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Lin WZ, Hung CM, Lin IH, Sun YJ, Liao ZX, Wu CC, Hou SY. Enhancing antibody detection sensitivity in lateral flow immunoassays using endospores of Bacillus subtilis as signal amplifiers. Talanta 2024; 276:126215. [PMID: 38723474 DOI: 10.1016/j.talanta.2024.126215] [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: 09/08/2023] [Revised: 03/28/2024] [Accepted: 05/05/2024] [Indexed: 06/14/2024]
Abstract
Antibody detection is the critical first step for tracking the spread of many diseases including COVID-19. Lateral flow immunoassay (LFIA) is the most commonly used method for rapid antibody detection because it is easy-to-use and inexpensive. However, LFIA has limited sensitivity when gold nanoparticles (AuNPs) are used as the signals. In this study, the endospores of Bacillus subtilis were used in combination with AuNP in a LFIA to detect antibodies. The endospores serve as a signal amplifier. The detection limit was about 10-8 M for anti-beta galactosidase antibody detection whereas the detection limit of conventional LFIA is about 10-6 M. Furthermore, the proposed methods have no additional user steps compared with the traditional LFIA. This method, therefore, improved the sensitivity 100-fold without compromising any advantages of LFIA. We believe that the proposed method will be useful for detection of antibodies against HIV, Zika virus, SARS-CoV-2, and so on.
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Affiliation(s)
- Wen-Zhi Lin
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, 11490, Taiwan; Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, 23742, Taiwan; Department of Biology and Anatomy, National Defense Medical Center, Taipei, 11490, Taiwan.
| | - Chin-Mao Hung
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, 23742, Taiwan; Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, 11490, Taiwan.
| | - I-Hsien Lin
- Graduate Institute of Chemical Engineering, Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, 10608, Taiwan.
| | - Yi-Jia Sun
- Graduate Institute of Biochemical and Biomedical Engineering, Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, 10608, Taiwan.
| | - Zheng-Xiu Liao
- Graduate Institute of Chemical Engineering, Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, 10608, Taiwan.
| | - Chia-Chun Wu
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, 23742, Taiwan; Department of Orthopaedic Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan.
| | - Shao-Yi Hou
- Graduate Institute of Biochemical and Biomedical Engineering, Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, 10608, Taiwan.
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2
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Dan H, Song X, Xiang G, Song C, Dai H, Shao Y, Huang D, Luo H. The response pattern of the microbial community structure and metabolic profile of jiupei to Bacillus subtilis JP1 addition during baijiu fermentation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:5021-5030. [PMID: 38296914 DOI: 10.1002/jsfa.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/07/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND Baijiu brewing is a complex and multifaceted multimicrobial co-fermentation process, in which various microorganisms interact to form an interdependent micro-ecosystem, subsequently influencing metabolic activities and compound production. Among these microorganisms, Bacillus, an important bacterial genus in the liquor brewing process, remains unclear in its role in shaping the brewing microbial community and its functional metabolism. RESULTS A baijiu fermentation system was constructed using B. subtilis JP1 isolated from native jiupei (grain mixture) combined with daqu (a saccharifying agent) and huangshui (a fermentation byproduct). Based on high-throughput amplicon sequencing analysis, it was evident that B. subtilis JP1 significantly influences bacterial microbial diversity and fungal community structure in baijiu fermentation. Of these, Aspergillus and Monascus emerge as the most markedly altered microbial genera in the jiupei community. Based on co-occurrence networks and bidirectional orthogonal partial least squares discriminant analysis models, it was demonstrated that the addition of B. subtilis JP1 intensified microbial interactions in jiupei fermentation, consequently enhancing the production of volatile flavor compounds such as heptanoic acid, butyl hexanoate and 3-methylthiopropanol in jiupei. CONCLUSION B. subtilis JP1 significantly alters the microbial community structure of jiupei, enhancing aroma formation during fermentation. These findings will contribute to a broader application in solid-state fermentation. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Hulin Dan
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
| | - Xuemiao Song
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
| | - Gangxing Xiang
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
| | | | | | - Yan Shao
- Luzhou Laojiao Co. Ltd, Luzhou, China
| | - Dan Huang
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Yibin, China
| | - Huibo Luo
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
- Liquor Brewing Biotechnology and Application Key Laboratory of Sichuan Province, Yibin, China
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3
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Smith DR, Kearns DB, Burton BM. ComI inhibits transformation in Bacillus subtilis by selectively killing competent cells. J Bacteriol 2024:e0041323. [PMID: 38874341 DOI: 10.1128/jb.00413-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
Many bacteria build elaborate molecular machines to import DNA via natural competence, yet this activity is often not identified until strains have been handled and domesticated in laboratory settings. For example, one of the best studied Gram-positive model organisms, Bacillus subtilis, has a poorly transformable ancestor. Transformation in the ancestral strain is inhibited by a transmembrane peptide, ComI, which is encoded on an extrachromosomal plasmid. Although ComI was shown to be necessary and sufficient to inhibit transformation when produced at high levels under an inducible promoter, the mechanism by which ComI inhibits transformation is unknown. Here, we examine the native regulation and mechanism of transformation inhibition by ComI. We find that under native regulation, ComI expression is restricted in the absence of the plasmid. In the presence of the plasmid, we find that ComI is expressed at higher levels in cells that are differentiating into a competent state. The subcellular localization of ComI, however, does not depend on any other competence proteins, and permeabilization activity is concentration-dependent. Time-lapse microscopy reveals that competent cells producing ComI are first permeabilized and then die. Based on these observations, we propose a new model for the mechanism of ComI in which response to competence activation leads to selective elimination of the competent subpopulation. IMPORTANCE Natural transformation mechanisms have been studied across several bacterial systems, but few examples of inhibition exist. This work investigates the mechanism of action of a plasmid-encoded transmembrane inhibitor of natural transformation. The data reveal that the peptide can cause cell permeabilization. Permeabilization is synergistic with entry of Bacillus subtilis into the "competent" state, such that cells with the ability to be transformed are preferentially killed. These findings reveal a self-preservation mechanism coupled to the physiological state of the cells that ensures that the population can maintain an unaltered plasmid and its predicted prophage.
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Affiliation(s)
- Dominique R Smith
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
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Plyuta VA, Sidorova DE, Koksharova OA, Khmel IA, Gnuchikh EY, Melkina OE. The effect of β-ionone on bacterial cells: the use of specific lux-biosensors. Res Microbiol 2024:104214. [PMID: 38740236 DOI: 10.1016/j.resmic.2024.104214] [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: 12/25/2023] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
The diversity of the biological activity of volatile organic compounds (VOCs), including unsaturated ketone β-ionone, promising pharmacological, biotechnological, and agricultural agent, has aroused considerable interest. However, the functional role and mechanisms of action of VOCs remain insufficiently studied. In this work, the response of bacterial cells to the action of β-ionone was studied using specific bioluminescent lux-biosensors containing stress-sensitive promoters. We determined that in Escherichia coli cells, β-ionone induces oxidative stress (PkatG and Pdps promoters) through a specific response mediated by the OxyR/OxyS regulon, but not SoxR/SoxS (PsoxS promoter). It has been shown that β-ionone at high concentrations (50 μM and above) causes a weak induction of the expression from the PibpA promoter and slightly induces the PcolD promoter in the E. coli biosensors; the observed effect is enhanced in the ΔoxyR mutants. This indicates the presence of some damage to proteins and DNA. β-Ionone was found to inhibit the bichaperone-dependent DnaKJE-ClpB refolding of heat-inactivated bacterial luciferase in E. coli wild-type and ΔibpB mutant strains. In the cells of the Gram-positive bacterium Bacillus subtilis 168 pNK-MrgA β-ionone does not cause oxidative stress. Thus, in this work, the specificity of bacterial cell stress responses to the action of β-ionone was shown.
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Affiliation(s)
- Vladimir A Plyuta
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Kurchatov Center for Genome Research, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Daria E Sidorova
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Kurchatov Center for Genome Research, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Olga A Koksharova
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1-40, 119991 Moscow, Russia.
| | - Inessa A Khmel
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Evgeniy Y Gnuchikh
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Kurchatov Center for Genome Research, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Olga E Melkina
- Complex of NBICS Technologies, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia; Kurchatov Center for Genome Research, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia.
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5
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Öberg R, Sil TB, Ohlin A, Andersson M, Malyshev D. Assessing CaDPA levels, metabolic activity, and spore detection through deuterium labeling. Analyst 2024; 149:1861-1871. [PMID: 38348676 DOI: 10.1039/d3an02162a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Many strains among spore-forming bacteria species are associated with food spoilage, foodborne disease, and hospital-acquired infections. Understanding the impact of environmental conditions and decontamination techniques on the metabolic activity, viability, and biomarkers of these spores is crucial for combatting them. To distinguish and track spores and to understand metabolic mechanisms, spores must be labeled. Staining or genetic modification are current methods for this, however, these methods can be time-consuming, and affect the viability and function of spore samples. In this work, we investigate the use of heavy water for permanent isotope labeling of spores and Raman spectroscopy for tracking sporulation/germination mechanisms. We also discuss the potential of this method in observing decontamination. We find that steady-state deuterium levels in the spore are achieved after only ∼48 h of incubation with 30% D2O-infused broth and sporulation, generating Raman peaks at cell silent region of 2200 and 2300 cm-1. These deuterium levels then decrease rapidly upon spore germination in non-deuterated media. We further find that unlike live spores, spores inactivated using various methods do not lose these Raman peaks upon incubation in growth media, suggesting these peaks may be used to indicate the viability of a spore sample. We further observe several Raman peaks exclusive to deuterated DPA, a spore-specific chemical biomarker, at e.g. 988 and 2300 cm-1, which can be used to track underlying changes in spores involving DPA. In conclusion, permanent spore labeling using deuterium offers a robust and non-invasive way of labeling bacterial spores for marking, viability determination, and characterising spore activity.
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Affiliation(s)
- Rasmus Öberg
- Department of Physics, Umeå University, 901 87, Umeå, Sweden.
- Swedish Defence Research Agency (FOI), Cementvägen 20, 906 21 Umeå, Sweden
| | - Timir Baran Sil
- Department of Physics, Umeå University, 901 87, Umeå, Sweden.
| | - André Ohlin
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | | | - Dmitry Malyshev
- Department of Physics, Umeå University, 901 87, Umeå, Sweden.
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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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Mardoukhi MSY, Rapp J, Irisarri I, Gunka K, Link H, Marienhagen J, de Vries J, Stülke J, Commichau FM. Metabolic rewiring enables ammonium assimilation via a non-canonical fumarate-based pathway. Microb Biotechnol 2024; 17:e14429. [PMID: 38483038 PMCID: PMC10938345 DOI: 10.1111/1751-7915.14429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/16/2024] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
Glutamate serves as the major cellular amino group donor. In Bacillus subtilis, glutamate is synthesized by the combined action of the glutamine synthetase and the glutamate synthase (GOGAT). The glutamate dehydrogenases are devoted to glutamate degradation in vivo. To keep the cellular glutamate concentration high, the genes and the encoded enzymes involved in glutamate biosynthesis and degradation need to be tightly regulated depending on the available carbon and nitrogen sources. Serendipitously, we found that the inactivation of the ansR and citG genes encoding the repressor of the ansAB genes and the fumarase, respectively, enables the GOGAT-deficient B. subtilis mutant to synthesize glutamate via a non-canonical fumarate-based ammonium assimilation pathway. We also show that the de-repression of the ansAB genes is sufficient to restore aspartate prototrophy of an aspB aspartate transaminase mutant. Moreover, in the presence of arginine, B. subtilis mutants lacking fumarase activity show a growth defect that can be relieved by aspB overexpression, by reducing arginine uptake and by decreasing the metabolic flux through the TCA cycle.
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Affiliation(s)
| | - Johanna Rapp
- Interfaculty Institute for Microbiology and Infection Medicine TübingenUniversity of TübingenTübingenGermany
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
- Campus Institute Data ScienceUniversity of GöttingenGöttingenGermany
| | - Katrin Gunka
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
| | - Hannes Link
- Interfaculty Institute for Microbiology and Infection Medicine TübingenUniversity of TübingenTübingenGermany
| | - Jan Marienhagen
- Institute of Bio‐ and Geosciences, IBG‐1: BiotechnologyForschungszentrum JülichJülichGermany
- Institut of BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
- Campus Institute Data ScienceUniversity of GöttingenGöttingenGermany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
| | - Fabian M. Commichau
- FG Molecular Microbiology, Institute for BiologyUniversity of HohenheimStuttgartGermany
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8
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Mishra A, Hughes AC, Amon JD, Rudner DZ, Wang X, Kearns DB. SwrA-mediated Multimerization of DegU and an Upstream Activation Sequence Enhance Flagellar Gene Expression in Bacillus subtilis. J Mol Biol 2024; 436:168419. [PMID: 38141873 DOI: 10.1016/j.jmb.2023.168419] [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: 08/30/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
The earliest genes in bacterial flagellar assembly are activated by narrowly-conserved proteins called master regulators that often act as heteromeric complexes. A complex of SwrA and the response-regulator transcription factor DegU is thought to form the master flagellar regulator in Bacillus subtilis but how the two proteins co-operate to activate gene expression is poorly-understood. Here we find using ChIP-Seq that SwrA interacts with a subset of DegU binding sites in the chromosome and does so in a DegU-dependent manner. Using this information, we identify a DegU-specific inverted repeat DNA sequence in the Pflache promoter region and show that SwrA synergizes with DegU phosphorylation to increase binding affinity. We further demonstrate that the SwrA/DegU footprint extends from the DegU binding site towards the promoter, likely through SwrA-induced DegU multimerization. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription by disrupting a previously-unrecognized upstream activation sequence (UAS). Thus, the SwrA-DegU heteromeric complex likely enables both remote binding and interaction between the activator and RNA polymerase. Small co-activator proteins like SwrA may allow selective activation of subsets of genes where activator multimerization is needed. Why some promoters require activator multimerization and some require UAS sequences is unknown.
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Affiliation(s)
- Ayushi Mishra
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Anna C Hughes
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Jeremy D Amon
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, IN 47408, USA.
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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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10
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Negi A, Pasam T, Farqadain SM, Mahalaxmi Y, Dandekar MP. In-vitro and preclinical testing of bacillus subtilis UBBS-14 probiotic in rats shows no toxicity. Toxicol Res (Camb) 2024; 13:tfae021. [PMID: 38406637 PMCID: PMC10891425 DOI: 10.1093/toxres/tfae021] [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: 10/24/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction Probiotics made from Bacillus subtilis provide a wide spread of health benefits, particularly in the treatment of diarrhea and gastrointestinal problems. Herein, we employed in vitro and in vivo paradigms to assess the potential adverse effects and toxicity of B. subtilis UBBS-14. Materials and methods According to Organization for Economic Co-operation and Development (OECD) 423 and 407 requirements, a preclinical investigation was conducted in male and female Sprague-Dawley rats. Acute toxicity was examined following a single peroral (PO) administration of 5,000 mg/kg body weight (bw) i.e. equivalent to 500 billion colony-forming units (CFU) per kg bw. Single administration of B. subtilis UBBS-14 showed no mortality or adverse effects until the 14-day observation period, indicating LD50 is >5,000 mg/kg bw. Results Incubation of B. subtilis UBBS-14 with Caco2, HT29, and Raw 264.7 cell lines, showed no cytotoxic effects. This probiotic strain was also found responsive to the majority of antibiotics. For a 28-day repeated dose toxicity study, rats were administered 100, 500, and 1,000 mg/kg bw daily once (10, 50, and 100 billion CFU/kg bw/day, respectively) doses of B. subtilis UBBS-14. No notable changes were seen in the morphology, weight, and histopathology of the critical internal organs. The haematological, biochemical, electrolyte (sodium, potassium, chloride, and calcium), and urine analytical results were within the normal range and equivalent to the vehicle-treated group. Conclusion B. subtilis UBBS-14's no-observed-effect level (NOEL) was thus determined to be >1,000 mg/kg bw/day following a 28-day oral dosing.
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Affiliation(s)
- Ankit Negi
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), NH 9, Balanagar Main Rd, Kukatpally Industrial Estate, Balanagar, Hyderabad, Telangana 500037, India
| | - Tulasi Pasam
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), NH 9, Balanagar Main Rd, Kukatpally Industrial Estate, Balanagar, Hyderabad, Telangana 500037, India
| | - Syed Muhammad Farqadain
- Unique Biotech Limited, Centre for Research and Development, Hyderabad, Telangana, 500 101, India
| | - Y Mahalaxmi
- Unique Biotech Limited, Centre for Research and Development, Hyderabad, Telangana, 500 101, India
| | - Manoj P Dandekar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), NH 9, Balanagar Main Rd, Kukatpally Industrial Estate, Balanagar, Hyderabad, Telangana 500037, India
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11
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Zhang L, Bao L, Li S, Liu Y, Liu H. Active substances of myxobacteria against plant diseases and their action mechanisms. Front Microbiol 2024; 14:1294854. [PMID: 38260911 PMCID: PMC10800785 DOI: 10.3389/fmicb.2023.1294854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Myxobacteria have a complex life cycle and unique social behavior, and obtain nutrients by preying on bacteria and fungi in soil. Chitinase, β-1,3 glucanase and β-1,6 glucanase produced by myxobacteria can degrade the glycosidic bond of cell wall of some plant pathogenic fungi, resulting in a perforated structure in the cell wall. In addition, isooctanol produced by myxobacteria can lead to the accumulation of intracellular reactive oxygen species in some pathogenic fungi and induce cell apoptosis. Myxobacteria can also perforate the cell wall of some plant pathogenic oomycetes by β-1,3 glucanase, reduce the content of intracellular soluble protein and protective enzyme activity, affect the permeability of oomycete cell membrane, and aggravate the oxidative damage of pathogen cells. Small molecule compounds such as diisobutyl phthalate and myxovirescin produced by myxobacteria can inhibit the formation of biofilm and lipoprotein of bacteria, and cystobactamids can inhibit the activity of DNA gyrase, thus changing the permeability of bacterial cell membrane. Myxobacteria, as a new natural compound resource bank, can control plant pathogenic fungi, oomycetes and bacteria by producing carbohydrate active enzymes and small molecular compounds, so it has great potential in plant disease control.
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Affiliation(s)
- Lele Zhang
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Liangliang Bao
- College of Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Songyuan Li
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Yang Liu
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Huirong Liu
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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12
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Nguyen TKC, Do HDK, Nguyen TLP, Pham TT, Mach BN, Nguyen TC, Pham TL, Katsande PM, Hong HA, Duong HT, Phan AN, Cutting SM, Vu MT, Nguyen VD. Genomic and vaccine preclinical studies reveal a novel mouse-adapted Helicobacter pylori model for the hpEastAsia genotype in Southeast Asia. J Med Microbiol 2024; 73. [PMID: 38235783 DOI: 10.1099/jmm.0.001786] [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] [Indexed: 01/19/2024] Open
Abstract
Introduction. Helicobacter pylori infection is a major global health concern, linked to the development of various gastrointestinal diseases, including gastric cancer. To study the pathogenesis of H. pylori and develop effective intervention strategies, appropriate animal pathogen models that closely mimic human infection are essential.Gap statement. This study focuses on the understudied hpEastAsia genotype in Southeast Asia, a region marked by a high H. pylori infection rate. No mouse-adapted model strains has been reported previously. Moreover, it recognizes the urgent requirement for vaccines in developing countries, where overuse of antimicrobials is fuelling the emergence of resistance.Aim. This study aims to establish a novel mouse-adapted H. pylori model specific to the hpEastAsia genotype prevalent in Southeast Asia, focusing on comparative genomic and histopathological analysis of pathogens coupled with vaccine preclinical studies.Methodology. We collected and sequenced the whole genome of clinical strains of H. pylori from infected patients in Vietnam and performed comparative genomic analyses of H. pylori strains in Southeast Asia. In parallel, we conducted preclinical studies to assess the pathogenicity of the mouse-adapted H. pylori strain and the protective effect of a new spore-vectored vaccine candidate on male Mlac:ICR mice and the host immune response in a female C57BL/6 mouse model.Results. Genome sequencing and comparison revealed unique and common genetic signatures, antimicrobial resistance genes and virulence factors in strains HP22 and HP34; and supported clarithromycin-resistant HP34 as a representation of the hpEastAsia genotype in Vietnam and Southeast Asia. HP34-infected mice exhibited gastric inflammation, epithelial erosion and dysplastic changes that closely resembled the pathology observed in human H. pylori infection. Furthermore, comprehensive immunological characterization demonstrated a robust host immune response, including both mucosal and systemic immune responses. Oral vaccination with candidate vaccine formulations elicited a significant reduction in bacterial colonization in the model.Conclusion. Our findings demonstrate the successful development of a novel mouse-adapted H. pylori model for the hpEastAsia genotype in Vietnam and Southeast Asia. Our research highlights the distinctive genotype and pathogenicity of clinical H. pylori strains in the region, laying the foundation for targeted interventions to address this global health burden.
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Affiliation(s)
- Thi Kim Cuc Nguyen
- Institute of Biotechnology and Environment, Nha Trang University, 2 Nguyen Dinh Chieu Street, Khanh Hoa, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, Ho Chi Minh City, Vietnam
| | - Thi Lan Phuong Nguyen
- Institute of Vaccines and Biological Medicals (IVAC), 9 Pasteur Street, Nha Trang, Khanh Hoa, Vietnam
| | - Thu Thuy Pham
- Institute of Biotechnology and Environment, Nha Trang University, 2 Nguyen Dinh Chieu Street, Khanh Hoa, Vietnam
| | - Bao Ngoc Mach
- NTT Hi-tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, Ho Chi Minh City, Vietnam
| | - Thi Chinh Nguyen
- Institute of Biotechnology and Environment, Nha Trang University, 2 Nguyen Dinh Chieu Street, Khanh Hoa, Vietnam
| | - Thi Lan Pham
- Institute of Biotechnology and Environment, Nha Trang University, 2 Nguyen Dinh Chieu Street, Khanh Hoa, Vietnam
| | - Paidamoyo M Katsande
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Huynh Anh Hong
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Huu Thai Duong
- Institute of Vaccines and Biological Medicals (IVAC), 9 Pasteur Street, Nha Trang, Khanh Hoa, Vietnam
| | - Anh N Phan
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Simon M Cutting
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Minh Thiet Vu
- NTT Hi-tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, Ho Chi Minh City, Vietnam
| | - Van Duy Nguyen
- Institute of Biotechnology and Environment, Nha Trang University, 2 Nguyen Dinh Chieu Street, Khanh Hoa, Vietnam
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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13
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Holland M, Farinella DN, Cruz-Lorenzo E, Laubscher MI, Doakes DA, Ramos MA, Kubota N, Levin TC. L. pneumophila resists its self-harming metabolite HGA via secreted factors and collective peroxide scavenging. mBio 2023; 14:e0120723. [PMID: 37728338 PMCID: PMC10653783 DOI: 10.1128/mbio.01207-23] [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: 05/10/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE Before environmental opportunistic pathogens can infect humans, they must first successfully grow and compete with other microbes in nature, often via secreted antimicrobials. We previously discovered that the bacterium Legionella pneumophila, the causative agent of Legionnaires' disease, can compete with other microbes via a secreted molecule called HGA. Curiously, L. pneumophila strains that produce HGA is not wholly immune to its toxicity, making it a mystery how these bacteria can withstand the "friendly fire" of potentially self-targeting antimicrobials during inter-bacterial battles. Here, we identify several strategies that allow the high-density bacterial populations that secrete HGA to tolerate its effects. Our study clarifies how HGA works. It also points to some explanations of why it is difficult to disinfect L. pneumophila from the built environment and prevent disease outbreaks.
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Affiliation(s)
- Mische Holland
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Danielle N. Farinella
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emily Cruz-Lorenzo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Madelyn I. Laubscher
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Darian A. Doakes
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Maria A. Ramos
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nanami Kubota
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Tera C. Levin
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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14
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Burton AT, Pospíšilová D, Sudzinova P, Snider EV, Burrage AM, Krásný L, Kearns DB. The alternative sigma factor SigN of Bacillus subtilis is intrinsically toxic. J Bacteriol 2023; 205:e0011223. [PMID: 37728605 PMCID: PMC10601692 DOI: 10.1128/jb.00112-23] [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: 03/28/2023] [Accepted: 07/13/2023] [Indexed: 09/21/2023] Open
Abstract
Sigma factors bind and direct the RNA polymerase core to specific promoter sequences, and alternative sigma factors direct transcription of different regulons of genes. Here, we study the pBS32 plasmid-encoded sigma factor SigN of Bacillus subtilis to determine how it contributes to DNA damage-induced cell death. We find that SigN causes cell death when expressed at high levels and does so in the absence of its regulon suggesting it is intrinsically toxic. One way toxicity was relieved was by curing the pBS32 plasmid, which eliminated a positive feedback loop that led to SigN hyper-accumulation. Another way toxicity was relieved was through mutating the chromosomally encoded transcriptional repressor protein AbrB, thereby derepressing a potent antisense transcript that antagonized SigN expression. SigN efficiently competed with the vegetative sigma factor SigA in vitro, and SigN accumulation in the absence of positive feedback reduced SigA-dependent transcription suggesting that toxicity may be due to competitive inhibition of one or more essential transcripts. Why B. subtilis encodes a toxic sigma factor is unclear but SigN may function in host-inhibition during lytic conversion, as phage lysogen genes are also encoded on pBS32. IMPORTANCE Alternative sigma factors activate entire regulons of genes to improve viability in response to environmental stimuli. The pBS32 plasmid-encoded alternative sigma factor SigN of Bacillus subtilis however, is activated by the DNA damage response and leads to cellular demise. Here we find that SigN impairs viability by hyper-accumulating and outcompeting the vegetative sigma factor for the RNA polymerase core. Why B. subtilis retains a plasmid with a deleterious alternative sigma factor is unknown.
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Affiliation(s)
- Aisha T. Burton
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Debora Pospíšilová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská, Prague, Czechia
| | - Petra Sudzinova
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská, Prague, Czechia
| | | | - Andrew M. Burrage
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Libor Krásný
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská, Prague, Czechia
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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15
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Kohm K, Jalomo-Khayrova E, Krüger A, Basu S, Steinchen W, Bange G, Frunzke J, Hertel R, Commichau F, Czech L. Structural and functional characterization of MrpR, the master repressor of the Bacillus subtilis prophage SPβ. Nucleic Acids Res 2023; 51:9452-9474. [PMID: 37602373 PMCID: PMC10516654 DOI: 10.1093/nar/gkad675] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
Prophages control their lifestyle to either be maintained within the host genome or enter the lytic cycle. Bacillus subtilis contains the SPβ prophage whose lysogenic state depends on the MrpR (YopR) protein, a key component of the lysis-lysogeny decision system. Using a historic B. subtilis strain harboring the heat-sensitive SPβ c2 mutant, we demonstrate that the lytic cycle of SPβ c2 can be induced by heat due to a single nucleotide exchange in the mrpR gene, rendering the encoded MrpRG136E protein temperature-sensitive. Structural characterization revealed that MrpR is a DNA-binding protein resembling the overall fold of tyrosine recombinases. MrpR has lost its recombinase function and the G136E exchange impairs its higher-order structure and DNA binding activity. Genome-wide profiling of MrpR binding revealed its association with the previously identified SPbeta repeated element (SPBRE) in the SPβ genome. MrpR functions as a master repressor of SPβ that binds to this conserved element to maintain lysogeny. The heat-inducible excision of the SPβ c2 mutant remains reliant on the serine recombinase SprA. A suppressor mutant analysis identified a previously unknown component of the lysis-lysogeny management system that is crucial for the induction of the lytic cycle of SPβ.
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Affiliation(s)
- Katharina Kohm
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Ekaterina Jalomo-Khayrova
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
| | - Aileen Krüger
- Institute of Bio- and Geosciences, iBG-1: Biotechnology, FZ Jülich, Germany
| | - Syamantak Basu
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, iBG-1: Biotechnology, FZ Jülich, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Laura Czech
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
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16
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Marathe A, Zarazúa-Osorio B, Srivastava P, Fujita M. The master regulator for entry into sporulation in Bacillus subtilis becomes a mother cell-specific transcription factor for forespore engulfment. Mol Microbiol 2023; 120:439-461. [PMID: 37485800 DOI: 10.1111/mmi.15132] [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: 12/29/2022] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The Spo0A transcription factor is activated by phosphorylation in starving Bacillus subtilis cells. The activated Spo0A (Spo0A~P) regulates genes controlling entry into sporulation and appears to control mother-cell-specific gene expression after asymmetric division, but the latter remains elusive. Here, we found that Spo0A~P directly binds to three conserved DNA sequences (0A1-3) in the promoter region of the mother cell-specific lytic transglycosylase gene spoIID, which is transcribed by σE -RNA polymerase (RNAP) and negatively controlled by the SpoIIID transcription factor and required for forespore engulfment. Systematic mutagenesis of the 0A boxes revealed that the 0A1 and 0A2 boxes located upstream of the promoter positively control the transcription of spoIID. In contrast, the 0A3 box located downstream of the promoter negatively controls the transcription of spoIID. The mutated SpoIIID binding site located between the -35 and -10 promoter elements causes increased expression of spoIID and reduced sporulation. When the mutations of 0A1, 0A2, and IIID sites are combined, sporulation is restored. Collectively, our data suggest that the mother cell-specific spoIID expression is precisely controlled by the coordination of three factors, Spo0A~P, SpoIIID, and σE -RNAP, for proper sporulation. The conservation of this mechanism across spore-forming species was discussed.
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Affiliation(s)
- Anuradha Marathe
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Priyanka Srivastava
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
- Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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17
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Mishra A, Hughes AC, Amon JD, Rudner DZ, Wang X, Kearns DB. SwrA extends DegU over an UP element to activate flagellar gene expression in Bacillus subtilis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552067. [PMID: 37577504 PMCID: PMC10418190 DOI: 10.1101/2023.08.04.552067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
SwrA activates flagellar gene expression in Bacillus subtilis to increase the frequency of motile cells in liquid and elevate flagellar density to enable swarming over solid surfaces. Here we use ChIP-seq to show that SwrA interacts with many sites on the chromosome in a manner that depends on the response regulator DegU. We identify a DegU-specific inverted repeat DNA sequence and show that SwrA synergizes with phosphorylation to increase DegU DNA binding affinity. We further show that SwrA increases the size of the DegU footprint expanding the region bound by DegU towards the promoter. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription more that could be explained by deactivation. We conclude that SwrA/DegU forms a heteromeric complex that enables both remote binding and interaction between the activator and RNA polymerase in the context of an interceding UP element. We speculate that multimeric activators that resolve cis-element spatial conflicts are common in bacteria and likely act on flagellar biosynthesis loci and other long operons of other multi-subunit complexes. IMPORTANCE In Bacteria, the sigma subunit of RNA polymerase recognizes specific DNA sequences called promoters that determine where gene transcription begins. Some promoters also have sequences immediately upstream called an UP element that is bound by the alpha subunit of RNA polymerase and is often necessary for transcription. Finally, promoters may be activated by transcription factors that bind DNA specific sequences and help recruit RNA polymerase to weak promoter elements. Here we show that the promoter for the 32 gene long flagellar operon in Bacillus subtilis requires an UP element and is activated by a heteromeric transcription factor of DegU and SwrA. Our evidence suggests that SwrA oligomerizes DegU over the DNA to allow RNA polymerase to interact with DegU and the UP element simultaneously. Heteromeric activator complexes are known but poorly-understood in bacteria and we speculate they may be needed to resolve spatial conflicts in the DNA sequence.
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18
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Warneke R, Garbers TB, Herzberg C, Aschenbrandt G, Ficner R, Stülke J. Ornithine is the central intermediate in the arginine degradative pathway and its regulation in Bacillus subtilis. J Biol Chem 2023; 299:104944. [PMID: 37343703 PMCID: PMC10404663 DOI: 10.1016/j.jbc.2023.104944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023] Open
Abstract
The Gram-positive bacterium Bacillus subtilis can utilize several proteinogenic and non-proteinogenic amino acids as sources of carbon, nitrogen, and energy. The utilization of the amino acids arginine, citrulline, and ornithine is catalyzed by enzymes encoded in the rocABC and rocDEF operons and by the rocG gene. The expression of these genes is controlled by the alternative sigma factor SigL. RNA polymerase associated with this sigma factor depends on ATP-hydrolyzing transcription activators to initiate transcription. The RocR protein acts as a transcription activator for the roc genes. However, the details of amino acid metabolism via this pathway are unknown. Here, we investigated the contributions of all enzymes of the Roc pathway to the degradation of arginine, citrulline, and ornithine. We identified the previously uncharacterized RocB protein as responsible for the conversion of citrulline to ornithine. In vitro assays with the purified enzyme suggest that RocB acts as a manganese-dependent N-carbamoyl-L-ornithine hydrolase that cleaves citrulline to form ornithine and carbamate. Moreover, the molecular effector that triggers transcription activation by RocR has not been unequivocally identified. Using a combination of transcription reporter assays and biochemical experiments, we demonstrate that ornithine is the molecular inducer of RocR activity. Taken together, our work suggests that binding of ATP to RocR triggers its hexamerization, and binding of ornithine then allows ATP hydrolysis and activation of roc gene transcription. Thus, ornithine is the central molecule of the roc degradative pathway as it is the common intermediate of arginine and citrulline degradation and the molecular effector of RocR.
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Affiliation(s)
- Robert Warneke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Tim Benedict Garbers
- Department of Molecular Structural Biology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Christina Herzberg
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Georg Aschenbrandt
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany.
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19
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Heydenreich R, Delbrück AI, Mathys A. Post-high-pressure temperature and time - Overlooked parameters in high pressure treatment of bacterial spores. Int J Food Microbiol 2023; 402:110279. [PMID: 37331115 DOI: 10.1016/j.ijfoodmicro.2023.110279] [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: 02/01/2023] [Revised: 05/19/2023] [Accepted: 06/03/2023] [Indexed: 06/20/2023]
Abstract
High pressure (HP) processing has high potential for bacterial spore inactivation with minimal thermal input. To advance HP germination and subsequent inactivation of spores, this study explored the physiological state of HP-treated spores using flow cytometry (FCM). Bacillus subtilis spores were treated at 550 MPa and 60 °C (very HP (vHP)) in buffer, incubated after the HP treatment, and stained for FCM analysis with SYTO16 indicating germination and propidium iodide (PI) indicating membrane damage. FCM subpopulations were analyzed depending on the HP dwell time (≤20 min), post-HP temperature (ice, 37 °C, 60 °C) and time (≤4 h), germination-relevant cortex-lytic enzymes (CLEs) and small-acid-soluble-proteins-(SASP)-degrading enzymes by using deletion strains. The effect of post-HP temperatures (ice, 37 °C) was additionally studied for moderate HP (150 MPa, 38 °C, 10 min). Post-HP incubation conditions strongly influenced the prevalence of five observed FCM subpopulations. Post-HP incubation on ice did not or only slowly shifted SYTO16-positive spores to higher SYTO16 levels. At 37 °C post-HP, this shift accelerated, and a shift to high PI intensities occurred depending on the HP dwell time. At 60 °C post-HP, the main shift was from SYTO16-positive to PI-positive subpopulations. The enzymes CwlJ and SleB, which are CLEs, seemed both necessary for PI or SYTO16 uptake, and to have different sensitivities to 550 MPa and 60 °C. Different extents of SASP degradation might explain the existence of two SYTO16-positive subpopulations. Shifts to higher SYTO16 intensities during post-HP incubation on ice or at 37 °C might rely on the activity and recovery of CLEs, SASP-degrading enzymes or their associated proteins from reversible HP-induced structural changes. These enzymes seemingly become active only during decompression or after vHP treatments (550 MPa, 60 °C). Based on our results, we provide a refined model of HP germination-inactivation of B. subtilis spores and an optimized FCM method for quantification of the safety-relevant subpopulation, i.e., vHP (550 MPa, 60 °C) superdormant spores. This study contributes to the development of mild spore inactivation processes by shedding light on overlooked parameters: post-HP incubation conditions. Post-HP conditions significantly influenced the physiological state of spores, likely due to varying enzymatic activity. This finding may explain inconsistencies in previous research and shows the importance of reporting post-HP conditions in future research. Furthermore, the addition of post-HP conditions as HP process parameter may open up new possibilities to optimize HP-based inactivation of spores for potential industrial applications in the food industry.
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Affiliation(s)
- Rosa Heydenreich
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Alessia I Delbrück
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland
| | - Alexander Mathys
- Sustainable Food Processing Laboratory, Institute of Food, Nutrition and Health, Department of Health Science and Technology, ETH Zurich, Zurich, Switzerland.
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20
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Driessen JL, Johnsen J, Pogrebnyakov I, Mohamed ET, Mussatto SI, Feist AM, Jensen SI, Nielsen AT. Adaptive laboratory evolution of Bacillus subtilis to overcome toxicity of lignocellulosic hydrolysate derived from Distiller's dried grains with solubles (DDGS). Metab Eng Commun 2023; 16:e00223. [PMID: 37234932 PMCID: PMC10206485 DOI: 10.1016/j.mec.2023.e00223] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/03/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Microbial tolerance to toxic compounds formed during biomass pretreatment is a significant challenge to produce bio-based products from lignocellulose cost effectively. Rational engineering can be problematic due to insufficient prerequisite knowledge of tolerance mechanisms. Therefore, adaptive laboratory evolution was applied to obtain 20 tolerant lineages of Bacillus subtilis strains able to utilize Distiller's Dried Grains with Solubles-derived (DDGS) hydrolysate. Evolved strains showed both improved growth performance and retained heterologous enzyme production using 100% hydrolysate-based medium, whereas growth of the starting strains was essentially absent. Whole-genome resequencing revealed that evolved isolates acquired mutations in the global regulator codY in 15 of the 19 sequenced isolates. Furthermore, mutations in genes related to oxidative stress (katA, perR) and flagella function appeared in both tolerance and control evolution experiments without toxic compounds. Overall, tolerance adaptive laboratory evolution yielded strains able to utilize DDGS-hydrolysate to produce enzymes and hence proved to be a valuable tool for the valorization of lignocellulose.
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Affiliation(s)
- Jasper L.S.P. Driessen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Josefin Johnsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Ivan Pogrebnyakov
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Elsayed T.T. Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Solange I. Mussatto
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800, Kongens Lyngby, Denmark
| | - Adam M. Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0412, USA
| | - Sheila I. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Alex T. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
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21
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Gao Y, Amon JD, Artzi L, Ramírez-Guadiana FH, Brock KP, Cofsky JC, Marks DS, Kruse AC, Rudner DZ. Bacterial spore germination receptors are nutrient-gated ion channels. Science 2023; 380:387-391. [PMID: 37104613 PMCID: PMC11154005 DOI: 10.1126/science.adg9829] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023]
Abstract
Bacterial spores resist antibiotics and sterilization and can remain metabolically inactive for decades, but they can rapidly germinate and resume growth in response to nutrients. Broadly conserved receptors embedded in the spore membrane detect nutrients, but how spores transduce these signals remains unclear. Here, we found that these receptors form oligomeric membrane channels. Mutations predicted to widen the channel initiated germination in the absence of nutrients, whereas those that narrow it prevented ion release and germination in response to nutrients. Expressing receptors with widened channels during vegetative growth caused loss of membrane potential and cell death, whereas the addition of germinants to cells expressing wild-type receptors triggered membrane depolarization. Therefore, germinant receptors act as nutrient-gated ion channels such that ion release initiates exit from dormancy.
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Affiliation(s)
- Yongqiang Gao
- Department of Microbiology, Harvard Medical ScF(2hool, 77 Avenue Louis Pasteur, Boston MA 02115
| | - Jeremy D. Amon
- Department of Microbiology, Harvard Medical ScF(2hool, 77 Avenue Louis Pasteur, Boston MA 02115
- Present Address: Moderna Genomics, 200 Technology Square, Cambridge MA 02139
| | - Lior Artzi
- Department of Microbiology, Harvard Medical ScF(2hool, 77 Avenue Louis Pasteur, Boston MA 02115
- Present Address: Evolved By Nature, 196 Boston Ave, Medford MA 02155
| | | | - Kelly P. Brock
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston MA 02115
- Present Address: Kernal Biologics, 238 Main Street, Cambrdige MA 02142
| | - Joshua C. Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston MA 02115
| | - Deborah S. Marks
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston MA 02115
| | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston MA 02115
| | - David Z. Rudner
- Department of Microbiology, Harvard Medical ScF(2hool, 77 Avenue Louis Pasteur, Boston MA 02115
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22
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Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C. A model industrial workhorse:
Bacillus subtilis
strain 168 and its genome after a quarter of a century. Microb Biotechnol 2023; 16:1203-1231. [PMID: 37002859 DOI: 10.1111/1751-7915.14257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).
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Affiliation(s)
- Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Alexandra Calteau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine Hong Kong University Pokfulam SAR Hong Kong China
| | - Colin Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute Newcastle University Baddiley Clark Building Newcastle upon Tyne UK
| | - John D. Helmann
- Department of Microbiology Cornell University Ithaca New York USA
| | - Claudine Médigue
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Bernhard O. Palsson
- Department of Bioengineering University of California San Diego La Jolla USA
| | | | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Abril Zuniga
- Department of Biology San Diego State University San Diego California USA
| | - Cristal Zuniga
- Bioinformatics and Medical Informatics Graduate Program San Diego State University San Diego California USA
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23
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Cheng YY, Zhou Z, Papadopoulos JM, Zuke JD, Falbel TG, Anantharaman K, Burton BM, Venturelli OS. Efficient plasmid transfer via natural competence in a microbial co-culture. Mol Syst Biol 2023; 19:e11406. [PMID: 36714980 PMCID: PMC9996237 DOI: 10.15252/msb.202211406] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/21/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species growth, and HGT efficiency over time. In the co-culture, plasmid release and HGT efficiency are significantly enhanced than in the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released in high concentrations, enabling efficient HGT. However, HGT is reduced in response to high donor lysis rates. HGT is independent of the donor viability state as both live and dead cells transfer the plasmid with high efficiency. In sum, plasmid HGT via natural transformation depends on the interplay of plasmid properties, donor stress responses and lysis rates, and interspecies interactions.
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Affiliation(s)
- Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - James M Papadopoulos
- Department of Chemical & Biological Engineering, University of Wisconsin, Madison, WI, USA
| | - Jason D Zuke
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Tanya G Falbel
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | | | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin, Madison, WI, USA.,Department of Chemical & Biological Engineering, University of Wisconsin, Madison, WI, USA
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24
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Abstract
By chance, we discovered a window of extracellular magnesium (Mg2+) availability that modulates the division frequency of Bacillus subtilis without affecting its growth rate. In this window, cells grown with excess Mg2+ produce shorter cells than do those grown in unsupplemented medium. The Mg2+-responsive adjustment in cell length occurs in both rich and minimal media as well as in domesticated and undomesticated strains. Of other divalent cations tested, manganese (Mn2+) and zinc (Zn2+) also resulted in cell shortening, but this occurred only at concentrations that affected growth. Cell length decreased proportionally with increasing Mg2+ from 0.2 mM to 4.0 mM, with little or no detectable change being observed in labile, intracellular Mg2+, based on a riboswitch reporter. Cells grown in excess Mg2+ had fewer nucleoids and possessed more FtsZ-rings per unit cell length, consistent with the increased division frequency. Remarkably, when shifting cells from unsupplemented to supplemented medium, more than half of the cell length decrease occurred in the first 10 min, consistent with rapid division onset. Relative to unsupplemented cells, cells growing at steady-state with excess Mg2+ showed an enhanced expression of a large number of SigB-regulated genes and the activation of the Fur, MntR, and Zur regulons. Thus, by manipulating the availability of one nutrient, we were able to uncouple the growth rate from the division frequency and identify transcriptional changes that suggest that cell division is accompanied by the general stress response and an enhanced demand to sequester and/or increase the uptake of iron, Mn2+, and Zn2+. IMPORTANCE The signals that cells use to trigger cell division are unknown. Although division is often considered intrinsic to the cell cycle, microorganisms can continue to grow and repeat rounds of DNA replication without dividing, indicating that cycles of division can be skipped. Here, we show that by manipulating a single nutrient, namely, Mg2+, cell division can be uncoupled from the growth rate. This finding can be applied to investigate the nature of the cell division signal(s).
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25
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Novel 3D Flipwell system that models gut mucosal microenvironment for studying interactions between gut microbiota, epithelia and immunity. Sci Rep 2023; 13:870. [PMID: 36650266 PMCID: PMC9845379 DOI: 10.1038/s41598-023-28233-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
Gut mucosa consists of stratified layers of microbes, semi-permeable mucus, epithelium and stroma abundant in immune cells. Although tightly regulated, interactions between gut commensals and immune cells play indispensable roles in homeostasis and cancer pathogenesis in the body. Thus, there is a critical need to develop a robust model for the gut mucosal microenvironment. Here, we report our novel co-culture utilizing 3D Flipwell system for establishing the stratified layers of discrete mucosal components. This method allows for analyzing synchronous effects of test stimuli on gut bacteria, mucus, epithelium and immune cells, as well as their crosstalks. In the present report, we tested the immuno-stimulatory effects of sepiapterin (SEP, the precursor of the cofactor of nitric oxide synthase (NOS)-BH4) on the gut mucosal community. We previously reported that SEP effectively reprogrammed tumor-associated macrophages and inhibited breast tumor cell growth. In our co-cultures, SEP largely promoted mucus integrity, bacterial binding, and M1-like polarization of macrophages. Conversely, these phenomena were absent in control-treated cultures. Our results demonstrate that this novel co-culture may serve as a robust in vitro system to recapitulate the effects of pharmacological agents on the gut mucosal microenvironment, and could potentially be expanded to test the effects outside the gut.
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26
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Fulano AM, Elbakush AM, Chen LH, Gomelsky M. The Listeria monocytogenes exopolysaccharide significantly enhances colonization and survival on fresh produce. Front Microbiol 2023; 14:1126940. [PMID: 37180237 PMCID: PMC10172500 DOI: 10.3389/fmicb.2023.1126940] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Fresh produce contaminated with Listeria monocytogenes has caused major listeriosis outbreaks in the last decades. Our knowledge about components of the listerial biofilms formed on fresh produce and their roles in causing foodborne illness remains incomplete. Here, we investigated, for the first time, the role of the listerial Pss exopolysaccharide (EPS) in plant surface colonization and stress tolerance. Pss is the main component of L. monocytogenes biofilms synthesized at elevated levels of the second messenger c-di-GMP. We developed a new biofilm model, whereby L. monocytogenes EGD-e and its derivatives are grown in the liquid minimal medium in the presence of pieces of wood or fresh produce. After 48-h incubation, the numbers of colony forming units of the Pss-synthesizing strain on pieces of wood, cantaloupe, celery and mixed salads were 2-12-fold higher, compared to the wild-type strain. Colonization of manmade materials, metals and plastics, was largely unaffected by the presence of Pss. The biofilms formed by the EPS-synthesizing strain on cantaloupe rind were 6-16-fold more tolerant of desiccation, which resembles conditions of whole cantaloupe storage and transportation. Further, listeria in the EPS-biofilms survived exposure to low pH, a condition encountered by bacteria on the contaminated produce during passage through the stomach, by 11-116-fold better than the wild-type strain. We surmise that L. monocytogenes strains synthesizing Pss EPS have an enormous, 102-104-fold, advantage over the non-synthesizing strains in colonizing fresh produce, surviving during storage and reaching small intestines of consumers where they may cause disease. The magnitude of the EPS effect calls for better understanding of factors inducing Pss synthesis and suggests that prevention of listerial EPS-biofilms may significantly enhance fresh produce safety.
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Affiliation(s)
- Alex M. Fulano
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States
| | | | - Li-Hong Chen
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States
| | - Mark Gomelsky
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States
- *Correspondence: Mark Gomelsky,
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27
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Podnar E, Erega A, Danevčič T, Kovačec E, Lories B, Steenackers H, Mandic-Mulec I. Nutrient Availability and Biofilm Polysaccharide Shape the Bacillaene-Dependent Antagonism of Bacillus subtilis against Salmonella Typhimurium. Microbiol Spectr 2022; 10:e0183622. [PMID: 36342318 PMCID: PMC9769773 DOI: 10.1128/spectrum.01836-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Salmonella enterica is one of the most common foodborne pathogens and, due to the spread of antibiotic resistance, new antimicrobial strategies are urgently needed to control it. In this study, we explored the probiotic potential of Bacillus subtilis PS-216 and elucidated the mechanisms that underlie the interactions between this soil isolate and the model pathogenic strain S. Typhimurium SL1344. The results reveal that B. subtilis PS-216 inhibits the growth and biofilm formation of S. Typhimurium through the production of the pks cluster-dependent polyketide bacillaene. The presence of S. Typhimurium enhanced the activity of the PpksC promoter that controls bacillaene production, suggesting that B. subtilis senses and responds to Salmonella. The level of Salmonella inhibition, overall PpksC activity, and PpksC induction by Salmonella were all higher in nutrient-rich conditions than in nutrient-depleted conditions. Although eliminating the extracellular polysaccharide production of B. subtilis via deletion of the epsA-O operon had no significant effect on inhibitory activity against Salmonella in nutrient-rich conditions, this deletion mutant showed an enhanced antagonism against Salmonella in nutrient-depleted conditions, revealing an intricate relationship between exopolysaccharide production, nutrient availability, and bacillaene synthesis. Overall, this work provides evidence on the regulatory role of nutrient availability, sensing of the competitor, and EpsA-O polysaccharide in the social outcome of bacillaene-dependent competition between B. subtilis and S. Typhimurium. IMPORTANCE Probiotic bacteria represent an alternative for controlling foodborne disease caused by Salmonella enterica, which constitutes a serious concern during food production due to its antibiotic resistance and resilience to environmental stress. Bacillus subtilis is gaining popularity as a probiotic, but its behavior in biofilms with pathogens such as Salmonella remains to be elucidated. Here, we show that the antagonism of B. subtilis is mediated by the polyketide bacillaene and that the production of bacillaene is a highly dynamic trait which depends on environmental factors such as nutrient availability and the presence of competitors. Moreover, the production of extracellular polysaccharides by B. subtilis further alters the influence of these factors. Hence, this work highlights the inhibitory effect of B. subtilis, which is condition-dependent, and the importance of evaluating probiotic strains under conditions relevant to the intended use.
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Affiliation(s)
- Eli Podnar
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andi Erega
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Danevčič
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Eva Kovačec
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Bram Lories
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Hans Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Ines Mandic-Mulec
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Chair of Microprocess Engineering and Technology (COMPETE), University of Ljubljana, Ljubljana, Slovenia
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28
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Disparate Regions of the Human Chemokine CXCL10 Exhibit Broad-Spectrum Antimicrobial Activity against Biodefense and Antibiotic-Resistant Bacterial Pathogens. ACS Infect Dis 2022; 9:122-139. [PMID: 36475632 PMCID: PMC9841529 DOI: 10.1021/acsinfecdis.2c00456] [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] [Indexed: 12/12/2022]
Abstract
CXCL10 is a pro-inflammatory chemokine produced by the host in response to microbial infection. In addition to canonical, receptor-dependent actions affecting immune-cell migration and activation, CXCL10 has also been found to directly kill a broad range of pathogenic bacteria. Prior investigations suggest that the bactericidal effects of CXCL10 occur through two distinct pathways that compromise the cell envelope. These observations raise the intriguing notion that CXCL10 features a separable pair of antimicrobial domains. Herein, we affirm this possibility through peptide-based mapping and structure/function analyses, which demonstrate that discrete peptides derived from the N- and C-terminal regions of CXCL10 mediate bacterial killing. The N-terminal derivative, peptide P1, exhibited marked antimicrobial activity against Bacillus anthracis vegetative bacilli and spores, as well as antibiotic-resistant clinical isolates of Klebsiella pneumoniae, Acinetobacter baumannii, Enterococcus faecium, and Staphylococcus aureus, among others. At bactericidal concentrations, peptide P1 had a minimal degree of chemotactic activity, but did not cause red blood cell hemolysis or cytotoxic effects against primary human cells. The C-terminal derivative, peptide P9, exhibited antimicrobial effects, but only against Gram-negative bacteria in low-salt medium─conditions under which the peptide can adopt an α-helical conformation. The introduction of a hydrocarbon staple induced and stabilized α-helicity; accordingly, stapled peptide P9 displayed significantly improved bactericidal effects against both Gram-positive and Gram-negative bacteria in media containing physiologic levels of salt. Together, our findings identify and characterize the antimicrobial regions of CXCL10 and functionalize these novel determinants as discrete peptides with potential therapeutic utility against difficult-to-treat pathogens.
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29
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Kenneally R, Lawrence Q, Brydon E, Wan KH, Mao JH, Verma SC, Khazaieli A, Celniker SE, Snijders AM. Inactivation of multiple human pathogens by Fathhome's dry sanitizer device: Rapid and eco-friendly ozone-based disinfection. MEDICINE IN MICROECOLOGY 2022; 14:100059. [PMID: 35945946 PMCID: PMC9354387 DOI: 10.1016/j.medmic.2022.100059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/30/2022] [Accepted: 07/24/2022] [Indexed: 11/25/2022] Open
Abstract
SARS-CoV-2 spread rapidly, causing millions of deaths across the globe. As a result, demand for medical supplies and personal protective equipment (PPE) surged and supplies dwindled. Separate entirely, hospital-acquired infections have become commonplace and challenging to treat. To explore the potential of novel sterilization techniques, this study evaluated the disinfection efficacy of Fathhome's ozone-based, dry-sanitizing device by dose and time response. Inactivation of human pathogens was tested on non-porous (plastic) surfaces. 95.42–100% inactivation was observed across all types of vegetative microorganisms and 27.36% inactivation of bacterial endospores tested, with no residual ozone detectable after completion. These results strongly support the hypothesis that Fathhome's commercial implementation of gas-based disinfection is suitable for rapid decontamination of a wide variety of pathogens on PPE and other industrially relevant materials.
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30
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Imai T, Tobe R, Honda K, Tanaka M, Kawamoto J, Mihara H. Group II truncated haemoglobin YjbI prevents reactive oxygen species-induced protein aggregation in Bacillus subtilis. eLife 2022; 11:70467. [PMID: 36125244 PMCID: PMC9536834 DOI: 10.7554/elife.70467] [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: 05/18/2021] [Accepted: 09/19/2022] [Indexed: 12/12/2022] Open
Abstract
Oxidative stress-mediated formation of protein hydroperoxides can induce irreversible fragmentation of the peptide backbone and accumulation of cross-linked protein aggregates, leading to cellular toxicity, dysfunction, and death. However, how bacteria protect themselves from damages caused by protein hydroperoxidation is unknown. Here, we show that YjbI, a group II truncated haemoglobin from Bacillus subtilis, prevents oxidative aggregation of cell-surface proteins by its protein hydroperoxide peroxidase-like activity, which removes hydroperoxide groups from oxidised proteins. Disruption of the yjbI gene in B. subtilis lowered biofilm water repellence, which associated with the cross-linked aggregation of the biofilm matrix protein TasA. YjbI was localised to the cell surface or the biofilm matrix, and the sensitivity of planktonically grown cells to generators of reactive oxygen species was significantly increased upon yjbI disruption, suggesting that YjbI pleiotropically protects labile cell-surface proteins from oxidative damage. YjbI removed hydroperoxide residues from the model oxidised protein substrate bovine serum albumin and biofilm component TasA, preventing oxidative aggregation in vitro. Furthermore, the replacement of Tyr63 near the haem of YjbI with phenylalanine resulted in the loss of its protein peroxidase-like activity, and the mutant gene failed to rescue biofilm water repellency and resistance to oxidative stress induced by hypochlorous acid in the yjbI-deficient strain. These findings provide new insights into the role of truncated haemoglobin and the importance of hydroperoxide removal from proteins in the survival of aerobic bacteria.
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Affiliation(s)
- Takeshi Imai
- Hyogo Prefectural Institute of Technology, Hyogo, Japan
| | - Ryuta Tobe
- Department of Biotechnology, Ritsumeikan University, Shiga, Japan
| | - Koji Honda
- Hyogo Prefectural Institute of Technology, Hyogo, Japan
| | - Mai Tanaka
- Department of Biotechnology, Ritsumeikan University, Shiga, Japan
| | - Jun Kawamoto
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Hisaaki Mihara
- Department of Biotechnology, Ritsumeikan University, Shiga, Japan
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31
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Genetic Screens Identify Additional Genes Implicated in Envelope Remodeling during the Engulfment Stage of Bacillus subtilis Sporulation. mBio 2022; 13:e0173222. [PMID: 36066101 PMCID: PMC9600426 DOI: 10.1128/mbio.01732-22] [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] [Indexed: 11/20/2022] Open
Abstract
During bacterial endospore formation, the developing spore is internalized into the mother cell through a phagocytic-like process called engulfment, which involves synthesis and hydrolysis of peptidoglycan. Engulfment peptidoglycan hydrolysis requires the widely conserved and well-characterized DMP complex, composed of SpoIID, SpoIIM, and SpoIIP. In contrast, although peptidoglycan synthesis has been implicated in engulfment, the protein players involved are less well defined. The widely conserved SpoIIIAH-SpoIIQ interaction is also required for engulfment efficiency, functioning like a ratchet to promote membrane migration around the forespore. Here, we screened for additional factors required for engulfment using transposon sequencing in Bacillus subtilis mutants with mild engulfment defects. We discovered that YrvJ, a peptidoglycan hydrolase, and the MurA paralog MurAB, involved in peptidoglycan precursor synthesis, are required for efficient engulfment. Cytological analyses suggest that both factors are important for engulfment when the DMP complex is compromised and that MurAB is additionally required when the SpoIIIAH-SpoIIQ ratchet is abolished. Interestingly, despite the importance of MurAB for sporulation in B. subtilis, phylogenetic analyses of MurA paralogs indicate that there is no correlation between sporulation and the number of MurA paralogs and further reveal the existence of a third MurA paralog, MurAC, within the Firmicutes. Collectively, our studies identify two new factors that are required for efficient envelop remodeling during sporulation and highlight the importance of peptidoglycan precursor synthesis for efficient engulfment in B. subtilis and likely other endospore-forming bacteria.
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32
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Fioravanti A, Mathelie-Guinlet M, Dufrêne YF, Remaut H. The Bacillus anthracis S-layer is an exoskeleton-like structure that imparts mechanical and osmotic stabilization to the cell wall. PNAS NEXUS 2022; 1:pgac121. [PMID: 36714836 PMCID: PMC9802277 DOI: 10.1093/pnasnexus/pgac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/02/2022] [Indexed: 02/05/2023]
Abstract
Surface layers (S-layers) are 2D paracrystalline protein monolayers covering the cell envelope of many prokaryotes and archaea. Proposed functions include a role in cell support, as scaffolding structure, as molecular sieve, or as virulence factor. Bacillus anthracis holds two S-layers, composed of Sap or EA1, which interchange in early and late exponential growth phase. We previously found that acute disruption of B. anthracis Sap S-layer integrity, by means of nanobodies, results in severe morphological cell surface defects and cell collapse. Remarkably, this loss of function is due to the destruction of the Sap lattice structure rather than detachment of monomers from the cell surface. Here, we combine force nanoscopy and light microscopy observations to probe the contribution of the S-layer to the mechanical, structural, and functional properties of the cell envelope, which have been so far elusive. Our experiments reveal that cells with a compromised S-layer lattice show a decreased compressive stiffness and elastic modulus. Furthermore, we find that S-layer integrity is required to resist cell turgor under hypotonic conditions. These results present compelling experimental evidence indicating that the S-layers can serve as prokaryotic exoskeletons that support the cell wall in conferring rigidity and mechanical stability to bacterial cells.
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Affiliation(s)
- Antonella Fioravanti
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marion Mathelie-Guinlet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Han Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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33
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Helfrich M, Entian KD, Stein T. Antibiotic profiling of wild-type bacilli led to the discovery of new lanthipeptide subtilin-producing Bacillus spizizenii strains whose 16S rDNA sequences differ from the B. spizizenii typing strain. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2022; 25:839-850. [PMID: 35902452 PMCID: PMC9526687 DOI: 10.1007/s10123-022-00266-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/12/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022]
Abstract
Two dozen field-collected Bacillus and a dozen Bacillus spizizenii wild-type strains from strain collections were selected on the basis of their antagonistic properties against the Gram-positive strain Micrococcus luteus. Based on their genetic and antibiotic profiles, they were characterized (subtilin encoding spaS gene sequences, mass spectrometric, and quantitative-reversed phase liquid chromatographic analyses, as well as the presence of the lanthionine cyclase protein SpaC by western blotting), seven novel producers of the lanthipeptide subtilin. Phylogenetic analyses of the subtilin-producing wild-type strains based on their 16S rRNA sequences showed that all seven strains could be classified as B. spizizenii: The field-collected strains HS and N5, as well as strains DSM 618, 1087, 6395, 6405, and 8439 from the German Collection of Microorganisms and Cell Cultures. To the best of our knowledge, all B. spizizenii strains described so far are characterized by the fact that they can produce a lanthipeptide of the subtilin family. Both the lanthipeptide structures and the organization and sequences of the 16S rRNA-encoding genes suggest a subdivision of B. spizizenii into subspecies: The subtilin-producing B. spizizenii strains are distinctly different from the entianin-producing B. spizizenii typing strain TU-B-10 T (DSM 15029 T).
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Affiliation(s)
- Markus Helfrich
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany
- Jennewein Biotechnologie GmbH, Maarweg 32, 53619, Rheinbreitbach, Germany
| | - Karl-Dieter Entian
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany
| | - Torsten Stein
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany.
- Chemistry & Molecular Biotechnology, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany.
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Alam KM, Yan Y, Lin M, Islam MA, Gaber A, Hossain A. Insight rifampicin-resistant (rpoB) mutation in Pseudomonas stutzeri leads to enhance the biosynthesis of secondary metabolites to survive against harsh environments. Arch Microbiol 2022; 204:437. [PMID: 35768665 DOI: 10.1007/s00203-022-03064-9] [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: 02/18/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 11/02/2022]
Abstract
In this study, a wild-type and five distinct rifampicin-resistant (Rifr) rpoB mutants of Pseudomonas stutzeri (i.e., Q518R, D521Y, D521V, H531R and I614T) ability were investigated against harsh environments (particularly nutritional complexity). Among these, the robust Rifr phenotype of P. Stutzeri was associated only with base replacements of the amino deposits. The use of carboxylic and amino acids significantly increased in various Rifr mutants than that of wild type of P. stutzeri. The assimilation of carbon and nitrogen (N) sources of Rifr mutants' confirmed that the organism maintains the adaptation in nutritionally complex environments. Acetylene reduction assay at different times also found the variability for N-fixation in all strains. Among them, the highest nitrogenase activity was determined in mutant 'D521V'. The assimilation of carbon and nitrogen sources of P. stutzeri and its Rifr mutants ensures that the organism maintains the adaptability in nutritionally complex environments through fixing more nitrogen.
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Affiliation(s)
- Khandakar Mohiul Alam
- Soils and Nutrition Division, Bangladesh Sugarcrop Research Institute, Pabna, 6620, Bangladesh
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South StHaidian District, Beijing, People's Republic of China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South StHaidian District, Beijing, People's Republic of China
| | - Md Ariful Islam
- On-Farm Research Division, Bangladesh Agricultural Research Institute, Pabna, 6600, Bangladesh
| | - Ahmed Gaber
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Akbar Hossain
- Department of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur, 5200, Bangladesh.
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35
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Nordgaard M, Blake C, Maróti G, Hu G, Wang Y, Strube ML, Kovács ÁT. Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization. iScience 2022; 25:104406. [PMID: 35663012 PMCID: PMC9157203 DOI: 10.1016/j.isci.2022.104406] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/22/2022] [Accepted: 05/05/2022] [Indexed: 12/16/2022] Open
Abstract
Bacillus subtilis is known to promote plant growth and protect plants against disease. B. subtilis rapidly adapts to Arabidopsis thaliana root colonization, as evidenced by improved root colonizers already after 12 consecutive transfers between seedlings in a hydroponic setup. Re-sequencing of single evolved isolates and endpoint populations revealed mutations in genes related to different bacterial traits, in accordance with evolved isolates displaying increased root colonization associated with robust biofilm formation in response to the plant polysaccharide xylan and impaired motility. Interestingly, evolved isolates suffered a fitness disadvantage in a non-selective environment, demonstrating an evolutionary cost of adaptation to the plant root. Finally, increased root colonization by an evolved isolate was also demonstrated in the presence of resident soil microbes. Our findings highlight how a plant growth-promoting rhizobacterium rapidly adapts to an ecologically relevant environment and reveal evolutionary consequences that are fundamental to consider when evolving strains for biocontrol purposes. Bacillus subtilis shows fast adaptation to Arabidopsis thaliana roots in a hydroponic setup Evolved isolates exhibit robust biofilms in response to xylan and impaired motility Adaptation to A. thaliana roots is accompanied by an evolutionary cost An evolved isolate shows higher root colonization in the presence of soil bacteria
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Affiliation(s)
- Mathilde Nordgaard
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Christopher Blake
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6726 Szeged, Hungary
| | - Guohai Hu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.,China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Yue Wang
- China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China.,BGI-Beijing, BGI-Shenzhen, 100101 Beijing, China
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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36
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Zhao X, Chen X, Xue Y, Wang X. Development of an efficient iterative genome editing method in Bacillus subtilis using the CRISPR-AsCpf1 system. J Basic Microbiol 2022; 62:824-832. [PMID: 35655368 DOI: 10.1002/jobm.202200134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 12/28/2022]
Abstract
Bacillus subtilis is a useful chassis in the fields of synthetic biology and metabolic engineering for chemical production. Here, we constructed CRISPR-AsCpf1-based expression plasmids with the temperature-sensitive replicon for iterative genome editing in B. subtilis. This method allowed gene insertion and large genomic deletion with an editing efficiency of up 80%-100% and rapid plasmid curing to facilitate the iterative genome editing in B. subtilis 168. Using the customized CRISPR-AsCpf1 system, we successfully and efficiently implemented the related gene editing in B. subtilis 168 for hyaluronic acid (HA) biosynthesis, HA synthase gene (hasA) insertion, UDP-glucose-dehydrogenase gene (tuaD) insertion, and eps gene cluster (epsA-O) deletion. The heterologous production of HA was realized by the engineered strain with a yield of 1.39 g/L. These results support the finding that the CRISPR-AsCpf1 system is highly efficient in bacteria genome editing and provide valuable guidance and essential references for genome engineering in B. subtilis using the CRISPR-AsCpf1 system.
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Affiliation(s)
- Xingcong Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xi Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yanbing Xue
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xuedong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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37
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Preclinical Safety Assessment of Bacillus subtilis BS50 for Probiotic and Food Applications. Microorganisms 2022; 10:microorganisms10051038. [PMID: 35630480 PMCID: PMC9144164 DOI: 10.3390/microorganisms10051038] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 12/12/2022] Open
Abstract
Despite the commercial rise of probiotics containing Bacillaceae spp., it remains important to assess the safety of each strain before clinical testing. Herein, we performed preclinical analyses to address the safety of Bacillus subtilis BS50. Using in silico analyses, we screened the 4.15 Mbp BS50 genome for genes encoding known Bacillus toxins, secondary metabolites, virulence factors, and antibiotic resistance. We also assessed the effects of BS50 lysates on the viability and permeability of cultured human intestinal epithelial cells (Caco-2). We found that the BS50 genome does not encode any known Bacillus toxins. The BS50 genome contains several gene clusters involved in the biosynthesis of secondary metabolites, but many of these antimicrobial metabolites (e.g., fengycin) are common to Bacillus spp. and may even confer health benefits related to gut microbiota health. BS50 was susceptible to seven of eight commonly prescribed antibiotics, and no antibiotic resistance genes were flanked by the complete mobile genetic elements that could enable a horizontal transfer. In cell culture, BS50 cell lysates did not diminish either Caco-2 viability or monolayer permeability. Altogether, BS50 exhibits a robust preclinical safety profile commensurate with commercial probiotic strains and likely poses no significant health risk to humans.
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38
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Rykov SV, Battalova IY, Mironov AS. Construction of Recombinant Bacillus subtilis Strains Producing Hyaluronic Acid. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422050088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Gao Y, Barajas-Ornelas RDC, Amon JD, Ramírez-Guadiana FH, Alon A, Brock KP, Marks DS, Kruse AC, Rudner DZ. The SpoVA membrane complex is required for dipicolinic acid import during sporulation and export during germination. Genes Dev 2022; 36:634-646. [PMID: 35654455 PMCID: PMC9186386 DOI: 10.1101/gad.349488.122] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022]
Abstract
In response to starvation, endospore-forming bacteria differentiate into stress-resistant spores that can remain dormant for years yet rapidly germinate and resume growth in response to nutrients. The small molecule dipicolinic acid (DPA) plays a central role in both the stress resistance of the dormant spore and its exit from dormancy during germination. The spoVA locus is required for DPA import during sporulation and has been implicated in its export during germination, but the molecular bases are unclear. Here, we define the minimal set of proteins encoded in the Bacillus subtilis spoVA operon required for DPA import and demonstrate that these proteins form a membrane complex. Structural modeling of these components combined with mutagenesis and in vivo analysis reveal that the C and Eb subunits form a membrane channel, while the D subunit functions as a cytoplasmic plug. We show that point mutations that impair the interactions between D and the C-Eb membrane complex reduce the efficiency of DPA import during sporulation and reciprocally accelerate DPA release during germination. Our data support a model in which DPA transport into spores involves cycles of unplugging and then replugging the C-Eb membrane channel, while nutrient detection during germination triggers DPA release by unplugging it.
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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
| | | | - Assaf Alon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kelly P Brock
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, 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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40
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Zhang Q, Kobras CM, Gebhard S, Mascher T, Wolf D. Regulation of heterologous subtilin production in Bacillus subtilis W168. Microb Cell Fact 2022; 21:57. [PMID: 35392905 PMCID: PMC8991943 DOI: 10.1186/s12934-022-01782-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/25/2022] [Indexed: 11/30/2022] Open
Abstract
Background Subtilin is a peptide antibiotic (lantibiotic) natively produced by Bacillus subtilis ATCC6633. It is encoded in a gene cluster spaBTCSIFEGRK (spa-locus) consisting of four transcriptional units: spaS (subtilin pre-peptide), spaBTC (modification and export), spaIFEG (immunity) and spaRK (regulation). Despite the pioneer understanding on subtilin biosynthesis, a robust platform to facilitate subtilin research and improve subtilin production is still a poorly explored spot. Results In this work, the intact spa-locus was successfully integrated into the chromosome of Bacillus subtilis W168, which is the by far best-characterized Gram-positive model organism with powerful genetics and many advantages in industrial use. Through systematic analysis of spa-promoter activities in B. subtilis W168 wild type and mutant strains, our work demonstrates that subtilin is basally expressed in B. subtilis W168, and the transition state regulator AbrB strongly represses subtilin biosynthesis in a growth phase-dependent manner. The deletion of AbrB remarkably enhanced subtilin gene expression, resulting in comparable yield of bioactive subtilin production as for B. subtilis ATCC6633. However, while in B. subtilis ATCC6633 AbrB regulates subtilin gene expression via SigH, which in turn activates spaRK, AbrB of B. subtilis W168 controls subtilin gene expression in SigH-independent manner, except for the regulation of spaBTC. Furthermore, the work shows that subtilin biosynthesis in B. subtilis W168 is regulated by the two-component regulatory system SpaRK and strictly relies on subtilin itself as inducer to fulfill the autoregulatory circuit. In addition, by incorporating the subtilin-producing system (spa-locus) and subtilin-reporting system (PpsdA-lux) together, we developed “online” reporter strains to efficiently monitor the dynamics of subtilin biosynthesis. Conclusions Within this study, the model organism B. subtilis W168 was successfully established as a novel platform for subtilin biosynthesis and the underlying regulatory mechanism was comprehensively characterized. This work will not only facilitate genetic (engineering) studies on subtilin, but also pave the way for its industrial production. More broadly, this work will shed new light on the heterologous production of other lantibiotics. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01782-9.
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Affiliation(s)
- Qian Zhang
- Institute of Microbiology, Technische Universität Dresden, 01217, Dresden, Germany
| | - Carolin M Kobras
- Department Biology I, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.,School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Susanne Gebhard
- Department Biology I, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.,Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität Dresden, 01217, Dresden, Germany
| | - Diana Wolf
- Institute of Microbiology, Technische Universität Dresden, 01217, Dresden, Germany.
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Surfactin Shows Relatively Low Antimicrobial Activity against Bacillus subtilis and Other Bacterial Model Organisms in the Absence of Synergistic Metabolites. Microorganisms 2022; 10:microorganisms10040779. [PMID: 35456828 PMCID: PMC9030240 DOI: 10.3390/microorganisms10040779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/30/2022] [Accepted: 04/02/2022] [Indexed: 11/17/2022] Open
Abstract
Surfactin is described as a powerful biosurfactant and is natively produced by Bacillus subtilis in notable quantities. Among other industrially relevant characteristics, antimicrobial properties have been attributed to surfactin-producing Bacillus isolates. To investigate this property, stress approaches were carried out with biotechnologically established strains of Corynebacterium glutamicum, Bacillus subtilis, Escherichia coli and Pseudomonas putida with the highest possible amounts of surfactin. Contrary to the popular opinion, the highest growth-reducing effects were detectable in B. subtilis and E. coli after surfactin treatment of 100 g/L with 35 and 33%, respectively, while P. putida showed no growth-specific response. In contrast, other antimicrobial biosurfactants, like rhamnolipids and sophorolipids, showed significantly stronger effects on bacterial growth. Since the addition of high amounts of surfactin in defined mineral salt medium reduced the cell growth of B. subtilis by about 40%, the initial stress response at the protein level was analyzed by mass spectrometry, showing induction of stress proteins under control of alternative sigma factors σB and σW as well as the activation of LiaRS two-component system. Overall, although surfactin is associated with antimicrobial properties, relatively low growth-reducing effects could be demonstrated after the surfactin addition, challenging the general claim of the antimicrobial properties of surfactin.
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Bremer E, Hoffmann T, Dempwolff F, Bedrunka P, Bange G. The many faces of the unusual biofilm activator RemA. Bioessays 2022; 44:e2200009. [PMID: 35289951 DOI: 10.1002/bies.202200009] [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: 01/11/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/08/2022]
Abstract
Biofilms can be viewed as tissue-like structures in which microorganisms are organized in a spatial and functional sophisticated manner. Biofilm formation requires the orchestration of a highly integrated network of regulatory proteins to establish cell differentiation and production of a complex extracellular matrix. Here, we discuss the role of the essential Bacillus subtilis biofilm activator RemA. Despite intense research on biofilms, RemA is a largely underappreciated regulatory protein. RemA forms donut-shaped octamers with the potential to assemble into dimeric superstructures. The presumed DNA-binding mode suggests that RemA organizes its target DNA into nucleosome-like structures, which are the basis for its role as transcriptional activator. We discuss how RemA affects gene expression in the context of biofilm formation, and its regulatory interplay with established components of the biofilm regulatory network, such as SinR, SinI, SlrR, and SlrA. We emphasize the additional role of RemA played in nitrogen metabolism and osmotic-stress adjustment.
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Affiliation(s)
- Erhard Bremer
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Felix Dempwolff
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Patricia Bedrunka
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Gupta R, Elkabetz D, Leibman-Markus M, Jami E, Bar M. Cytokinin-microbiome interactions regulate developmental functions. ENVIRONMENTAL MICROBIOME 2022; 17:2. [PMID: 35033189 PMCID: PMC8760676 DOI: 10.1186/s40793-022-00397-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/05/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND The interaction of plants with the complex microbial networks that inhabit them is important for plant health. While the reliance of plants on their microbial inhabitants for defense against invading pathogens is well documented, the acquisition of data concerning the relationships between plant developmental stage or aging, and microbiome assembly, is still underway. The plant hormone cytokinin (CK) regulates various plant growth and developmental processes. Here, examining the relationships between plant development and microbiome assembly, we observed developmental-age dependent changes in the phyllopshere microbiome. We show that age-related shifts in microbiome content vary based on content of, or sensitivity to, CK. RESULTS We found a developmental age associated decline in microbial richness and diversity, accompanied by a decline in the presence of growth promoting and resistance inducing Bacilli in the phyllosphere. This decline was absent from CK-rich or CK-hypersensitive genotypes. Bacillus isolates we obtained from CK rich genotypes were found to alter the expression of developmental genes to support morphogenesis and alter the leaf developmental program when applied to seedlings, and enhance yield and agricultural productivity when applied to mature plants. CONCLUSIONS Our results support the notion that CK supports developmental functions in part via the bacterial community.
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Affiliation(s)
- Rupali Gupta
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Dorin Elkabetz
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
- Department of Plant Pathology and Microbiology, Hebrew University of Jerusalem, Rehovot, Israel
| | - Meirav Leibman-Markus
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Elie Jami
- Department of Ruminant Science, Animal Science Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel.
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Gupta R, Elkabetz D, Leibman-Markus M, Sayas T, Schneider A, Jami E, Kleiman M, Bar M. Cytokinin drives assembly of the phyllosphere microbiome and promotes disease resistance through structural and chemical cues. THE ISME JOURNAL 2022; 16:122-137. [PMID: 34272494 PMCID: PMC8692462 DOI: 10.1038/s41396-021-01060-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023]
Abstract
The plant hormone cytokinin (CK) is an important developmental regulator, promoting morphogenesis and delaying differentiation and senescence. From developmental processes, to growth, to stress tolerance, CKs are central in plant life. CKs are also known to mediate plant immunity and disease resistance, and several classes of microbes can also produce CKs, affecting the interaction with their plant hosts. While host species and genotype can be a driving force in shaping the plant microbiome, how plant developmental hormones such as CK can shape the microbiome is largely uninvestigated. Here, we examined the relationship between CK and the phyllosphere microbiome, finding that CK acts as a selective force in microbiome assembly, increasing richness, and promoting the presence of Firmicutes. CK-mediated immunity was found to partially depend on the microbial community, and bacilli isolated from previously described CK-rich plant genotypes, which overexpress a CK biosynthesis gene or have increased CK sensitivity, induced plant immunity, and promoted disease resistance. Using a biomimetic system, we investigated the relationship between the leaf microstructure, which is differentially patterned upon changes in CK content or signaling, and the growth of different phyllosphere microbes. We found that leaf structures derived from CK-rich plant genotypes support bacilli in the biomimetic system. CK was able to promote the growth, swarming, and biofilm formation of immunity inducing bacillus isolates in vitro. Overall, our results indicate that host genotype and hormonal profiles can act as a strong selective force in microbiome assembly, underlying differential immunity profiles, and pathogen resistance as a result.
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Affiliation(s)
- Rupali Gupta
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Dorin Elkabetz
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
- Department of Plant Pathology and Microbiology, Hebrew University of Jerusalem, Rehovot, Israel
| | - Meirav Leibman-Markus
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Tali Sayas
- Department of Vegetable and Field crops, Plant Sciences Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Anat Schneider
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
- Department of Plant Pathology and Microbiology, Hebrew University of Jerusalem, Rehovot, Israel
| | - Elie Jami
- Department of Ruminant Science, Animal Science Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Maya Kleiman
- Department of Vegetable and Field crops, Plant Sciences Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
- Agro-NanoTechnology and Advanced Materials Center, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Plant Protection Institute, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel.
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45
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Itaya M. <i>Bacillus subtilis</i> 168 as a unique platform enabling synthesis and dissemination of genomes. J GEN APPL MICROBIOL 2022; 68:45-53. [DOI: 10.2323/jgam.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Mitsuhiro Itaya
- Graduate School of Science and Technology, Shinshu University
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46
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Artzi L, Alon A, Brock KP, Green AG, Tam A, Ramírez-Guadiana FH, Marks D, Kruse A, Rudner DZ. Dormant spores sense amino acids through the B subunits of their germination receptors. Nat Commun 2021; 12:6842. [PMID: 34824238 PMCID: PMC8617281 DOI: 10.1038/s41467-021-27235-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 11/01/2021] [Indexed: 01/19/2023] Open
Abstract
Bacteria from the orders Bacillales and Clostridiales differentiate into stress-resistant spores that can remain dormant for years, yet rapidly germinate upon nutrient sensing. How spores monitor nutrients is poorly understood but in most cases requires putative membrane receptors. The prototypical receptor from Bacillus subtilis consists of three proteins (GerAA, GerAB, GerAC) required for germination in response to L-alanine. GerAB belongs to the Amino Acid-Polyamine-Organocation superfamily of transporters. Using evolutionary co-variation analysis, we provide evidence that GerAB adopts a structure similar to an L-alanine transporter from this superfamily. We show that mutations in gerAB predicted to disrupt the ligand-binding pocket impair germination, while mutations predicted to function in L-alanine recognition enable spores to respond to L-leucine or L-serine. Finally, substitutions of bulkier residues at these positions cause constitutive germination. These data suggest that GerAB is the L-alanine sensor and that B subunits in this broadly conserved family function in nutrient detection.
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Affiliation(s)
- Lior Artzi
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Assaf Alon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA, 02115, USA
| | - Kelly P Brock
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA
| | - Anna G Green
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA
| | - Amy Tam
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA
| | | | - Debora Marks
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA, 02115, USA
| | - Andrew Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA, 02115, USA
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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Genetic evidence for signal transduction within the Bacillus subtilis GerA germinant receptor. J Bacteriol 2021; 204:e0047021. [PMID: 34780301 DOI: 10.1128/jb.00470-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial spores can rapidly exit dormancy through the process of germination. This process begins with the activation of nutrient receptors embedded in the spore membrane. The prototypical germinant receptor in Bacillus subtilis responds to L-alanine and is thought to be a complex of proteins encoded by the genes in the gerA operon: gerAA, gerAB, and gerAC. The GerAB subunit has recently been shown to function as the nutrient sensor, but beyond contributing to complex stability, no additional functions have been attributed to the other two subunits. Here, we investigate the role of GerAA. We resurrect a previously characterized allele of gerA (termed gerA*) that carries a mutation in gerAA and show it constitutively activates germination even in the presence of a wild-type copy of gerA. Using an enrichment strategy to screen for suppressors of gerA*, we identified mutations in all three gerA genes that restore a functional receptor. Characterization of two distinct gerAB suppressors revealed that one (gerAB[E105K]) reduces the GerA complex's ability to respond to L-alanine, while another (gerAB[F259S]) disrupts the germinant signal downstream of L-alanine recognition. These data argue against models in which GerAA is directly or indirectly involved in germinant sensing. Rather, our data suggest that GerAA is responsible for transducing the nutrient signal sensed by GerAB. While the steps downstream of gerAA have yet to be uncovered, these results validate the use of a dominant-negative genetic approach in elucidating the gerA signal transduction pathway. Importance Endospore formers are a broad group of bacteria that can enter dormancy upon starvation and exit dormancy upon sensing the return of nutrients. How dormant spores sense and respond to these nutrients is poorly understood. Here, we identify a key step in the signal transduction pathway that is activated after spores detect the amino acid L-alanine. We present a model that provides a more complete picture of this process that is critical for allowing dormant spores to germinate and resume growth.
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Bacillus spp. Inhibit Edwardsiella tarda Quorum-Sensing and Fish Infection. Mar Drugs 2021; 19:md19110602. [PMID: 34822473 PMCID: PMC8623655 DOI: 10.3390/md19110602] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 01/26/2023] Open
Abstract
The disruption of pathogen communication or quorum-sensing (QS) via quorum-quenching (QQ) molecules has been proposed as a promising strategy to fight bacterial infections. Bacillus spp. have recognizable biotechnology applications, namely as probiotic health-promoting agents or as a source of natural antimicrobial molecules, including QQ molecules. This study characterized the QQ potential of 200 Bacillus spp., isolated from the gut of different aquaculture fish species, to suppress fish pathogens QS. Approximately 12% of the tested Bacillus spp. fish isolates (FI). were able to interfere with synthetic QS molecules. Ten isolates were further selected as producers of extracellular QQ-molecules and their QQ capacity was evaluated against the QS of important aquaculture bacterial pathogens, namely Aeromonas spp., Vibrio spp., Photobacterium damselae, Edwardsiela tarda, and Shigella sonnei. The results revealed that A. veronii and E. tarda produce QS molecules that are detectable by the Chr. violaceum biosensor, and which were degraded when exposed to the extracellular extracts of three FI isolates. Moreover, the same isolates, identified as B. subtilis, B. vezelensis, and B. pumilus, significantly reduced the pathogenicity of E. tarda in zebrafish larvae, increasing its survival by 50%. Taken together, these results identified three Bacillus spp. capable of extracellularly quenching aquaculture pathogen communication, and thus become a promising source of bioactive molecules for use in the biocontrol of aquaculture bacterial diseases.
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Ermoli F, Bontà V, Vitali G, Calvio C. SwrA as global modulator of the two-component system DegSU in Bacillus subtilis. Res Microbiol 2021; 172:103877. [PMID: 34487843 DOI: 10.1016/j.resmic.2021.103877] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/28/2022]
Abstract
The two-component system DegSU of Bacillus subtilis controls more than one hundred genes involved in several different cellular behaviours. Over the last four decades, the degU32Hy allele, supposedly encoding a constitutively active mutant of the response regulator DegU, was exploited to define the impact of this system on cell physiology. Those studies concluded that phosphorylated DegU (DegU∼P) induced degradative enzyme expression while repressing flagellar motility and competence. Recent experiments, however, demonstrated that flagella expression is enhanced by DegU∼P if SwrA, a protein only encoded by wild strains, is present. Yet, to promote motility, SwrA must interact with DegU∼P produced by a wild-type degU allele, as it cannot correctly cooperate with the mutant DegU32Hy protein. In this work, the impact of DegSU was reanalysed in the presence or absence of SwrA employing a DegS kinase mutant, degS200Hy, to force the activation of the TCS. Our results demonstrate that the role of SwrA in B. subtilis physiology is wider than expected and affects several other DegSU targets. SwrA reduces subtilisin, cellulases and xylanases production while, besides motility, it also positively modulates competence for DNA uptake, remarkably relieving the inhibition caused by DegU∼P alone and restoring transformability in degS200Hy strains.
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Affiliation(s)
- Francesca Ermoli
- Dept. of Biology and Biotechnology, Laboratories of Genetics and Microbiology, University of Pavia, Via Ferrata 9, 27100 Pavia (I), Italy.
| | - Valeria Bontà
- Dept. of Biology and Biotechnology, Laboratories of Genetics and Microbiology, University of Pavia, Via Ferrata 9, 27100 Pavia (I), Italy.
| | - Giulia Vitali
- Dept. of Biology and Biotechnology, Laboratories of Genetics and Microbiology, University of Pavia, Via Ferrata 9, 27100 Pavia (I), Italy.
| | - Cinzia Calvio
- Dept. of Biology and Biotechnology, Laboratories of Genetics and Microbiology, University of Pavia, Via Ferrata 9, 27100 Pavia (I), Italy.
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Mou S, Jenkins CC, Okaro U, Dhummakupt ES, Mach PM, DeShazer D. The Burkholderia pseudomallei hmqA-G Locus Mediates Competitive Fitness against Environmental Gram-Positive Bacteria. Microbiol Spectr 2021; 9:e0010221. [PMID: 34160272 PMCID: PMC8552763 DOI: 10.1128/spectrum.00102-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/21/2022] Open
Abstract
Burkholderia pseudomallei is an opportunistic pathogen that is responsible for the disease melioidosis in humans and animals. The microbe is a tier 1 select agent because it is highly infectious by the aerosol route, it is inherently resistant to multiple antibiotics, and no licensed vaccine currently exists. Naturally acquired infections result from contact with contaminated soil or water sources in regions of endemicity. There have been few reports investigating the molecular mechanism(s) utilized by B. pseudomallei to survive and persist in ecological niches harboring microbial competitors. Here, we report the isolation of Gram-positive bacteria from multiple environmental sources and show that ∼45% of these isolates are inhibited by B. pseudomallei in head-to-head competition assays. Two competition-deficient B. pseudomallei transposon mutants were identified that contained insertion mutations in the hmqA-G operon. This large biosynthetic gene cluster encodes the enzymes that produce a family of secondary metabolites called 4-hydroxy-3-methyl-2-alkylquinolines (HMAQs). Liquid chromatography and mass spectrometry conducted on filter-sterilized culture supernatants revealed five HMAQs and N-oxide derivatives that were produced by the parental strain but were absent in an isogenic hmqD deletion mutant. The results demonstrate that B. pseudomallei inhibits the growth of environmental Gram-positive bacteria in a contact-independent manner via the production of HMAQs by the hmqA-G operon. IMPORTANCE Burkholderia pseudomallei naturally resides in water, soil, and the rhizosphere and its success as an opportunistic pathogen is dependent on the ability to persist in these harsh habitats long enough to come into contact with a susceptible host. In addition to adapting to limiting nutrients and diverse chemical and physical challenges, B. pseudomallei also has to interact with a variety of microbial competitors. Our research shows that one of the ways in which B. pseudomallei competes with Gram-positive environmental bacteria is by exporting a diverse array of closely related antimicrobial secondary metabolites.
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Affiliation(s)
- Sherry Mou
- Foundational Sciences Directorate, Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Conor C. Jenkins
- Excet Inc., Springfield, Virginia, USA
- DEVCOM Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - Udoka Okaro
- Foundational Sciences Directorate, Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | | | - Phillip M. Mach
- DEVCOM Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - David DeShazer
- Foundational Sciences Directorate, Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
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