1
|
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
|
2
|
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
|
3
|
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
|
4
|
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
|
5
|
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
|
6
|
Kolet SP, Jadhav DD, Priyadarshini B, Swarge BN, Thulasiram HV. Fungi mediated production and practical purification of (R)-(−)-3-quinuclidinol. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|