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Smart microscopes spot fleeting biology. Nature 2023; 614:378-380. [PMID: 36750675 DOI: 10.1038/d41586-023-00336-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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2
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Labana P, Dornan MH, Lafrenière M, Czarny TL, Brown ED, Pezacki JP, Boddy CN. Armeniaspirols inhibit the AAA+ proteases ClpXP and ClpYQ leading to cell division arrest in Gram-positive bacteria. Cell Chem Biol 2021; 28:1703-1715.e11. [PMID: 34293284 DOI: 10.1016/j.chembiol.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/22/2021] [Accepted: 06/29/2021] [Indexed: 01/16/2023]
Abstract
Multi-drug-resistant bacteria present an urgent threat to modern medicine, creating a desperate need for antibiotics with new modes of action. As natural products remain an unsurpassed source for clinically viable antibiotic compounds, we investigate the mechanism of action of armeniaspirol. The armeniaspirols are a structurally unique class of Gram-positive antibiotic discovered from Streptomyces armeniacus for which resistance cannot be readily obtained. We show that armeniaspirol inhibits the ATP-dependent proteases ClpXP and ClpYQ in vitro and in the model Gram-positive Bacillus subtilis. This inhibition dysregulates the divisome and elongasome supported by an upregulation of key proteins FtsZ, DivIVA, and MreB inducing cell division arrest. The inhibition of ClpXP and ClpYQ to dysregulate cell division represents a unique antibiotic mechanism of action and armeniaspirol is the only known natural product inhibitor of the coveted anti-virulence target ClpP. Thus, armeniaspirol possesses a promising lead scaffold for antibiotic development with unique pharmacology.
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Affiliation(s)
- Puneet Labana
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Mark H Dornan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Matthew Lafrenière
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tomasz L Czarny
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - John P Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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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] [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.
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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;
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Wang M, Yu H, Li X, Shen Z. Single-gene regulated non-spore-forming Bacillus subtilis: Construction, transcriptome responses, and applications for producing enzymes and surfactin. Metab Eng 2020; 62:235-248. [DOI: 10.1016/j.ymben.2020.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 01/01/2023]
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Alteration of Proteomes in First-Generation Cultures of Bacillus pumilus Spores Exposed to Outer Space. mSystems 2019; 4:4/4/e00195-19. [PMID: 31186338 PMCID: PMC6561321 DOI: 10.1128/msystems.00195-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bacillus pumilus SAFR-032 was originally isolated from the Jet Propulsion Lab Spacecraft Assembly Facility and thoroughly characterized for its enhanced resistance to UV irradiation and oxidative stress. This unusual resistance of SAFR-032 is of particular concern in the context of planetary protection and calls for development of novel disinfection techniques to prevent extraterrestrial contamination. Previously, spores of SAFR-032 were exposed for 18 months to a variety of space conditions on board the International Space Station to investigate their resistance to Mars-like conditions and space travel. Here, proteomic characterization of vegetative SAFR-032 cells from space-surviving spores is presented in comparison to a ground control. Vegetative cells of the first passage were processed and subjected to quantitative proteomics using tandem mass tags. Approximately 60% of all proteins encoded by SAFR-032 were identified, and 301 proteins were differentially expressed among the strains. We found that proteins predicted to be involved in carbohydrate transport/metabolism and energy production/conversion had lower abundance than those of the ground control. For three proteins, we showed that the expected metabolic activities were decreased, as expected with direct enzymatic assays. This was consistent with a decrease of ATP production in the space-surviving strains. The same space-surviving strains showed increased abundance of proteins related to survival, growth advantage, and stress response. Such alterations in the proteomes provide insights into possible molecular mechanisms of B. pumilus SAFR-032 to adapt to and resist extreme extraterrestrial environments.IMPORTANCE Spore-forming bacteria are well known for their resistance to harsh environments and are of concern for spreading contamination to extraterrestrial bodies during future life detection missions. Bacillus pumilus has been regularly isolated from spacecraft-associated surfaces and exhibited unusual resistance to ultraviolet light and other sterilization techniques. A better understanding of the mechanisms of microbial survival and enhanced resistance is essential for developing novel disinfection protocols for the purpose of planetary protection. While genomic analyses did not reveal the unique characteristics that explain elevated UV resistance of space-exposed B. pumilus, the proteomics study presented here provided intriguing insight on key metabolic changes. The observed proteomics aberrations reveal a complex biological phenomenon that plays a role in bacterial survival and adaptation under long-term exposure to outer space. This adaptive ability of microorganisms needs to be considered by those tasked with eliminating forward contamination.
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Sun QL, Sun YY, Zhang J, Luan ZD, Lian C, Liu SQ, Yu C. High temperature-induced proteomic and metabolomic profiles of a thermophilic Bacillus manusensis isolated from the deep-sea hydrothermal field of Manus Basin. J Proteomics 2019; 203:103380. [PMID: 31102757 DOI: 10.1016/j.jprot.2019.103380] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/16/2019] [Accepted: 05/06/2019] [Indexed: 12/23/2022]
Abstract
Thermophiles are organisms that grow optimally at 50 °C-80 °C and studies on the survival mechanisms of thermophiles have drawn great attention. Bacillus manusensis S50-6 is the type strain of a new thermophilic species isolated from hydrothermal vent in Manus Basin. In this study, we examined the growth and global responses of S50-6 to high temperature on molecular level using multi-omics method (genomics, proteomics, and metabolomics). S50-6 grew optimally at 50 °C (Favorable, F) and poorly at 65 °C (Non-Favorable, NF); it formed spores at F but not at NF condition. At NF condition, S50-6 formed long filaments containing undivided cells. A total of 1621 proteins were identified at F and NF conditions, and 613 proteins were differentially expressed between F and NF. At NF condition, proteins of glycolysis, rRNA mature and modification, and DNA/protein repair were up-regulated, whereas proteins of sporulation and amino acid/nucleotide metabolism were down-regulated. Consistently, many metabolites associated with amino acid and nucleotide metabolic processes were down-regulated at NF condition. Our results revealed molecular strategies of deep-sea B. manusensis to survive at unfavorable high temperature and provided new insights into the thermotolerant mechanisms of thermophiles. SIGNIFICANCE: In this study, we systematically characterized the genomic, proteomic and metabolomic profiles of a thermophilic deep-sea Bacillus manusensis under different temperatures. Based on these analysis, we propose a model delineating the global responses of B. manusensis to unfavorable high temperature. Under unfavorable high temperature, glycolysis is a more important energy supply pathway; protein synthesis is subjected to more stringent regulation by increased tRNA modification; protein and DNA repair associated proteins are enhanced in production to promote heat survival. In contrast, energy-costing pathways, such as sporulation, are repressed, and basic metabolic pathways, such as amino acid and nucleotide metabolisms, are slowed down. Our results provide new insights into the thermotolerant mechanisms of thermophilic Bacillus.
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Affiliation(s)
- Qing-Lei Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Yuan-Yuan Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhen-Dong Luan
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Chao Lian
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Shi-Qi Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Chao Yu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
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Culley S, Tosheva KL, Matos Pereira P, Henriques R. SRRF: Universal live-cell super-resolution microscopy. Int J Biochem Cell Biol 2018; 101:74-79. [PMID: 29852248 PMCID: PMC6025290 DOI: 10.1016/j.biocel.2018.05.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 11/30/2022]
Abstract
Super-resolution microscopy techniques break the diffraction limit of conventional optical microscopy to achieve resolutions approaching tens of nanometres. The major advantage of such techniques is that they provide resolutions close to those obtainable with electron microscopy while maintaining the benefits of light microscopy such as a wide palette of high specificity molecular labels, straightforward sample preparation and live-cell compatibility. Despite this, the application of super-resolution microscopy to dynamic, living samples has thus far been limited and often requires specialised, complex hardware. Here we demonstrate how a novel analytical approach, Super-Resolution Radial Fluctuations (SRRF), is able to make live-cell super-resolution microscopy accessible to a wider range of researchers. We show its applicability to live samples expressing GFP using commercial confocal as well as laser- and LED-based widefield microscopes, with the latter achieving long-term timelapse imaging with minimal photobleaching.
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Affiliation(s)
- Siân Culley
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK; Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kalina L Tosheva
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK; Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Pedro Matos Pereira
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK; Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK; Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK; The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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Vega-Cabrera LA, Wood CD, Pardo-López L. Spo0M: structure and function beyond regulation of sporulation. Curr Genet 2017; 64:17-23. [PMID: 28577219 DOI: 10.1007/s00294-017-0718-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/29/2022]
Abstract
In this mini-review, we present a perspective on the recent findings relating Spo0M structure and function that will stimulate and guide further studies in the characterization of this interesting protein. Cell division and sporulation constitute two of the best studied processes in the model organism Bacillus subtilis; however, there are many missing pieces in the giant regulatory puzzle that governs the independent and shared networks between them. Spo0M is a little studied protein that has been related to both, cell division and sporulation, but its biochemical function and its direct interactions have not been yet defined. Structural analysis of Spo0M revealed the presence of an arrestin-like domain and an FP domain (a dimerization domain present in proteasome elements), motifs more commonly found in eukaryotic proteins. The aim of this perspective is to present open questions regarding the functional and structural features of Spo0M that make this protein a good candidate for the ancestor of arrestins in bacteria and an important element in developmental and differentiation processes of Bacillus subtilis.
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Affiliation(s)
- Luz Adriana Vega-Cabrera
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Apdo. Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Christopher D Wood
- Laboratorio Nacional de Microscopía Avanzada, Universidad Nacional Autónoma de México, Av. Universidad #2001, Apdo. Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Liliana Pardo-López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Apdo. Postal 510-3, 62250, Cuernavaca, Morelos, Mexico.
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