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Pospíšil J, Sax A, Hubálek M, Krásný L, Vohradský J. Whole proteome analysis of germinating and outgrowing Bacillus subtilis 168. Proteomics 2024:e2400031. [PMID: 39044338 DOI: 10.1002/pmic.202400031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/21/2024] [Accepted: 07/08/2024] [Indexed: 07/25/2024]
Abstract
In this study, we present a high-resolution dataset and bioinformatic analysis of the proteome of Bacillus subtilis 168 trp+ (BSB1) during germination and spore outgrowth. Samples were collected at 14 different time points (ranging from 0 to 130 min) in three biological replicates after spore inoculation into germination medium. A total of 2191 proteins were identified and categorized based on their expression kinetics. We observed four distinct clusters that were analyzed for functional categories and KEGG pathways annotations. The examination of newly synthesized proteins between successive time points revealed significant changes, particularly within the first 50 min. The dataset provides an information base that can be used for modeling purposes and inspire the design of new experiments.
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Affiliation(s)
- Jiří Pospíšil
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Alice Sax
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Jiří Vohradský
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
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2
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Cui Z, Kawada M, Hui Y, Sim S. Programming aliphatic polyester degradation by engineered bacterial spores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603759. [PMID: 39071336 PMCID: PMC11275931 DOI: 10.1101/2024.07.16.603759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Enzymatic degradation of plastics is a sustainable approach to addressing the growing issue of plastic accumulation. The primary challenges for using enzymes as catalysts are issues with their stability and recyclability, further exacerbated by their costly production and delicate structures. Here, we demonstrate an approach that leverages engineered spores that display target enzymes in high density on their surface to catalyze aliphatic polyester degradation and create self-degradable materials. Engineered spores display recombinant enzymes on their surface, eliminating the need for costly purification processes. The intrinsic physical and biological characteristics of spores enable easy separation from the reaction mixture, repeated reuse, and renewal. Engineered spores displaying lipases completely degrade aliphatic polyesters and retain activity through four cycles, with full activity recovered through germination and sporulation. Directly incorporating spores into polyesters results in robust materials that are completely degradable. Our study offers a straightforward and sustainable biocatalytic approach to plastic degradation.
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Liu S, Zhao L, Li M, Zhu Y, Liang D, Ma Y, Sun L, Zhao G, Tu Q. Probiotic Bacillus as fermentation agents: Status, potential insights, and future perspectives. Food Chem X 2024; 22:101465. [PMID: 38798797 PMCID: PMC11127159 DOI: 10.1016/j.fochx.2024.101465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
Probiotic Bacillus strains can solve the problems of single flavor and long fermentation time of fermented products caused by the lack of certain functional genes and insufficient metabolism ability of fermenter strains (Lactobacillus and Bifidobacterium) at the present stage. There is a lack of systematic evaluation and review of probiotic Bacillus as food fermentation agents. In this paper, it is observed that probiotic Bacillus strains are involved to varying degrees in liquid-state, semi-solid state, and solid-state fermentation and are widely present in solid-state fermented foods. Probiotic Bacillus strains not only produce abundant proteases and lipases, but also effective antifungal lipopeptides and extracellular polymers, thus enhancing the flavor, nutritional value and safety of fermented foods. Bacillus with probiotic qualities is an underutilized group of probiotic food fermentation agents, which give a potential for the development of fermentation technology in the food business and the integration of ancient traditional fermentation techniques.
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Affiliation(s)
- Shijie Liu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China
- International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Lijun Zhao
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China
- International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Miaoyun Li
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China
- International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Yaodi Zhu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China
- International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Dong Liang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China
- International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Yangyang Ma
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China
- International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - LingXia Sun
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China
- International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Gaiming Zhao
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China
- International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Qiancheng Tu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China
- International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
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Liu S, Zhu Y, Zhao L, Li M, Liang D, Li M, Zhao G, Ma Y, Tu Q. Characteristic substance analysis and rapid detection of bacteria spores in cooked meat products by surface enhanced Raman scattering based on Ag@AuNP array substrate. Anal Chim Acta 2024; 1308:342616. [PMID: 38740451 DOI: 10.1016/j.aca.2024.342616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/13/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Bacterial spores are the main potential hazard in medium- and high-temperature sterilized meat products, and their germination and subsequent reproduction and metabolism can lead to food spoilage. Moreover, the spores of some species pose a health and safety threat to consumers. The rapid detection, prevention, and control of bacterial spores has always been a scientific problem and a major challenge for the medium and high-temperature meat industry. Early and sensitive identification of spores in meat products is a decisive factor in contributing to consumer health and safety. RESULTS In this study, we developed a novel and stable Ag@AuNP array substrate by using a two-step synthesis approach and a liquid-interface self-assembly method that can directly detect bacterial spores in actual meat product samples without the need for additional in vitro bacterial culture. The results indicate that the Ag@AuNP array substrate exhibits high reproducibility and Raman enhancement effects (1.35 × 105). The differentiation in the Surface enhanced Raman scattering (SERS) spectra of five bacterial spores primarily arises from proteins in the spore coat and inner membrane, peptidoglycan of cortex, and Ca2⁺-DPA within the spore core. The correct recognition rate of linear discriminant analysis for spores in the meat product matrix can reach 100 %. The average recovery accuracy of the SERS quantitative model was at around 101.77 %, and the limit of detection can reach below 10 CFU/mL. SIGNIFICANCE It provides a promising technological strategy for the characteristic substance analysis and timely monitoring of spores in meat products.
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Affiliation(s)
- Shijie Liu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Yaodi Zhu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Lijun Zhao
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Miaoyun Li
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China.
| | - Dong Liang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Mengya Li
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Gaiming Zhao
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Yangyang Ma
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Qiancheng Tu
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China; International Joint Laboratory of Meat Processing and Safety in Henan Province, Henan Agricultural University, Zhengzhou, 450002, PR China
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Shrestha A, Mehdizadeh Gohari I, Li J, Navarro M, Uzal FA, McClane BA. The biology and pathogenicity of Clostridium perfringens type F: a common human enteropathogen with a new(ish) name. Microbiol Mol Biol Rev 2024:e0014023. [PMID: 38864615 DOI: 10.1128/mmbr.00140-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024] Open
Abstract
SUMMARYIn the 2018-revised Clostridium perfringens typing classification system, isolates carrying the enterotoxin (cpe) and alpha toxin genes but no other typing toxin genes are now designated as type F. Type F isolates cause food poisoning and nonfoodborne human gastrointestinal (GI) diseases, which most commonly involve type F isolates carrying, respectivefooly, a chromosomal or plasmid-borne cpe gene. Compared to spores of other C. perfringens isolates, spores of type F chromosomal cpe isolates often exhibit greater resistance to food environment stresses, likely facilitating their survival in improperly prepared or stored foods. Multiple factors contribute to this spore resistance phenotype, including the production of a variant small acid-soluble protein-4. The pathogenicity of type F isolates involves sporulation-dependent C. perfringens enterotoxin (CPE) production. C. perfringens sporulation is initiated by orphan histidine kinases and sporulation-associated sigma factors that drive cpe transcription. CPE-induced cytotoxicity starts when CPE binds to claudin receptors to form a small complex (which also includes nonreceptor claudins). Approximately six small complexes oligomerize on the host cell plasma membrane surface to form a prepore. CPE molecules in that prepore apparently extend β-hairpin loops to form a β-barrel pore, allowing a Ca2+ influx that activates calpain. With low-dose CPE treatment, caspase-3-dependent apoptosis develops, while high-CPE dose treatment induces necroptosis. Those effects cause histologic damage along with fluid and electrolyte losses from the colon and small intestine. Sialidases likely contribute to type F disease by enhancing CPE action and, for NanI-producing nonfoodborne human GI disease isolates, increasing intestinal growth and colonization.
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Affiliation(s)
- Archana Shrestha
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Iman Mehdizadeh Gohari
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jihong Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mauricio Navarro
- Instituto de Patologia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Francisco A Uzal
- California Animal Health and Food Safety Laboratory System, School of Veterinary Medicine, University of California Davis, San Bernardino, California, USA
| | - Bruce A McClane
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Eichenberger P. Spore germination: Two ion channels are better than one. Genes Dev 2024; 38:1-3. [PMID: 38316519 PMCID: PMC10903942 DOI: 10.1101/gad.351554.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Germination is the process by which spores emerge from dormancy. Although spores can remain dormant for decades, the study of germination is an active field of research. In this issue of Genes & Development, Gao and colleagues (pp. 31-45) address a perplexing question: How can a dormant spore initiate germination in response to environmental cues? Three distinct complexes are involved: GerA, a germinant-gated ion channel; 5AF/FigP, a second ion channel required for amplification; and SpoVA, a channel for dipicolinic acid (DPA). DPA release is followed by rehydration of the spore core, thus allowing the resumption of metabolic activity.
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Gao Y, Amon JD, Brogan AP, Artzi L, Ramírez-Guadiana FH, Cofsky JC, Kruse AC, Rudner DZ. SpoVAF and FigP assemble into oligomeric ion channels that enhance spore germination. Genes Dev 2024; 38:31-45. [PMID: 38242633 PMCID: PMC10903944 DOI: 10.1101/gad.351353.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/04/2024] [Indexed: 01/21/2024]
Abstract
Bacterial spores can remain dormant for decades yet rapidly germinate and resume growth in response to nutrients. GerA family receptors that sense and respond to these signals have recently been shown to oligomerize into nutrient-gated ion channels. Ion release initiates exit from dormancy. Here, we report that a distinct ion channel, composed of SpoVAF (5AF) and its newly discovered partner protein, YqhR (FigP), amplifies the response. At high germinant concentrations, 5AF/FigP accelerate germination; at low concentrations, this complex becomes critical for exit from dormancy. 5AF is homologous to the channel-forming subunit of GerA family receptors and is predicted to oligomerize around a central pore. 5AF mutations predicted to widen the channel cause constitutive germination during spore formation and membrane depolarization in vegetative cells. Narrow-channel mutants are impaired in germination. A screen for suppressors of a constitutively germinating 5AF mutant identified FigP as an essential cofactor of 5AF activity. We demonstrate that 5AF and FigP interact and colocalize with GerA family receptors in spores. Finally, we show that 5AF/FigP accelerate germination in B. subtilis spores that have nutrient receptors from another species. Our data support a model in which nutrient-triggered ion release by GerA family receptors activates 5AF/FigP ion release, amplifying the response to germinant signals.
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Affiliation(s)
- Yongqiang Gao
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jeremy D Amon
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Anna P Brogan
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Lior Artzi
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Joshua C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA;
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8
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Tezuka T, Mitsuyama K, Date R, Ohnishi Y. A unique sigma/anti-sigma system in the actinomycete Actinoplanes missouriensis. Nat Commun 2023; 14:8483. [PMID: 38123564 PMCID: PMC10733313 DOI: 10.1038/s41467-023-44291-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Bacteria of the genus Actinoplanes form sporangia that contain dormant sporangiospores which, upon contact with water, release motile spores (zoospores) through a process called sporangium dehiscence. Here, we set out to study the molecular mechanisms behind sporangium dehiscence in Actinoplanes missouriensis and discover a sigma/anti-sigma system with unique features. Protein σSsdA contains a functional sigma factor domain and an anti-sigma factor antagonist domain, while protein SipA contains an anti-sigma factor domain and an anti-sigma factor antagonist domain. Remarkably, the two proteins interact with each other via the anti-sigma factor antagonist domain of σSsdA and the anti-sigma factor domain of SipA. Although it remains unclear whether the SipA/σSsdA system plays direct roles in sporangium dehiscence, the system seems to modulate oxidative stress responses in zoospores. In addition, we identify a two-component regulatory system (RsdK-RsdR) that represses initiation of sporangium dehiscence.
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Affiliation(s)
- Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo, Japan.
| | - Kyota Mitsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Risa Date
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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9
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Whole-genome alignment with primates reveals DNA elements conserved in humans. Nature 2023:10.1038/d41586-023-03641-y. [PMID: 38030758 DOI: 10.1038/d41586-023-03641-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
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10
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Huang J, Sheng K, Zhang Y, Song M, Ali A, Huang T, Huang M. Inactivation Effect of Germination Combined with Cold Plasma Treatment on Bacillus licheniformis Spores. Foods 2023; 12:4319. [PMID: 38231775 DOI: 10.3390/foods12234319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
Food spoilage, primarily caused by spore-forming bacteria, has become a critical concern since it results in substantial economic losses within the food industry. Past investigations have successfully identified Bacillus licheniformis as the main bacterium responsible for spoilage in roast chicken. In this study, we screened a new sterilization combination from 16 germinants and 4 cold plasma conditions, respectively. Among them, the combination of "A"GFNa-1 (composed of 60 mmol/L L-alanine, 10 mmol/L D-glucose, 10 mmol/L D-fructose, and 1 g/L NaCl) with cold plasma treatment (packed with 100% argon at 70 kV) proved effective in deactivating B. licheniformis spores, resulting in a reduction of approximately 2.1 log CFU/mL. Furthermore, we exposed the spores to different conditions: CK (no germination, no cold plasma), MF (germination only), CP (no germination, 100% argon packed, 70 kV cold plasma treatment for 3 min), and MF + CP (germination for 5 h, 100% argon packed, 70 kV cold plasma treatment for 3 min). The results of heat inactivation and dipicolinic acid (DPA) release rate demonstrated that cold plasma treatment effectively inactivated both spores and vegetative cells without inducing germination. Additionally, the reduced survival under hyperosmotic conditions and the presence of distinct red fluorescence patterns observed through confocal laser scanning microscopy (CLSM) collectively suggest that cold plasma treatment disrupts the inner membrane structure and leads to the inactivation of B. licheniformis. Overall, our findings indicate a spore clearance rate of 99.2% and suggest that the combination of efficient germinants and cold plasma treatment holds promise as a viable approach to mitigate spore contamination in the food industry.
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Affiliation(s)
- Jichao Huang
- College of Engineering, Nanjing Agricultural University, Nanjing 210095, China
| | - Kairan Sheng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yali Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengmeng Song
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ahtisham Ali
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianran Huang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Huang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Zhou B, Xiong Y, Nevo Y, Kahan T, Yakovian O, Alon S, Bhattacharya S, Rosenshine I, Sinai L, Ben-Yehuda S. Dormant bacterial spores encrypt a long-lasting transcriptional program to be executed during revival. Mol Cell 2023; 83:4158-4173.e7. [PMID: 37949068 DOI: 10.1016/j.molcel.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/16/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Sporulating bacteria can retreat into long-lasting dormant spores that preserve the capacity to germinate when propitious. However, how the revival transcriptional program is memorized for years remains elusive. We revealed that in dormant spores, core RNA polymerase (RNAP) resides in a central chromosomal domain, where it remains bound to a subset of intergenic promoter regions. These regions regulate genes encoding for most essential cellular functions, such as rRNAs and tRNAs. Upon awakening, RNAP recruits key transcriptional components, including sigma factor, and progresses to express the adjacent downstream genes. Mutants devoid of spore DNA-compacting proteins exhibit scattered RNAP localization and subsequently disordered firing of gene expression during germination. Accordingly, we propose that the spore chromosome is structured to preserve the transcriptional program by halting RNAP, prepared to execute transcription at the auspicious time. Such a mechanism may sustain long-term transcriptional programs in diverse organisms displaying a quiescent life form.
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Affiliation(s)
- Bing Zhou
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, P.O.B. 12272, 9112001 Jerusalem, Israel
| | - Yifei Xiong
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, P.O.B. 12272, 9112001 Jerusalem, Israel
| | - Yuval Nevo
- Info-CORE, Bioinformatics Unit of the I-CORE Computation Center at the Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Tamar Kahan
- Bioinformatics Unit, Faculty of Medicine, The Hebrew University of Jerusalem, 9112001 Jerusalem, Israel
| | - Oren Yakovian
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, P.O.B. 12272, 9112001 Jerusalem, Israel; The Racah Institute of Physics, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Sima Alon
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, P.O.B. 12272, 9112001 Jerusalem, Israel
| | - Saurabh Bhattacharya
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, P.O.B. 12272, 9112001 Jerusalem, Israel
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, P.O.B. 12272, 9112001 Jerusalem, Israel
| | - Lior Sinai
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, P.O.B. 12272, 9112001 Jerusalem, Israel.
| | - Sigal Ben-Yehuda
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, P.O.B. 12272, 9112001 Jerusalem, Israel.
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12
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Kilian M, Bischofs IB. Co-evolution at protein-protein interfaces guides inference of stoichiometry of oligomeric protein complexes by de novo structure prediction. Mol Microbiol 2023; 120:763-782. [PMID: 37777474 DOI: 10.1111/mmi.15169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
The quaternary structure with specific stoichiometry is pivotal to the specific function of protein complexes. However, determining the structure of many protein complexes experimentally remains a major bottleneck. Structural bioinformatics approaches, such as the deep learning algorithm Alphafold2-multimer (AF2-multimer), leverage the co-evolution of amino acids and sequence-structure relationships for accurate de novo structure and contact prediction. Pseudo-likelihood maximization direct coupling analysis (plmDCA) has been used to detect co-evolving residue pairs by statistical modeling. Here, we provide evidence that combining both methods can be used for de novo prediction of the quaternary structure and stoichiometry of a protein complex. We achieve this by augmenting the existing AF2-multimer confidence metrics with an interpretable score to identify the complex with an optimal fraction of native contacts of co-evolving residue pairs at intermolecular interfaces. We use this strategy to predict the quaternary structure and non-trivial stoichiometries of Bacillus subtilis spore germination protein complexes with unknown structures. Co-evolution at intermolecular interfaces may therefore synergize with AI-based de novo quaternary structure prediction of structurally uncharacterized bacterial protein complexes.
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Affiliation(s)
- Max Kilian
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
- BioQuant Center for Quantitative Analysis of Molecular and Cellular Biosystems, Heidelberg University, Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Ilka B Bischofs
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
- BioQuant Center for Quantitative Analysis of Molecular and Cellular Biosystems, Heidelberg University, Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
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Li YQ, He L, Aryal M, Wicander J, Korza G, Setlow P. Thioflavin-T does not report on electrochemical potential and memory of dormant or germinating bacterial spores. mBio 2023; 14:e0222023. [PMID: 37830807 PMCID: PMC10653816 DOI: 10.1128/mbio.02220-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Bacillus and Clostridium spores cause food spoilage and disease because of spores' dormancy and resistance to microbicides. However, when spores "come back to life" in germination, their resistance properties are lost. Thus, understanding the mechanisms of spore germination could facilitate the development of "germinate to eradicate" strategies. One germination feature is the memory of a pulsed germinant stimulus leading to greater germination following a second pulse. Recent observations of increases in spore binding of the potentiometric dye thioflavin-T early in their germination of spores led to the suggestion that increasing electrochemical potential is how spores "remember" germinant pulses. However, new work finds no increased thioflavin-T binding in the physiological germination of Coatless spores or of intact spores germinating with dodecylamine, even though spore memory is seen in both cases. Thus, using thioflavin-T uptake by germinating spores to assess the involvement of electrochemical potential in memory of germinant exposure, as suggested recently, is questionable.
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Affiliation(s)
- Yong-qing Li
- School of Electrical Engineering and Intelligentization, Dongguan University of Technology, Dongguan, Guangdong, China
- Department of Physics, East Carolina University, Greenville, North Carolina, USA
| | - Lin He
- School of Electrical Engineering and Intelligentization, Dongguan University of Technology, Dongguan, Guangdong, China
| | - Makunda Aryal
- Department of Physics, East Carolina University, Greenville, North Carolina, USA
| | - James Wicander
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - George Korza
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
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Moir A, Christie G. A coating of lipoproteins provides a stabilizing environment on the inner membrane of Bacillus subtilis spores. J Bacteriol 2023; 205:e0016723. [PMID: 37730539 PMCID: PMC10601610 DOI: 10.1128/jb.00167-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023] Open
Abstract
A new study by M. J. Flores, K. Duricy, S. Choudhary, M. Laue, and D. L. Popham (J Bacteriol 205:e00142-23, 2023, https://doi.org/10.1128/jb.00142-23) demonstrates a role for the YlaJ/YhcN family of lipoproteins in the immobilization of the spore's inner membrane. In the absence of these lipoproteins, membrane fluidity increases and membrane-associated proteins like the GerA receptor complexes are more exposed to inimical conditions. The role of these proteins in stabilizing the Bacillus spore inner membrane is now being explored.
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Affiliation(s)
- Anne Moir
- School of Biosciences, University of Sheffield, Firth Court, Sheffield, United Kingdom
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
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Flores MJ, Duricy K, Choudhary S, Laue M, Popham DL. A Family of Spore Lipoproteins Stabilizes the Germination Apparatus by Altering Inner Spore Membrane Fluidity in Bacillus subtilis Spores. J Bacteriol 2023; 205:e0014223. [PMID: 37338384 PMCID: PMC10601750 DOI: 10.1128/jb.00142-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/26/2023] [Indexed: 06/21/2023] Open
Abstract
Dormant bacterial spores undergo the process of germination to return to a vegetative state. In most species, germination involves the sensing of nutrient germinants, the release of various cations and a calcium-dipicolinic acid (DPA) complex, spore cortex degradation, and full rehydration of the spore core. These steps are mediated by membrane-associated proteins, and all these proteins have exposure on the outer surface of the membrane, a hydrated environment where they are potentially subject to damage during dormancy. A family of lipoproteins, including YlaJ, which is expressed from the sleB operon in some species, are present in all sequenced Bacillus and Clostridium genomes that contain sleB. B. subtilis possesses four proteins in this family, and prior studies have demonstrated two of these are required for efficient spore germination and these proteins contain a multimerization domain. Genetic studies of strains lacking all combinations of these four genes now reveal all four play roles in ensuring efficient germination, and affect multiple steps in this process. Electron microscopy does not reveal significant changes in spore morphology in strains lacking lipoproteins. Generalized polarization measurements of a membrane dye probe indicate the lipoproteins decrease spore membrane fluidity. These data suggest a model in which the lipoproteins form a macromolecular structure on the outer surface of the inner spore membrane, where they act to stabilize the membrane and potentially interact with other germination proteins, and thus stabilize the function of multiple components of the germination machinery. IMPORTANCE Bacterial spores exhibit extreme longevity and resistance to many killing agents, and are thus problematic agents of several diseases and of food spoilage. However, to cause disease or spoilage, germination of the spore and return to the vegetative state is necessary. The proteins responsible for initiation and progression of germination are thus potential targets for spore-killing processes. A family of membrane-bound lipoproteins that are conserved across most spore-forming species was studied in the model organism Bacillus subtilis. The results indicate that these proteins reduce the membrane fluidity and increase the stability of other membrane associated proteins that are required for germination. Further understanding of such protein interactions on the spore membrane surface will enhance our understanding of the germination process and its potential as a decontamination method target.
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Affiliation(s)
- Matthew J. Flores
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Kate Duricy
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Shreya Choudhary
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Michael Laue
- Advanced Light and Electron Microscopy (ZBS 4), Robert Koch Institute, Berlin, Germany
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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Lewis D. Biggest ever study of primate genomes has surprises for humanity. Nature 2023:10.1038/d41586-023-01776-6. [PMID: 37264125 DOI: 10.1038/d41586-023-01776-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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Moir A. Spore germination receptors - a new paradigm. Trends Microbiol 2023:S0966-842X(23)00165-8. [PMID: 37270332 DOI: 10.1016/j.tim.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/05/2023]
Abstract
David Rudner and his team (Gao et al.) predict a pentameric structure for the GerA alanine-responsive germination receptor of Bacillus subtilis and demonstrate that it behaves as a nutrient-gated ion channel, finally establishing a function for this novel family of receptors and focussing research on early ion movements in germination.
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Affiliation(s)
- Anne Moir
- School of Biosciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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