kraupner
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute of Life Sciences, 1098 XH, Amsterdam, the Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, University of Amsterdam, Swammerdam Institute of Life Sciences, 1098 XH, Amsterdam, the Netherlands
| |
Collapse
|
46
|
Brul S. Editorial overview: The rise of the ‘omics’ technologies and their relevance to food. Curr Opin Food Sci 2016. [DOI: 10.1016/j.cofs.2016.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
47
|
Feng Y, Hodiamont CJ, van Hest RM, Brul S, Schultsz C, ter Kuile BH. Development of Antibiotic Resistance during Simulated Treatment of Pseudomonas aeruginosa in Chemostats. PLoS One 2016; 11:e0149310. [PMID: 26872140 PMCID: PMC4752458 DOI: 10.1371/journal.pone.0149310] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/29/2016] [Indexed: 11/24/2022] Open
Abstract
During treatment of infections with antibiotics in critically ill patients in the intensive care resistance often develops. This study aims to establish whether under those conditions this resistance can develop de novo or that genetic exchange between bacteria is by necessity involved. Chemostat cultures of Pseudomonas aeruginosa were exposed to treatment regimes with ceftazidime and meropenem that simulated conditions expected in patient plasma. Development of antibiotic resistance was monitored and mutations in resistance genes were searched for by sequencing PCR products. Even at the highest concentrations that can be expected in patients, sufficient bacteria survived in clumps of filamentous cells to recover and grow out after 3 to 5 days. At the end of a 7 days simulated treatment, the minimal inhibitory concentration (MIC) had increased by a factor between 10 and 10,000 depending on the antibiotic and the treatment protocol. The fitness costs of resistance were minimal. In the resistant strains, only three mutations were observed in genes associated with beta-lactam resistance. The development of resistance often observed during patient treatment can be explained by de novo acquisition of resistance and genetic exchange of resistance genes is not by necessity involved. As far as conclusions based on an in vitro study using P. aeruginosa and only two antibiotics can be generalized, it seems that development of resistance can be minimized by treating with antibiotics in the highest concentration the patient can endure for the shortest time needed to eliminate the infection.
Collapse
Affiliation(s)
- Yanfang Feng
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Caspar J. Hodiamont
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Reinier M. van Hest
- Department of Hospital Pharmacy & Clinical Pharmacology, Academic Medical Center, Amsterdam, the Netherlands
| | - Stanley Brul
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Constance Schultsz
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
- Department of Global Health-Amsterdam Institute for Global Health and Development, Academic Medical Center, Amsterdam, The Netherlands
| | - Benno H. ter Kuile
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Office for Risk Assessment and Research Coordination Netherlands Food and Consumer Product Safety Authority, Utrecht, The Netherlands
- * E-mail: ;
| |
Collapse
|
48
|
Zheng L, Abhyankar W, Ouwerling N, Dekker HL, van Veen H, van der Wel NN, Roseboom W, de Koning LJ, Brul S, de Koster CG. Bacillus subtilis Spore Inner Membrane Proteome. J Proteome Res 2016; 15:585-94. [PMID: 26731423 DOI: 10.1021/acs.jproteome.5b00976] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The endospore is the dormant form of Bacillus subtilis and many other Firmicutes. By sporulation, these spore formers can survive very harsh physical and chemical conditions. Yet, they need to go through germination to return to their growing form. The spore inner membrane (IM) has been shown to play an essential role in triggering the initiation of germination. In this study, we isolated the IM of bacterial spores, in parallel with the isolation of the membrane of vegetative cells. With the use of GeLC-MS/MS, over 900 proteins were identified from the B. subtilis spore IM preparations. By bioinformatics-based membrane protein predictions, ca. one-third could be predicted to be membrane-localized. A large number of unique proteins as well as proteins common to the two membrane proteomes were identified. In addition to previously known IM proteins, a number of IM proteins were newly identified, at least some of which are likely to provide new insights into IM physiology, unveiling proteins putatively involved in spore germination machinery and hence putative germination inhibition targets.
Collapse
Affiliation(s)
| | | | | | | | - Henk van Veen
- Electron Microscopy Centre Amsterdam, Department of Cell Biology and Histology, Academic Medical Center , 1105 AZ Amsterdam, The Netherlands
| | - Nicole N van der Wel
- Electron Microscopy Centre Amsterdam, Department of Cell Biology and Histology, Academic Medical Center , 1105 AZ Amsterdam, The Netherlands
| | | | | | | | | |
Collapse
|
49
|
Pandey R, Pieper GH, Beek AT, Vischer NO, Smelt JP, Manders EM, Brul S. Quantifying the effect of sorbic acid, heat and combination of both on germination and outgrowth of Bacillus subtilis spores at single cell resolution. Food Microbiol 2015; 52:88-96. [DOI: 10.1016/j.fm.2015.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 05/10/2015] [Accepted: 06/19/2015] [Indexed: 11/26/2022]
|
50
|
de Boer R, Smith RL, De Vos WH, Manders EMM, Brul S, van der Spek H. Caenorhabditis elegans as a Model System for Studying Drug Induced Mitochondrial Toxicity. PLoS One 2015; 10:e0126220. [PMID: 25970180 PMCID: PMC4430419 DOI: 10.1371/journal.pone.0126220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 03/30/2015] [Indexed: 01/23/2023] Open
Abstract
Today HIV-1 infection is recognized as a chronic disease with obligatory lifelong treatment to keep viral titers below detectable levels. The continuous intake of antiretroviral drugs however, leads to severe and even life-threatening side effects, supposedly by the deleterious impact of nucleoside-analogue type compounds on the functioning of the mitochondrial DNA polymerase. For detailed investigation of the yet partially understood underlying mechanisms, the availability of a versatile model system is crucial. We therefore set out to develop the use of Caenorhabditis elegans to study drug induced mitochondrial toxicity. Using a combination of molecular-biological and functional assays, combined with a quantitative analysis of mitochondrial network morphology, we conclude that anti-retroviral drugs with similar working mechanisms can be classified into distinct groups based on their effects on mitochondrial morphology and biochemistry. Additionally we show that mitochondrial toxicity of antiretroviral drugs cannot be exclusively attributed to interference with the mitochondrial DNA polymerase.
Collapse
Affiliation(s)
- Richard de Boer
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Ruben L. Smith
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Winnok H. De Vos
- Cell Biology and Histology Group, Department of Veterinary Sciences, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
- Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, Coupure Links, 653, 9000, Ghent, Belgium
| | - Erik M. M. Manders
- van Leeuwenhoek Center for Advanced Microscopy, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Hans van der Spek
- Molecular Biology & Microbial Food Safety, Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|