1
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Rosazza T, Earl C, Eigentler L, Davidson FA, Stanley-Wall NR. Reciprocal sharing of extracellular proteases and extracellular matrix molecules facilitates Bacillus subtilis biofilm formation. Mol Microbiol 2024; 122:184-200. [PMID: 38922753 DOI: 10.1111/mmi.15288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Extracellular proteases are a class of public good that support growth of Bacillus subtilis when nutrients are in a polymeric form. Bacillus subtilis biofilm matrix molecules are another class of public good that are needed for biofilm formation and are prone to exploitation. In this study, we investigated the role of extracellular proteases in B. subtilis biofilm formation and explored interactions between different public good producer strains across various conditions. We confirmed that extracellular proteases support biofilm formation even when glutamic acid provides a freely available nitrogen source. Removal of AprE from the NCIB 3610 secretome adversely affects colony biofilm architecture, while sole induction of WprA activity into an otherwise extracellular protease-free strain is sufficient to promote wrinkle development within the colony biofilm. We found that changing the nutrient source used to support growth affected B. subtilis biofilm structure, hydrophobicity and architecture. We propose that the different phenotypes observed may be due to increased protease dependency for growth when a polymorphic protein presents the sole nitrogen source. We however cannot exclude that the phenotypic changes are due to alternative matrix molecules being made. Co-culture of biofilm matrix and extracellular protease mutants can rescue biofilm structure, yet reliance on extracellular proteases for growth influences population coexistence dynamics. Our findings highlight the intricate interplay between these two classes of public goods, providing insights into microbial social dynamics during biofilm formation across different ecological niches.
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Affiliation(s)
- Thibault Rosazza
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chris Earl
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lukas Eigentler
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, UK
| | - Fordyce A Davidson
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
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2
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Bedore AM, Waters CM. Plasmid-free cheater cells commonly evolve during laboratory growth. Appl Environ Microbiol 2024; 90:e0231123. [PMID: 38446071 PMCID: PMC11022567 DOI: 10.1128/aem.02311-23] [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: 12/20/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, extracellular beta-lactamases produced by resistant cells that subsequently degrade penicillin and related antibiotics allow neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show in multiple bacterial species that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface-grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss was still observed. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.IMPORTANCEPlasmids are routinely used in microbiology as readouts of cell biology or tools to manipulate cell function. Central to these studies is the assumption that all cells in an experiment contain the plasmid. Plasmid maintenance in a host cell typically depends on a plasmid-encoded antibiotic resistance marker, which provides a selective advantage when the plasmid-containing cell is grown in the presence of antibiotic. Here, we find that growth of plasmid-containing bacteria on a surface and to a lesser extent in liquid culture in the presence of three distinct antibiotic families leads to the evolution of a significant number of plasmid-free cells, which rely on the resistance mechanisms of the plasmid-containing cells. This process generates a heterogenous population of plasmid-free and plasmid-containing bacteria, an outcome which could confound further experimentation.
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Affiliation(s)
- Amber M. Bedore
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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3
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Lynn BK, De Leenheer P, Schuster M. Putting theory to the test: An integrated computational/experimental chemostat model of the tragedy of the commons. PLoS One 2024; 19:e0300887. [PMID: 38598418 PMCID: PMC11006152 DOI: 10.1371/journal.pone.0300887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024] Open
Abstract
Cooperation via shared public goods is ubiquitous in nature, however, noncontributing social cheaters can exploit the public goods provided by cooperating individuals to gain a fitness advantage. Theory predicts that this dynamic can cause a Tragedy of the Commons, and in particular, a 'Collapsing' Tragedy defined as the extinction of the entire population if the public good is essential. However, there is little empirical evidence of the Collapsing Tragedy in evolutionary biology. Here, we experimentally demonstrate this outcome in a microbial model system, the public good-producing bacterium Pseudomonas aeruginosa grown in a continuous-culture chemostat. In a growth medium that requires extracellular protein digestion, we find that P. aeruginosa populations maintain a high density when entirely composed of cooperating, protease-producing cells but completely collapse when non-producing cheater cells are introduced. We formulate a mechanistic mathematical model that recapitulates experimental observations and suggests key parameters, such as the dilution rate and the cost of public good production, that define the stability of cooperative behavior. We combine model prediction with experimental validation to explain striking differences in the long-term cheater trajectories of replicate cocultures through mutational events that increase cheater fitness. Taken together, our integrated empirical and theoretical approach validates and parametrizes the Collapsing Tragedy in a microbial population, and provides a quantitative, mechanistic framework for generating testable predictions of social behavior.
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Affiliation(s)
- Bryan K. Lynn
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - Patrick De Leenheer
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Mathematics, Oregon State University, Corvallis, Oregon, United States of America
| | - Martin Schuster
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
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4
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Kumari K, Dey J, Mahapatra SR, Ma Y, Sharma PK, Misra N, Singh RP. Protein profiling and immunoinformatic analysis of the secretome of a metal-resistant environmental isolate Pseudomonas aeruginosa S-8. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01152-5. [PMID: 38457114 DOI: 10.1007/s12223-024-01152-5] [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: 06/14/2023] [Accepted: 02/03/2024] [Indexed: 03/09/2024]
Abstract
The bacterial secretome represents a comprehensive catalog of proteins released extracellularly that have multiple important roles in virulence and intercellular communication. This study aimed to characterize the secretome of an environmental isolate Pseudomonas aeruginosa S-8 by analyzing trypsin-digested culture supernatant proteins using nano-LC-MS/MS tool. Using a combined approach of bioinformatics and mass spectrometry, 1088 proteins in the secretome were analyzed by PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb tool for their subcellular localization and further categorization of secretome proteins according to signal peptides. Using the gene ontology tool, secretome proteins were categorized into different functional categories. KEGG pathway analysis identified the secreted proteins into different metabolic functional pathways. Moreover, our LC-MS/MS data revealed the secretion of various CAZymes into the extracellular milieu, which suggests its strong biotechnological applications to breakdown complex carbohydrate polymers. The identified immunodominant epitopes from the secretome of P. aeruginosa showed the characteristic of being non-allergenic, highly antigenic, nontoxic, and having a low risk of triggering autoimmune responses, which highlights their potential as successful vaccine targets. Overall, the identification of secreted proteins of P. aeruginosa could be important for both diagnostic purposes and the development of an effective candidate vaccine.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, 835215, India
| | - Jyotirmayee Dey
- School of Biotechnology, Deemed to Be University, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, 751024, India
| | - Soumya Ranjan Mahapatra
- School of Biotechnology, Deemed to Be University, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, 751024, India
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Namrata Misra
- School of Biotechnology, Deemed to Be University, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, 751024, India
| | - Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, 201309, India.
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5
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Chua W, Marsh CO, Poh SE, Koh WL, Lee MLY, Koh LF, Tang XZE, See P, Ser Z, Wang SM, Sobota RM, Dawson TL, Yew YW, Thng S, O'Donoghue AJ, Oon HH, Common JE, Li H. A Malassezia pseudoprotease dominates the secreted hydrolase landscape and is a potential allergen on skin. Biochimie 2024; 216:181-193. [PMID: 37748748 DOI: 10.1016/j.biochi.2023.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Malassezia globosa is abundant and prevalent on sebaceous areas of the human skin. Genome annotation reveals that M. globosa possesses a repertoire of secreted hydrolytic enzymes relevant for lipid and protein metabolism. However, the functional significance of these enzymes is uncertain and presence of these genes in the genome does not always translate to expression at the cutaneous surface. In this study we utilized targeted RNA sequencing from samples isolated directly from the skin to quantify gene expression of M. globosa secreted proteases, lipases, phospholipases and sphingomyelinases. Our findings indicate that the expression of these enzymes is dynamically regulated by the environment in which the fungus resides, as different growth phases of the planktonic culture of M. globosa show distinct expression levels. Furthermore, we observed significant differences in the expression of these enzymes in culture compared to healthy sebaceous skin sites. By examining the in situ gene expression of M. globosa's secreted hydrolases, we identified a predicted aspartyl protease, MGL_3331, which is highly expressed on both healthy and disease-affected dermatological sites. However, molecular modeling and biochemical studies revealed that this protein has a non-canonical active site motif and lacks measurable proteolytic activity. This pseudoprotease MGL_3331 elicits a heightened IgE-reactivity in blood plasma isolated from patients with atopic dermatitis compared to healthy individuals and invokes a pro-inflammatory response in peripheral blood mononuclear cells. Overall, our study highlights the importance of studying fungal proteins expressed in physiologically relevant environments and underscores the notion that secreted inactive enzymes may have important functions in influencing host immunity.
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Affiliation(s)
- Wisely Chua
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Carl O Marsh
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Si En Poh
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Winston Lc Koh
- Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopolis Street, #07-01, Matrix, 138671, Singapore
| | - Melody Li Ying Lee
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Li Fang Koh
- A∗STAR Skin Research Labs, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06, Immunos, 138648, Singapore
| | - Xin-Zi Emily Tang
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Peter See
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Zheng Ser
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Shi Mei Wang
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Thomas L Dawson
- A∗STAR Skin Research Labs, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06, Immunos, 138648, Singapore; College of Pharmacy, Department of Drug Discovery, Medical University of South Carolina, USA
| | - Yik Weng Yew
- National Skin Centre, National Healthcare Group, 1 Mandalay Rd, 308205, Singapore; Skin Research Institute of Singapore, Skin Research Institute of Singapore (SRIS), 17-01 LKC CSB, 11 Mandalay Rd, 308232, Singapore
| | - Steven Thng
- National Skin Centre, National Healthcare Group, 1 Mandalay Rd, 308205, Singapore; Skin Research Institute of Singapore, Skin Research Institute of Singapore (SRIS), 17-01 LKC CSB, 11 Mandalay Rd, 308232, Singapore
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States
| | - Hazel H Oon
- National Skin Centre, National Healthcare Group, 1 Mandalay Rd, 308205, Singapore; Skin Research Institute of Singapore, Skin Research Institute of Singapore (SRIS), 17-01 LKC CSB, 11 Mandalay Rd, 308232, Singapore
| | - John E Common
- A∗STAR Skin Research Labs, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06, Immunos, 138648, Singapore; Skin Research Institute of Singapore, Skin Research Institute of Singapore (SRIS), 17-01 LKC CSB, 11 Mandalay Rd, 308232, Singapore
| | - Hao Li
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, 61 Biopolis Drive, Proteos, 138673, Singapore; Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
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6
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Bedore AM, Waters CM. Plasmid-free cheater cells commonly evolve during laboratory growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541508. [PMID: 37292590 PMCID: PMC10245762 DOI: 10.1101/2023.05.19.541508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, secretion of beta-lactamase from resistant cells, and subsequent degradation of nearby penicillin and related antibiotics, allows neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss still occurred. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.
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Affiliation(s)
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA, 48824
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7
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Zhang B, Lu D, Duan H. Recent advances in responsive antibacterial materials: design and application scenarios. Biomater Sci 2023; 11:356-379. [PMID: 36408610 DOI: 10.1039/d2bm01573k] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bacterial infection is one of the leading causes of death globally, although modern medicine has made considerable strides in the past century. As traditional antibiotics are suffering from the emergence of drug resistance, new antibacterial strategies are of great interest. Responsive materials are appealing alternatives that have shown great potential in combating resistant bacteria and avoiding the side effects of traditional antibiotics. In this review, the responsive antibacterial materials are introduced in terms of stimulus signals including intrinsic (pH, enzyme, ROS, etc.) and extrinsic (light, temperature, magnetic fields, etc.) stimuli. Their biomedical applications in therapeutics and medical devices are then discussed. Finally, the author's perspective of the challenge and the future of such a system is provided.
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Affiliation(s)
- Bo Zhang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
| | - Derong Lu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
| | - Hongwei Duan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
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8
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Secretome of Paenibacillus sp. S-12 provides an insight about its survival and possible pathogenicity. Folia Microbiol (Praha) 2023:10.1007/s12223-023-01032-4. [PMID: 36642775 DOI: 10.1007/s12223-023-01032-4] [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: 09/11/2022] [Accepted: 01/01/2023] [Indexed: 01/17/2023]
Abstract
Our aim in this study was to characterize and investigate the secretome of Paenibacillus sp. S-12 by nanoLC-MS/MS tool-based analysis of trypsin digested culture supernatant proteins. Using a bioinformatics and combined approach of mass spectrometry, we identified 657 proteins in the secretome. Bioinformatic tools such as PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb were used for the subcellular localization and categorization of secretome on basis of signal peptides. Among the identified proteins, more than 25% of the secretome proteins were associated with virulence proteins including flagellar, adherence, and immune modulators. Gene ontology analysis using Blast2GO tools categorized 60 proteins of the secretome into biological processes, cellular components, and molecular functions. KEGG pathway analysis identified the enzymes or proteins involved in various biosynthesis and degradation pathways. Functional analysis of secretomes reveals a large number of proteins involved in the uptake and exchange of nutrients, colonization, and chemotaxis. A good number of proteins were involved in survival and defense mechanism against oxidative stress, the production of toxins and antimicrobial compounds. The present study is the first report of the in-depth protein profiling of Paenibacillus bacterium. In summary, the current findings of Paenibacillus sp. S-12 secretome provide basic information to understand its survival and the possible pathogenic mechanism.
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9
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Liao H, Li C, Ai S, Li X, Ai X, Ai Y. A simulated ecological restoration of bare cut slope reveals the dosage and temporal effects of cement on ecosystem multifunctionality in a mountain ecosystem. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116672. [PMID: 36343402 DOI: 10.1016/j.jenvman.2022.116672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 09/23/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Cement is a critical building material used in the restorations of bare cut slopes. Yet, how cement affects ecosystem's functions and their undertakers remains elusive. Here, we revealed the dosage and temporal effects of cement on plant and soil traits, extracellular enzymes, greenhouse gas fluxes and microbiome using simulation experiments. The results showed that soil pH increased with the cement content at 1st day but relatively constant values around 7 to 7.5 were detected in the flowing days. The β-1,4-glucosidase, phenol oxidase, leucine aminopeptidase and acid phosphatase showed high activities under high cement content, and they generally increased with the cultivations except for acid phosphatase. CH4 fluxes at 16th day were less than zero, and they increased to peak around at 37th to 44th days followed by decreasing until reaching to relatively stable fluctuations around 0. Despite of decrease patterns, N2O fluxes stayed around zero across the temporal gradient except for the maximum around at 30th day in 2%, 5% and 8% cement treatment. Microbial diversity decreased with the cement content, in which there were a recovery trend for bacteria. By integrating above- and belowground ecosystem traits into a multifunctionality index, we identified a potential optimum cement content (11%). PLSPM showed that multifunctionality was affected by the shifts in soil bacterial community, enzyme activity and greenhouse gases while these components were effected by other environmental changes resulted from cement. Our results demonstrate that cement determines multifunctionality through mediating microbial community and activity, providing new insights for designing in situ experiments and ecological restoration strategies for bare cut slopes.
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Affiliation(s)
- Haijun Liao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China; CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Chaonan Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Shenghao Ai
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.
| | - Xiangzhen Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Xiaoyan Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China.
| | - Yingwei Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China.
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10
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The human pathobiont Malassezia furfur secreted protease Mfsap1 regulates cell dispersal and exacerbates skin inflammation. Proc Natl Acad Sci U S A 2022; 119:e2212533119. [PMID: 36442106 PMCID: PMC9894114 DOI: 10.1073/pnas.2212533119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Malassezia form the dominant eukaryotic microbial community on the human skin. The Malassezia genus possesses a repertoire of secretory hydrolytic enzymes involved in protein and lipid metabolism which alter the external cutaneous environment. The exact role of most Malassezia secreted enzymes, including those in interaction with the epithelial surface, is not well characterized. In this study, we compared the expression level of secreted proteases, lipases, phospholipases, and sphingomyelinases of Malassezia globosa in healthy subjects and seborrheic dermatitis or atopic dermatitis patients. We observed upregulated gene expression of the previously characterized secretory aspartyl protease MGSAP1 in both diseased groups, in lesional and non-lesional skin sites, as compared to healthy subjects. To explore the functional roles of MGSAP1 in skin disease, we generated a knockout mutant of the homologous protease MFSAP1 in the genetically tractable Malassezia furfur. We observed the loss of MFSAP1 resulted in dramatic changes in the cell adhesion and dispersal in both culture and a human 3D reconstituted epidermis model. In a murine model of Malassezia colonization, we further demonstrated Mfsap1 contributes to inflammation as observed by reduced edema and inflammatory cell infiltration with the knockout mutant versus wildtype. Taken together, we show that this dominant secretory Malassezia aspartyl protease has an important role in enabling a planktonic cellular state that can potentially aid in colonization and additionally as a virulence factor in barrier-compromised skin, further highlighting the importance of considering the contextual relevance when evaluating the functions of secreted microbial enzymes.
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11
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Moffett AS, Thomas PJ, Hinczewski M, Eckford AW. Cheater suppression and stochastic clearance through quorum sensing. PLoS Comput Biol 2022; 18:e1010292. [PMID: 35901008 PMCID: PMC9333318 DOI: 10.1371/journal.pcbi.1010292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
The evolutionary consequences of quorum sensing in regulating bacterial cooperation are not fully understood. In this study, we reveal unexpected effects of regulating public good production through quorum sensing on bacterial population dynamics, showing that quorum sensing can be a collectively harmful alternative to unregulated production. We analyze a birth-death model of bacterial population dynamics accounting for public good production and the presence of non-producing cheaters. Our model demonstrates that when demographic noise is a factor, the consequences of controlling public good production according to quorum sensing depend on the cost of public good production and the growth rate of populations in the absence of public goods. When public good production is inexpensive, quorum sensing is a destructive alternative to unconditional production, in terms of the mean population extinction time. When costs are higher, quorum sensing becomes a constructive strategy for the producing strain, both stabilizing cooperation and decreasing the risk of population extinction. Quorum sensing is a process through which bacteria can regulate gene expression according to their population density. The reasons for why bacteria use quorum sensing to regulate production of “public goods”, biochemical products that benefit nearby bacteria, are not entirely clear. We use mathematical modeling to explore how quorum sensing compares to other strategies for controlling production of public goods, namely unconditional production independent on population density, in small populations of bacteria where the random nature of growth is significant. Our model captures both how likely “cheater” strains, which do not produce public goods but benefit from them, are to take over a population and how long on average the population will last before going extinct. We find that depending on how expensive public good production is and how critical public goods are for growth, quorum sensing can decrease or increase the mean time to extinction compared with unconditional production, while always reducing the likelihood of cheaters taking over. Our results could have important implications for the growth of bacterial infections, for example Pseudomonas aeruginosa infections of the lungs of cystic fibrosis patients.
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Affiliation(s)
- Alexander S. Moffett
- Department of Electrical Engineering and Computer Science, York University, Toronto, Ontario, Canada
| | - Peter J. Thomas
- Department of Mathematics, Applied Mathematics, and Statistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Andrew W. Eckford
- Department of Electrical Engineering and Computer Science, York University, Toronto, Ontario, Canada
- * E-mail:
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12
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Peukert C, Popat Gholap S, Green O, Pinkert L, van den Heuvel J, van Ham M, Shabat D, Brönstrup M. Enzyme-Activated, Chemiluminescent Siderophore-Dioxetane Probes Enable the Selective and Highly Sensitive Detection of Bacterial Pathogens. Angew Chem Int Ed Engl 2022; 61:e202201423. [PMID: 35358362 PMCID: PMC9322335 DOI: 10.1002/anie.202201423] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Indexed: 12/18/2022]
Abstract
The sensitive detection of bacterial infections is a prerequisite for their successful treatment. The use of a chemiluminescent readout was so far hampered by an insufficient probe enrichment at the pathogens. We coupled siderophore moieties, that harness the unique iron transport system of bacteria, with enzyme‐activatable dioxetanes and obtained seven trifunctional probes with high signal‐to‐background ratios (S/B=426‐859). Conjugates with efficient iron transport capability into bacteria were identified through a growth recovery assay. All ESKAPE pathogens were labelled brightly by desferrioxamine conjugates, while catechols were weaker due to self‐quenching. Bacteria could also be detected inside lung epithelial cells. The best probe 8 detected 9.1×103 CFU mL−1 of S. aureus and 5.0×104 CFU mL−1 of P. aeruginosa, while the analogous fluorescent probe 10 was 205–305fold less sensitive. This qualifies siderophore dioxetane probes for the selective and sensitive detection of bacteria.
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Affiliation(s)
- Carsten Peukert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Sachin Popat Gholap
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ori Green
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lukas Pinkert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Joop van den Heuvel
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Marco van Ham
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Doron Shabat
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
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13
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Assessing Hydrolyzed Gluten Content in Dietary Enzyme Supplements Following Fermentation. FERMENTATION 2022. [DOI: 10.3390/fermentation8050203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Partially digested gluten fragments from grains including wheat, rye, spelt and barley are responsible for triggering an inflammatory response in the intestinal tract of Celiac Disease (CD) and Non-Celiac Gluten Sensitive (NCGS) individuals. Fermentation is an effective method to metabolize gluten, with enzymes from bacterial or fungal species being released to help in this process. However, the levels of gluten in commercially available enzymes, including those involved in gluten fermentation, are unknown. In this study we investigated gluten levels in commercially available dietary enzymes combined with assessing their effect on inflammatory response in human cell culture assays. Using antibodies that recognize different gluten epitopes (G12, R5, 2D4, MloBS and Skerritt), we employed ELISA and immunoblotting methodologies to determine gluten content in crude gluten, crude gliadin, pepsin-trypsin digested gluten and a selection of commercially available enzymes. We further investigated the effect of these compounds on inflammatory response in immortalized immune and intestinal human cell lines, as well as in peripheral blood mononuclear cells (PBMCs) from coeliac individuals. All tested supplemental enzyme products reported a gluten concentration that was equivalent to or below 20 parts per million (ppm) as compared with an intact wheat reference standard and a pepsin-trypsin digested standard. Similarly, the inflammatory response to IL-8 and TNF-α inflammatory cytokines in mammalian cell lines and PBMCs from coeliac individuals to the commercial enzymes was not significantly different to 20 ppm of crude gluten, crude gliadin or pepsin-trypsin digested gluten. This combined approach provides insight into the extent of gluten breakdown in the fermentation process and the safety of these products to gluten-sensitive individuals.
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14
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Peukert C, Gholap SP, Green O, Pinkert L, van den Heuvel J, van Ham M, Shabat D, Broenstrup M. Enzyme‐activated, Chemiluminescent Siderophore‐Dioxetane Probes Enable the Selective and Highly Sensitive Detection of Bacterial ESKAPE Pathogens. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Carsten Peukert
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH Chemical Biology GERMANY
| | - Sachin Popat Gholap
- Tel Aviv University Raymond and Beverly Sackler Faculty of Exact Sciences School of Chemistry ISRAEL
| | - Ori Green
- Tel Aviv University Raymond and Beverly Sackler Faculty of Exact Sciences School of Chemistry ISRAEL
| | - Lukas Pinkert
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH Chemical Biology GERMANY
| | - Joop van den Heuvel
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH SFPR GERMANY
| | - Marco van Ham
- Helmholtz-Zentrum für Infektionsforschung GmbH: Helmholtz-Zentrum fur Infektionsforschung GmbH SFPR GERMANY
| | - Doron Shabat
- Tel Aviv University Raymond and Beverly Sackler Faculty of Exact Sciences School of Chemistry ISRAEL
| | - Mark Broenstrup
- Helmholtz-Zentrum fur Infektionsforschung GmbH Chemical Biology Inhoffenstraße 7 38124 Braunschweig GERMANY
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15
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Li C, Liao H, Xu L, Wang C, He N, Wang J, Li X. The adjustment of life history strategies drives the ecological adaptations of soil microbiota to aridity. Mol Ecol 2022; 31:2920-2934. [PMID: 35344623 DOI: 10.1111/mec.16445] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Abstract
Soil microbiota increase their fitness to local habitats by adjusting their life history strategies. Yet, how such adjustments drive their ecological adaptations in xeric grasslands remains elusive. In this study, shifts in the traits that potentially represent microbial life history strategies were studied along two aridity gradients with different climates using metagenomic and trait-based approaches. The results indicated that resource acquisition (e.g., higher activities of β-D-glucosidase and N-acetyl-beta-D-glucosidase, higher degradation rates of cellulose and chitin as well as genes involved in cell motilities, biodegradations, transportations and competitions) and growth yield (e.g., higher biomass and respiration) strategies were depleted with a higher aridity. However, cellular and high growth potential maintenance (e.g., higher metabolic quotients and genes related to DNA replication, transcription, translation, central carbon metabolisms and biosynthesis) and stress tolerance (e.g., genes involved in DNA damage repair, cation transporter, sporulation and osmolyte biosynthesis) strategies were enriched with a higher aridity. This implied that microbiota have lower growth yields but are probably well primed for rapid responses to pulse rainfalls in more arid soils, whereas those in less arid soils may have stronger resource acquisition and growth yield abilities. By integrating a large amount of evidence involved in taxonomic, metagenomic, genomic and biochemical properties, this study demonstrated that the ecological adaptations of soil microbiota to aridity made by adjusting and optimizing their life history strategies are universal in xeric grasslands and provided an underlying mechanistic understanding of soil microbial responses to climate changes.
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Affiliation(s)
- Chaonan Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Haijun Liao
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Lin Xu
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Changting Wang
- Institute of Qinghai-Tibet Plateau, Southwest Minzu University, Chengdu, 610041, China
| | - Nianpeng He
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Junming Wang
- Section of Climate Science, Illinois State Water Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, 61802, USA
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
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16
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van Leeuwen HC, Roelofs D, Corver J, Hensbergen P. Phylogenetic analysis of the bacterial Pro-Pro-endopeptidase domain reveals a diverse family including secreted and membrane anchored proteins. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100024. [PMID: 34841315 PMCID: PMC8610288 DOI: 10.1016/j.crmicr.2021.100024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 11/21/2022] Open
Abstract
Bacterial Pro-Pro-endopeptidase (PPEP) is the latest member of the metalloendopeptidase class (E.C. 3.4.24.89). PPEP homologs are found in two firmicutes orders, clostridiales and bacillales spread over 9 genera and more than 130 species. Some PPEP homologs have acquired additional anchor domains that bind noncovalently to various elements of the bacterial peptidoglycan cell wall. Prototype family members, PPEP-1 and PPEP-2, target bacterial surface adhesion proteins, but homologs could target other extracellular proteins.
Pro-Pro-endopeptidases (PPEP, EC 3.4.24.89) are secreted, zinc metalloproteases that have the unusual capacity to cleave a peptide bond between two prolines, a bond that is generally less sensitive to proteolytic cleavage. Two well studied members of the family are PPEP-1 and PPEP-2, produced by Clostridioides difficile, a human pathogen, and Paenibacillus alvei, a bee secondary invader, respectively. Both proteases seem to be involved in mediating bacterial adhesion by cleaving cell surface anchor proteins on the bacterium itself. By using basic alignment and phylogenetic profiling analysis, this work shows that the complete family of proteins that contain a PPEP domain includes proteins from more than 130 species spread over 9 genera. These analyses also suggest that the PPEP domain spread through horizontal gene transfer events between species within the Firmicutes’ classes Bacilli and Clostridia. Bacterial species containing PPEP homologs are found in diverse habitats, varying from human pathogens and gut microbiota to free-living bacteria, which were isolated from various environments, including extreme conditions such as hot springs, desert soil and salt lakes. The phylogenetic tree reveals the relationships between family members and suggests that smaller subgroups could share cleavage specificity, substrates and functional similarity. Except for PPEP-1 and PPEP-2, no cleavage specificity, specific physiological target, or function has been assigned for any of the other PPEP-family members. Some PPEP proteins have acquired additional domains that recognize and bind noncovalently to various elements of the bacterial peptidoglycan cell-wall, anchoring these PPEPs. Secreted or anchored to the cell-wall surface PPEP proteins seem to perform various functions.
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Affiliation(s)
- Hans C van Leeuwen
- Department of CBRN Protection, Netherlands Organization for Applied Scientific Research TNO, Lange Kleiweg 137, 2288 GJ Rijswijk, the Netherlands
| | - Dick Roelofs
- KeyGene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands
| | - Jeroen Corver
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC Leiden, the Netherlands
| | - Paul Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC Leiden, the Netherlands
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17
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Dukovski I, Bajić D, Chacón JM, Quintin M, Vila JCC, Sulheim S, Pacheco AR, Bernstein DB, Riehl WJ, Korolev KS, Sanchez A, Harcombe WR, Segrè D. A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS). Nat Protoc 2021; 16:5030-5082. [PMID: 34635859 PMCID: PMC10824140 DOI: 10.1038/s41596-021-00593-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/16/2021] [Indexed: 02/08/2023]
Abstract
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. This protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.
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Affiliation(s)
- Ilija Dukovski
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Djordje Bajić
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Jeremy M Chacón
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Michael Quintin
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Snorre Sulheim
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Alan R Pacheco
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - David B Bernstein
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - William J Riehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kirill S Korolev
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Physics, Boston University, Boston, MA, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - William R Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Department of Physics, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
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18
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Gardner JG, Schreier HJ. Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems. Appl Microbiol Biotechnol 2021; 105:8109-8127. [PMID: 34611726 DOI: 10.1007/s00253-021-11614-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/24/2022]
Abstract
Our current understanding of enzymatic polysaccharide degradation has come from a huge number of in vitro studies with purified enzymes. While this vast body of work has been invaluable in identifying and characterizing novel mechanisms of action and engineering desirable traits into these enzymes, a comprehensive picture of how these enzymes work as part of a native in vivo system is less clear. Recently, several model bacteria have emerged with genetic systems that allow for a more nuanced study of carbohydrate active enzymes (CAZymes) and how their activity affects bacterial carbon metabolism. With these bacterial model systems, it is now possible to not only study a single nutrient system in isolation (i.e., carbohydrate degradation and carbon metabolism), but also how multiple systems are integrated. Given that most environmental polysaccharides are carbon rich but nitrogen poor (e.g., lignocellulose), the interplay between carbon and nitrogen metabolism in polysaccharide-degrading bacteria can now be studied in a physiologically relevant manner. Therefore, in this review, we have summarized what has been experimentally determined for CAZyme regulation, production, and export in relation to nitrogen metabolism for two Gram-positive (Caldicellulosiruptor bescii and Clostridium thermocellum) and two Gram-negative (Bacteroides thetaiotaomicron and Cellvibrio japonicus) polysaccharide-degrading bacteria. By comparing and contrasting these four bacteria, we have highlighted the shared and unique features of each, with a focus on in vivo studies, in regard to carbon and nitrogen assimilation. We conclude with what we believe are two important questions that can act as guideposts for future work to better understand the integration of carbon and nitrogen metabolism in polysaccharide-degrading bacteria. KEY POINTS: • Regardless of CAZyme deployment system, the generation of a local pool of oligosaccharides is a common strategy among Gram-negative and Gram-positive polysaccharide degraders as a means to maximally recoup the energy expenditure of CAZyme production and export. • Due to the nitrogen deficiency of insoluble polysaccharide-containing substrates, Gram-negative and Gram-positive polysaccharide degraders have a diverse set of strategies for supplementation and assimilation. • Future work needs to precisely characterize the energetic expenditures of CAZyme deployment and bolster our understanding of how carbon and nitrogen metabolism are integrated in both Gram-negative and Gram-positive polysaccharide-degrading bacteria, as both of these will significantly influence a given bacterium's suitability for biotechnology applications.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.
| | - Harold J Schreier
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.,Department of Marine Biotechnology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD, USA
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19
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Abstract
The human skin is our outermost layer and serves as a protective barrier against external insults. Advances in next generation sequencing have enabled the discoveries of a rich and diverse community of microbes - bacteria, fungi and viruses that are residents of this surface. The genomes of these microbes also revealed the presence of many secretory enzymes. In particular, proteases which are hydrolytic enzymes capable of protein cleavage and degradation are of special interest in the skin environment which is enriched in proteins and lipids. In this minireview, we will focus on the roles of these skin-relevant microbial secreted proteases, both in terms of their widely studied roles as pathogenic agents in tissue invasion and host immune inactivation, and their recently discovered roles in inter-microbial interactions and modulation of virulence factors. From these studies, it has become apparent that while microbial proteases are capable of a wide range of functions, their expression is tightly regulated and highly responsive to the environments the microbes are in. With the introduction of new biochemical and bioinformatics tools to study protease functions, it will be important to understand the roles played by skin microbial secretory proteases in cutaneous health, especially the less studied commensal microbes with an emphasis on contextual relevance.
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20
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Dey R, Mukherjee S, Barman S, Haldar J. Macromolecular Nanotherapeutics and Antibiotic Adjuvants to Tackle Bacterial and Fungal Infections. Macromol Biosci 2021; 21:e2100182. [PMID: 34351064 DOI: 10.1002/mabi.202100182] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/13/2021] [Indexed: 12/19/2022]
Abstract
The escalating rise in the population of multidrug-resistant (MDR) pathogens coupled with their biofilm forming ability has struck the global health as nightmare. Alongwith the threat of aforementioned menace, the sluggish development of new antibiotics and the continuous deterioration of the antibiotic pipeline has stimulated the scientific community toward the search of smart and innovative alternatives. In near future, membrane targeting antimicrobial polymers, inspired from antimicrobial peptides, can stand out significantly to combat against the MDR superbugs. Many of these amphiphilic polymers can form nanoaggregates through self-assembly with superior and selective antimicrobial efficacy. Additionally, these macromolecular nanoaggregrates can be utilized to engineer smart antibiotic-delivery system for on-demand drug-release, exploiting the infection site's micoenvironment. This strategy substantially increases the local concentration of antibiotics and reduces the associated off-target toxicity. Furthermore, amphiphilc macromolecules can be utilized to rejuvinate obsolete antibiotics to tackle the drug-resistant infections. This review article highlights the recent developments in macromolecular architecture to design numerous nanostructures with broad-spectrum antimicrobial activity, their application in fabricating smart drug delivery systems and their efficacy as antibiotic adjuvants to circumvent antimicrobial resistance. Finally, the current challenges and future prospects are briefly discussed for further exploration and their practical application in clinical settings.
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Affiliation(s)
- Rajib Dey
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka, 560064, India
| | - Sudip Mukherjee
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka, 560064, India
| | - Swagatam Barman
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka, 560064, India
| | - Jayanta Haldar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka, 560064, India.,Antimicrobial Research Laboratory, School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka, 560064, India
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21
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Mudge MC, Nunn BL, Firth E, Ewert M, Hales K, Fondrie WE, Noble WS, Toner J, Light B, Junge KA. Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments. Environ Microbiol 2021; 23:3840-3866. [PMID: 33760340 PMCID: PMC8475265 DOI: 10.1111/1462-2920.15485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/22/2021] [Indexed: 11/26/2022]
Abstract
Colwellia psychrerythraea is a marine psychrophilic bacterium known for its remarkable ability to maintain activity during long-term exposure to extreme subzero temperatures and correspondingly high salinities in sea ice. These microorganisms must have adaptations to both high salinity and low temperature to survive, be metabolically active, or grow in the ice. Here, we report on an experimental design that allowed us to monitor culturability, cell abundance, activity and proteomic signatures of C. psychrerythraea strain 34H (Cp34H) in subzero brines and supercooled sea water through long-term incubations under eight conditions with varying subzero temperatures, salinities and nutrient additions. Shotgun proteomics found novel metabolic strategies used to maintain culturability in response to each independent experimental variable, particularly in pathways regulating carbon, nitrogen and fatty acid metabolism. Statistical analysis of abundances of proteins uniquely identified in isolated conditions provide metabolism-specific protein biosignatures indicative of growth or survival in either increased salinity, decreased temperature, or nutrient limitation. Additionally, to aid in the search for extant life on other icy worlds, analysis of detected short peptides in -10°C incubations after 4 months identified over 500 potential biosignatures that could indicate the presence of terrestrial-like cold-active or halophilic metabolisms on other icy worlds.
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Affiliation(s)
- Miranda C. Mudge
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Molecular and Cellular Biology, University of Washington, Seattle, WA
| | - Brook L. Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA
- Astrobiology Program, University of Washington, Seattle, WA
| | - Erin Firth
- Applied Physics Lab, Polar Science Center, University of Washington, Seattle, WA
| | - Marcela Ewert
- Applied Physics Lab, Polar Science Center, University of Washington, Seattle, WA
| | - Kianna Hales
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA
| | - Jonathan Toner
- Department of Earth and Space Sciences, University of Washington, Seattle, WA
| | - Bonnie Light
- Applied Physics Lab, Polar Science Center, University of Washington, Seattle, WA
| | - Karen A. Junge
- Applied Physics Lab, Polar Science Center, University of Washington, Seattle, WA
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22
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Proteomics of extracellular vesicles produced by Granulicatella adiacens, which causes infective endocarditis. PLoS One 2020; 15:e0227657. [PMID: 33216751 PMCID: PMC7679012 DOI: 10.1371/journal.pone.0227657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 10/16/2020] [Indexed: 12/31/2022] Open
Abstract
When oral bacteria accidentally enter the bloodstream due to transient tissue damage during dental procedures, they have the potential to attach to the endocardium or an equivalent surface of an indwelling prosthesis and cause infection. Many bacterial species produce extracellular vesicles (EVs) as part of normal physiology, but also use it as a virulence strategy. In this study, it was hypothesized that Granulicatella adiacens produce EVs that possibly help it in virulence. Therefore, the objectives were to isolate and characterize EVs produced by G. adiacens and to investigate its immune-stimulatory effects. The reference strain G. adiacens CCUG 27809 was cultured on chocolate blood agar for 2 days. From subsequent broth culture, the EVs were isolated using differential centrifugation and filtration protocol and then observed using scanning electron microscopy. Proteins in the vesicle preparation were identified by nano LC-ESI-MS/MS. The EVs proteome was analyzed and characterized using different bioinformatics tools. The immune-stimulatory effect of the EVs was studied via ELISA quantification of IL-8, IL-1β and CCL5, major proinflammatory cytokines, produced from stimulated human PBMCs. It was revealed that G. adiacens produced EVs, ranging in diameter from 30 to 250 nm. Overall, G. adiacens EVs contained 112 proteins. The proteome consists of several ribosomal proteins, DNA associated proteins, binding proteins, and metabolic enzymes. It was also shown that these EVs carry putative virulence factors including moonlighting proteins. These EVs were able to induce the production of IL-8, IL-1β and CCL5 from human PBMCs. Further functional characterization of the G. adiacens EVs may provide new insights into virulence mechanisms of this important but less studied oral bacterial species.
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23
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Van den Bossche S, Vandeplassche E, Ostyn L, Coenye T, Crabbé A. Bacterial Interference With Lactate Dehydrogenase Assay Leads to an Underestimation of Cytotoxicity. Front Cell Infect Microbiol 2020; 10:494. [PMID: 33042868 PMCID: PMC7523407 DOI: 10.3389/fcimb.2020.00494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/10/2020] [Indexed: 12/21/2022] Open
Abstract
Models to study host-pathogen interactions in vitro are an important tool for investigating the infectious disease process and evaluating the efficacy of antimicrobial compounds. In these models, the viability of mammalian cells is often determined using the lactate dehydrogenase (LDH) cytotoxicity assay. In the present study we evaluated whether bacteria could interfere with the LDH assay. As a model for host-pathogen interactions, we co-cultured lung epithelial cells with eight bacteria encountered in the lower respiratory tract. We show that LDH activity is affected by Pseudomonas aeruginosa, Klebsiella pneumoniae, Stenotrophomonas maltophilia, and Streptococcus pneumoniae, and that this depends on the density of the start inoculum and the duration of infection. Two different mechanisms were discovered through which bacteria interfered with LDH activity, i.e., acidification of the cell culture medium (by K. pneumoniae and S. pneumoniae) and protease production (by P. aeruginosa and S. maltophilia). In addition, we developed and validated a modified protocol to evaluate cytotoxicity using the LDH assay, where bacterial interference with LDH quantification is avoided.
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Affiliation(s)
| | - Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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24
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Sauvage S, Hardouin J. Exoproteomics for Better Understanding Pseudomonas aeruginosa Virulence. Toxins (Basel) 2020; 12:E571. [PMID: 32899849 PMCID: PMC7551764 DOI: 10.3390/toxins12090571] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/25/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is the most common human opportunistic pathogen associated with nosocomial diseases. In 2017, the World Health Organization has classified P. aeruginosa as a critical agent threatening human health, and for which the development of new treatments is urgently necessary. One interesting avenue is to target virulence factors to understand P. aeruginosa pathogenicity. Thus, characterising exoproteins of P. aeruginosa is a hot research topic and proteomics is a powerful approach that provides important information to gain insights on bacterial virulence. The aim of this review is to focus on the contribution of proteomics to the studies of P. aeruginosa exoproteins, highlighting its relevance in the discovery of virulence factors, post-translational modifications on exoproteins and host-pathogen relationships.
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Affiliation(s)
- Salomé Sauvage
- Polymers, Biopolymers, Surface Laboratory, UMR 6270 CNRS, University of Rouen, CEDEX, F-76821 Mont-Saint-Aignan, France;
- PISSARO Proteomics Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Polymers, Biopolymers, Surface Laboratory, UMR 6270 CNRS, University of Rouen, CEDEX, F-76821 Mont-Saint-Aignan, France;
- PISSARO Proteomics Facility, IRIB, F-76820 Mont-Saint-Aignan, France
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The use of proteomics for the identification of promising vaccine and diagnostic biomarkers in Plasmodium falciparum. Parasitology 2020; 147:1255-1262. [PMID: 32618524 DOI: 10.1017/s003118202000102x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plasmodium falciparum is the main cause of severe malaria in humans that can lead to death. There is growing evidence of drug-resistance in P. falciparum treatment, and the design of effective vaccines remains an ongoing strategy to control the disease. On the other hand, the recognition of specific diagnostic markers for P. falciparum can accelerate the diagnosis of this parasite in the early stages of infection. Therefore, the identification of novel antigenic proteins especially by proteomic tools is urgent for vaccination and diagnosis of P. falciparum. The proteome diversity of the life cycle stages of P. falciparum, the altered proteome of P. falciparum-infected human sera and altered proteins in P. falciparum-infected erythrocytes could be proposed as appropriate proteins for the aforementioned aims. Accordingly, this review highlights and proposes different proteins identified using proteomic approaches as promising markers in the diagnosis and vaccination of P. falciparum. It seems that most of the candidates identified in this study were able to elicit immune responses in the P. falciparum-infected hosts and they also played major roles in the life cycle, pathogenicity and key pathways of this parasite.
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Muselius B, Sukumaran A, Yeung J, Geddes-McAlister J. Iron Limitation in Klebsiella pneumoniae Defines New Roles for Lon Protease in Homeostasis and Degradation by Quantitative Proteomics. Front Microbiol 2020; 11:546. [PMID: 32390954 PMCID: PMC7194016 DOI: 10.3389/fmicb.2020.00546] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/12/2020] [Indexed: 01/24/2023] Open
Abstract
Nutrient adaptation is key in limiting environments for the promotion of microbial growth and survival. In microbial systems, iron is an essential component for many cellular processes, and bioavailability varies greatly among different conditions. In the bacterium, Klebsiella pneumoniae, the impact of iron limitation is known to alter transcriptional expression of iron-acquisition pathways and influence secretion of iron-binding siderophores, however, a comprehensive view of iron limitation at the protein level remains to be defined. Here, we apply a mass-spectrometry-based quantitative proteomics strategy to profile the global impact of iron limitation on the cellular proteome and extracellular environment (secretome) of K. pneumoniae. Our data define the impact of iron on proteins involved in transcriptional regulation and emphasize the modulation of a vast array of proteins associated with iron acquisition, transport, and binding. We also identify proteins in the extracellular environment associated with conventional and non-conventional modes of secretion, as well as vesicle release. In particular, we demonstrate a new role for Lon protease in promoting iron homeostasis outside of the cell. Characterization of a Lon protease mutant in K. pneumoniae validates roles in bacterial growth, cell division, and virulence, and uncovers novel degradation candidates of Lon protease associated with improved iron utilization strategies in the absence of the enzyme. Overall, we provide evidence of unique connections between Lon and iron in a bacterial system and suggest a new role for Lon protease in the extracellular environment during nutrient limitation.
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Macias-Benitez S, Garcia-Martinez AM, Caballero Jimenez P, Gonzalez JM, Tejada Moral M, Parrado Rubio J. Rhizospheric Organic Acids as Biostimulants: Monitoring Feedbacks on Soil Microorganisms and Biochemical Properties. FRONTIERS IN PLANT SCIENCE 2020; 11:633. [PMID: 32547578 PMCID: PMC7270406 DOI: 10.3389/fpls.2020.00633] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/24/2020] [Indexed: 05/19/2023]
Abstract
The biostimulant potential of three different organic acids (OAs) present in the rhizosphere, specifically lactic, oxalic, and citric acids, have been studied. The results showed a rapid and complete metabolism of these three acids with soil microorganisms using them as a source of carbon and energy. Biostimulation was confirmed by soil biochemical studies which showed an increase in enzymatic activities, such as dehydrogenase and phosphatase, lactic and citric acids being those that produced the greatest biostimulation. With regard to microbiota composition, amplicon sequencing of the 16S rRNA gene showed changes in the structure of soil microbial communities. Applying OAs produced a decrease in richness and diversity indices, inducing specific changes in the structure of the microbiological communities. Applying lactic acid induced rapid changes in microbiota composition at both phylum and family taxonomic levels, favoring the proliferation of microorganisms involved in its degradation and soil fertility, such as the genus Bacillus and the family Micrococcaceae. Once the lactic acid was degraded, the biodiversity tended to return to similar phyla, but specific distinctive families and genera remained, leaving a pattern of induction of taxa described as plant growth-promoting bacteria (PGPB), such as the Sinorhizobium and Lysobacter genera, and the Pseudomonaceae family. Similar behavior was found with citric acid, which favored the proliferation and dominance of microorganisms of the Clostridiaceae family, involved in its degradation, as well as microorganisms of both the Micrococcaceae and Pseudomonadaceae families which were found on day 7, leaving a similar pattern of induction as that found after the mineralization of lactic acid. On the other hand, oxalic acid induced long-lasting changes in the bacterial community composition. This was characterized by an increase in the proportion of the Burkholderiales order, which includes microorganisms involved in the degradation of this acid and microorganisms described as PGPB. This study presents evidence supporting the use of OAs as potential soil fertility inducers, due both to their effects in enhancing the dominance of taxa described as PGPB and to their stimulating soil microbial activity.
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Affiliation(s)
- Sandra Macias-Benitez
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, Seville, Spain
| | - Ana María Garcia-Martinez
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, Seville, Spain
| | - Pablo Caballero Jimenez
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, Seville, Spain
| | - Juan Miguel Gonzalez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Manuel Tejada Moral
- Departamento de Cristalografía, Mineralogía y Química Agrícola, E.T.S.I.A, Universidad de Sevilla, Seville, Spain
| | - Juan Parrado Rubio
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, Seville, Spain
- *Correspondence: Juan Parrado Rubio,
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Mahmoudi N, Enke TN, Beaupré SR, Teske AP, Cordero OX, Pearson A. Illuminating microbial species‐specific effects on organic matter remineralization in marine sediments. Environ Microbiol 2019; 22:1734-1747. [DOI: 10.1111/1462-2920.14871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Nagissa Mahmoudi
- Department of Earth and Planetary Sciences McGill University Montreal QC H3A 0E8
| | - Tim N. Enke
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology (MIT) Cambridge Massachusetts 02139
| | - Steven R. Beaupré
- School of Marine and Atmospheric Sciences Stony Brook University Stony Brook New York 11794
| | - Andreas P. Teske
- Department of Marine Sciences University of North Carolina Chapel Hill North Carolina 27599
| | - Otto X. Cordero
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology (MIT) Cambridge Massachusetts 02139
| | - Ann Pearson
- Department of Earth and Planetary Sciences Harvard University Cambridge Massachusetts 02138
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Kindler O, Pulkkinen O, Cherstvy AG, Metzler R. Burst statistics in an early biofilm quorum sensing model: the role of spatial colony-growth heterogeneity. Sci Rep 2019; 9:12077. [PMID: 31427659 PMCID: PMC6700081 DOI: 10.1038/s41598-019-48525-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/07/2019] [Indexed: 01/01/2023] Open
Abstract
Quorum-sensing bacteria in a growing colony of cells send out signalling molecules (so-called “autoinducers”) and themselves sense the autoinducer concentration in their vicinity. Once—due to increased local cell density inside a “cluster” of the growing colony—the concentration of autoinducers exceeds a threshold value, cells in this clusters get “induced” into a communal, multi-cell biofilm-forming mode in a cluster-wide burst event. We analyse quantitatively the influence of spatial disorder, the local heterogeneity of the spatial distribution of cells in the colony, and additional physical parameters such as the autoinducer signal range on the induction dynamics of the cell colony. Spatial inhomogeneity with higher local cell concentrations in clusters leads to earlier but more localised induction events, while homogeneous distributions lead to comparatively delayed but more concerted induction of the cell colony, and, thus, a behaviour close to the mean-field dynamics. We quantify the induction dynamics with quantifiers such as the time series of induction events and burst sizes, the grouping into induction families, and the mean autoinducer concentration levels. Consequences for different scenarios of biofilm growth are discussed, providing possible cues for biofilm control in both health care and biotechnology.
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Affiliation(s)
- Oliver Kindler
- Institute for Physics & Astronomy, University of Potsdam, D-14476, Potsdam-Golm, Germany
| | - Otto Pulkkinen
- Institute for Molecular Medicine Finland and Helsinki Institute for Information Technology, University of Helsinki, FI-00014, Helsinki, Finland
| | - Andrey G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, D-14476, Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, D-14476, Potsdam-Golm, Germany.
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El-Helow ER, Atalla RG, Sabra WA, Lotfy WA. Kinetic studies on the expression of alginate and extracellular proteins by Pseudomonas aeruginosa FRD1 and PAO1. J GEN APPL MICROBIOL 2019; 66:15-23. [PMID: 31366850 DOI: 10.2323/jgam.2019.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Pseudomonas aeruginosa is characterized by its capability to produce extracellular virulence proteins and to establish biofilm-based infections that do not respond easily to conventional treatments. However, the physiological conditions that decrease the fitness of such a persistent pathogen would assist the host to defend itself and reduce the infection prevalence. Therefore, developing treatments against P. aeruginosa requires a quantitative understanding of the relationship between bacterial growth kinetics and secretion of alginate and proteins, in addition to the ecological factors that control their synthesis. For this purpose, we examined various environmental factors that affect the specific product yield coefficients (expressed as g product/OD600) of alginate and extracellular proteins using a mucoid (FRD1) and a non-mucoid (PAO1) clinical isolate of P. aeruginosa, respectively. The results suggested magnesium sulfate, trace elements and hydrogen peroxide as significant variables that positively affect alginate synthesis by the FRD1 cells. However, the production of extracellular proteins by PAO1 was negatively affected by the concentration of ferrous sulfate. For understanding the kinetics of expressing alginate and extracellular proteins by the cells, a well-controlled 5 L tank bioreactor was used. The results suggested that under the bioreactor controlled conditions, both alginate and extracellular proteins are expressed parallel to biomass increase in the cells of P. aeruginosa.
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Affiliation(s)
- Ehab R El-Helow
- Department of Botany and Microbiology, Faculty of Science, Alexandria University
| | - Ramy G Atalla
- Department of Botany and Microbiology, Faculty of Science, Alexandria University
| | - Wael A Sabra
- Department of Botany and Microbiology, Faculty of Science, Alexandria University
| | - Walid A Lotfy
- Microbiology Department, Faculty of Dentistry, Pharos University in Alexandria
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Karched M, Bhardwaj RG, Tiss A, Asikainen S. Proteomic Analysis and Virulence Assessment of Granulicatella adiacens Secretome. Front Cell Infect Microbiol 2019; 9:104. [PMID: 31069174 PMCID: PMC6491454 DOI: 10.3389/fcimb.2019.00104] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/26/2019] [Indexed: 12/31/2022] Open
Abstract
Despite reports on the occurrence of Granulicatella adiacens in infective endocarditis, few mechanistic studies on its virulence characteristics or pathogenicity are available. Proteins secreted by this species may act as determinants of host-microbe interaction and play a role in virulence. Our aim in this study was to investigate and functionally characterize the secretome of G. adiacens. Proteins in the secretome preparation were digested by trypsin and applied to nanoLC-ESI-MS/MS. By using a combined mass spectrometry and bioinformatics approach, we identified 101 proteins. Bioinformatics tools predicting subcellular localization revealed that 18 of the secreted proteins possessed signal sequence. More than 20% of the secretome proteins were putative virulence proteins including serine protease, superoxide dismutase, aminopeptidase, molecular chaperone DnaK, and thioredoxin. Ribosomal proteins, molecular chaperones, and glycolytic enzymes, together known as "moonlighting proteins," comprised fifth of the secretome proteins. By Gene Ontology analysis, more than 60 proteins of the secretome were grouped in biological processes or molecular functions. KEGG pathway analysis disclosed that the secretome consisted of enzymes involved in biosynthesis of antibiotics. Cytokine profiling revealed that secreted proteins stimulated key cytokines, such as IL-1β, MCP-1, TNF-α, and RANTES from human PBMCs. In summary, the results from the current investigation of the G. adiacens secretome provide a basis for understanding possible pathogenic mechanisms of G. adiacens.
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Affiliation(s)
- Maribasappa Karched
- Oral Microbiology Research Laboratory, Faculty of Dentistry, Kuwait University, Kuwait City, Kuwait
| | - Radhika G Bhardwaj
- Oral Microbiology Research Laboratory, Faculty of Dentistry, Kuwait University, Kuwait City, Kuwait
| | - Ali Tiss
- Functional Proteomics and Metabolomics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Sirkka Asikainen
- Oral Microbiology Research Laboratory, Faculty of Dentistry, Kuwait University, Kuwait City, Kuwait
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Marshall RC, Whitworth DE. Is "Wolf-Pack" Predation by Antimicrobial Bacteria Cooperative? Cell Behaviour and Predatory Mechanisms Indicate Profound Selfishness, Even when Working Alongside Kin. Bioessays 2019; 41:e1800247. [PMID: 30919490 DOI: 10.1002/bies.201800247] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/10/2019] [Indexed: 01/27/2023]
Abstract
For decades, myxobacteria have been spotlighted as exemplars of social "wolf-pack" predation, communally secreting antimicrobial substances into the shared public milieu. This behavior has been described as cooperative, becoming more efficient if performed by more cells. However, laboratory evidence for cooperativity is limited and of little relevance to predation in a natural setting. In contrast, there is accumulating evidence for predatory mechanisms promoting "selfish" behavior during predation, which together with conflicting definitions of cooperativity, casts doubt on whether microbial "wolf-pack" predation really is cooperative. Here, it is hypothesized that public-goods-mediated predation is not cooperative, and it is argued that a holistic model of microbial predation is needed, accounting for predator and prey relatedness, social phenotypes, spatial organization, activity/specificity/transport of secreted toxins, and prey resistance mechanisms. Filling such gaps in our knowledge is vital if the evolutionary benefits of potentially costly microbial behaviors mediated by public goods are to be properly understood.
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Affiliation(s)
- Rupert C Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DA, UK
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DA, UK
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Wang R, Chen YC, Lai YJ, Lu TJ, Huang ST, Lo YC. Dekkera bruxellensis, a beer yeast that specifically bioconverts mogroside extracts into the intense natural sweetener siamenoside I. Food Chem 2019; 276:43-49. [DOI: 10.1016/j.foodchem.2018.09.163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/13/2018] [Accepted: 09/26/2018] [Indexed: 12/18/2022]
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Roberts MF, Khan HM, Goldstein R, Reuter N, Gershenson A. Search and Subvert: Minimalist Bacterial Phosphatidylinositol-Specific Phospholipase C Enzymes. Chem Rev 2018; 118:8435-8473. [DOI: 10.1021/acs.chemrev.8b00208] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Rebecca Goldstein
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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