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Balobanov V, Chertkova R, Egorova A, Dolgikh D, Bychkova V, Kirpichnikov M. The Kinetics of Amyloid Fibril Formation by de Novo Protein Albebetin and Its Mutant Variants. Biomolecules 2020; 10:E241. [PMID: 32033353 PMCID: PMC7072675 DOI: 10.3390/biom10020241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/01/2020] [Accepted: 02/03/2020] [Indexed: 11/17/2022] Open
Abstract
Engineering of amyloid structures is one of the new perspective areas of protein engineering. Studying the process of amyloid formation can help find ways to manage it in the interests of medicine and biotechnology. One of the promising candidates for the structural basis of artificial functional amyloid fibrils is albebetin (ABB), an artificial protein engineered under the leadership of O.B. Ptitsyn. Various aspects of the amyloid formation of this protein and some methods for controlling this process are investigated in this paper. Four stages of amyloid fibrils formation by this protein from the first non-fibrillar aggregates to mature fibrils and large micron-sized complexes have been described in detail. Dependence of albebetin amyloids formation on external conditions and some mutations also have been described. The introduction of similar point mutations in the two structurally identical α-β-β motifs of ABB lead to different amiloidogenesis kinetics. The inhibitory effect of a disulfide bond and high pH on amyloid fibrils formation, that can be used to control this process, was shown. The results of this work are a good basis for the further design and use of ABB-based amyloid constructs.
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Affiliation(s)
- Vitalii Balobanov
- Institute of Protein Research, Pushchino, Moscow 142290, Russia (V.B.)
| | - Rita Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho–Maklaya st. 16/10, Moscow 117997, Russia
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow 117312, Russia
| | - Anna Egorova
- Institute of Protein Research, Pushchino, Moscow 142290, Russia (V.B.)
| | - Dmitry Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho–Maklaya st. 16/10, Moscow 117997, Russia
- Biology Department, Lomonosov Moscow State University, Leninskie gory, 1/12, Moscow 119899, Russia
| | | | - Mikhail Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho–Maklaya st. 16/10, Moscow 117997, Russia
- Biology Department, Lomonosov Moscow State University, Leninskie gory, 1/12, Moscow 119899, Russia
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202
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Sayed MA, Abdelsalam HK, El-Bassuony AAH. Antimicrobial activity of Novel spinel nanoferrites against pathogenic fungi and bacteria. World J Microbiol Biotechnol 2020; 36:25. [DOI: 10.1007/s11274-020-2803-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/16/2020] [Indexed: 10/25/2022]
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203
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Das S, Czuni L, Báló V, Papp G, Gazdag Z, Papp N, Kőszegi T. Cytotoxic Action of Artemisinin and Scopoletin on Planktonic Forms and on Biofilms of Candida Species. Molecules 2020; 25:E476. [PMID: 31979177 PMCID: PMC7038054 DOI: 10.3390/molecules25030476] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
We investigated the antifungal activities of purified plant metabolites artemisinin (Ar) and scopoletin (Sc) including inhibition, effects on metabolic activities, viability, and oxidative stress on planktonic forms and on preformed biofilms of seven Candida species. The characteristic minimum inhibitory concentration (MIC90) of Ar and Sc against Candida species ranged from 21.83-142.1 µg/mL and 67.22-119.4 µg/mL, respectively. Drug concentrations causing ≈10% CFU decrease within 60 minutes of treatments were also determined (minimum effective concentration, MEC10) using 100-fold higher CFUs than in the case of MIC90 studies. Cytotoxic effects on planktonic and on mature biofilms of Candida species at MEC10 concentrations were further evaluated with fluorescent live/dead discrimination techniques. Candida glabrata, Candida guilliermondii, and Candida parapsilosis were the species most sensitive to Ar and Sc. Ar and Sc were also found to promote the accumulation of intracellular reactive oxygen species (ROS) by increasing oxidative stress at their respective MEC10 concentrations against the tested planktonic Candida species. Ar and Sc possess dose-dependent antifungal action but the underlying mechanism type (fungistatic and fungicidal) is not clear yet. Our data suggest that Ar and Sc found in herbal plants might have potential usage in the fight against Candida biofilms.
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Affiliation(s)
- Sourav Das
- Department of Laboratory Medicine, University of Pécs, Medical School, 7624 Pécs, Ifjúság u. 13., Hungary;
- János Szentágothai Research Center, University of Pécs, 7624 Pécs, Ifjúság u. 20., Hungary
| | - Lilla Czuni
- Department of General and Environmental Microbiology, Institute of Biology, University of Pécs, 7624 Pécs, Ifjúság u. 6., Hungary; (L.C.); (V.B.); (G.P.); (Z.G.)
- Microbial Biotechnology Research Group, János Szentágothai Research Center, University of Pécs, 7624 Pécs, Ifjúság u. 20., Hungary
| | - Viktória Báló
- Department of General and Environmental Microbiology, Institute of Biology, University of Pécs, 7624 Pécs, Ifjúság u. 6., Hungary; (L.C.); (V.B.); (G.P.); (Z.G.)
| | - Gábor Papp
- Department of General and Environmental Microbiology, Institute of Biology, University of Pécs, 7624 Pécs, Ifjúság u. 6., Hungary; (L.C.); (V.B.); (G.P.); (Z.G.)
- Microbial Biotechnology Research Group, János Szentágothai Research Center, University of Pécs, 7624 Pécs, Ifjúság u. 20., Hungary
| | - Zoltán Gazdag
- Department of General and Environmental Microbiology, Institute of Biology, University of Pécs, 7624 Pécs, Ifjúság u. 6., Hungary; (L.C.); (V.B.); (G.P.); (Z.G.)
- Microbial Biotechnology Research Group, János Szentágothai Research Center, University of Pécs, 7624 Pécs, Ifjúság u. 20., Hungary
| | - Nóra Papp
- Department of Pharmacognosy, University of Pécs, Faculty of Pharmacy, 7624 Pécs, Rókus u. 2, Hungary
| | - Tamás Kőszegi
- Department of Laboratory Medicine, University of Pécs, Medical School, 7624 Pécs, Ifjúság u. 13., Hungary;
- János Szentágothai Research Center, University of Pécs, 7624 Pécs, Ifjúság u. 20., Hungary
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204
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Mechanomicrobiology: how bacteria sense and respond to forces. Nat Rev Microbiol 2020; 18:227-240. [DOI: 10.1038/s41579-019-0314-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2019] [Indexed: 12/26/2022]
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205
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Goya ME, Xue F, Sampedro-Torres-Quevedo C, Arnaouteli S, Riquelme-Dominguez L, Romanowski A, Brydon J, Ball KL, Stanley-Wall NR, Doitsidou M. Probiotic Bacillus subtilis Protects against α-Synuclein Aggregation in C. elegans. Cell Rep 2020; 30:367-380.e7. [PMID: 31940482 PMCID: PMC6963774 DOI: 10.1016/j.celrep.2019.12.078] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/23/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Recent discoveries have implicated the gut microbiome in the progression and severity of Parkinson's disease; however, how gut bacteria affect such neurodegenerative disorders remains unclear. Here, we report that the Bacillus subtilis probiotic strain PXN21 inhibits α-synuclein aggregation and clears preformed aggregates in an established Caenorhabditis elegans model of synucleinopathy. This protection is seen in young and aging animals and is partly mediated by DAF-16. Multiple B. subtilis strains trigger the protective effect via both spores and vegetative cells, partly due to a biofilm formation in the gut of the worms and the release of bacterial metabolites. We identify several host metabolic pathways differentially regulated in response to probiotic exposure, including sphingolipid metabolism. We further demonstrate functional roles of the sphingolipid metabolism genes lagr-1, asm-3, and sptl-3 in the anti-aggregation effect. Our findings provide a basis for exploring the disease-modifying potential of B. subtilis as a dietary supplement.
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Affiliation(s)
- María Eugenia Goya
- University of Edinburgh, Centre for Discovery Brain Sciences, Edinburgh, Scotland
| | - Feng Xue
- University of Edinburgh, Centre for Discovery Brain Sciences, Edinburgh, Scotland
| | | | | | | | - Andrés Romanowski
- University of Edinburgh, School of Biological Sciences, Edinburgh, Scotland
| | - Jack Brydon
- University of Edinburgh, Institute of Genetics & Molecular Medicine, Edinburgh, Scotland
| | - Kathryn L Ball
- University of Edinburgh, Institute of Genetics & Molecular Medicine, Edinburgh, Scotland
| | | | - Maria Doitsidou
- University of Edinburgh, Centre for Discovery Brain Sciences, Edinburgh, Scotland.
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206
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Huang YM, Hong XZ, Shen J, Geng LJ, Pan YH, Ling W, Zhao HL. Amyloids in Site-Specific Autoimmune Reactions and Inflammatory Responses. Front Immunol 2020; 10:2980. [PMID: 31993048 PMCID: PMC6964640 DOI: 10.3389/fimmu.2019.02980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022] Open
Abstract
Amyloid deposition is a histological hallmark of common human disorders including Alzheimer's disease (AD) and type 2 diabetes. Although some reports highlight that amyloid fibrils might activate the innate immunity system via pattern recognition receptors, here, we provide multiple lines of evidence for the protection by site-specific amyloid protein analogs and fibrils against autoimmune attacks: (1) strategies targeting clearance of the AD-related brain amyloid plaque induce high risk of deadly autoimmune destructions in subjects with cognitive dysfunction; (2) administration of amyloidogenic peptides with either full length or core hexapeptide structure consistently ameliorates signs of experimental autoimmune encephalomyelitis; (3) experimental autoimmune encephalomyelitis is exacerbated following genetic deletion of amyloid precursor proteins; (4) absence of islet amyloid coexists with T-cell-mediated insulitis in autoimmune diabetes and autoimmune polyendocrine syndrome; (5) use of islet amyloid polypeptide agonists rather than antagonists improves diabetes care; and (6) common suppressive signaling pathways by regulatory T cells are activated in both local and systemic amyloidosis. These findings indicate dual modulation activity mediated by amyloid protein monomers, oligomers, and fibrils to maintain immune homeostasis. The protection from autoimmune destruction by amyloid proteins offers a novel therapeutic approach to regenerative medicine for common degenerative diseases.
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Affiliation(s)
- Yan-Mei Huang
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Center for Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, China
| | - Xue-Zhi Hong
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Department of Rheumatology and Immunology, The First Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Jian Shen
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Department of Pathology, The First Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Li-Jun Geng
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Center for Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, China
| | - Yan-Hong Pan
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Center for Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, China
| | - Wei Ling
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Department of Endocrinology, Xiangya Medical School, Central South University, Changsha, China
| | - Hai-Lu Zhao
- Department of Immunology, Guangxi Area of Excellence, Guilin Medical University, Guilin, China.,Center for Systems Medicine, Guangxi Key Laboratory of Excellence, Guilin Medical University, Guilin, China.,Institute of Basic Medical Sciences, Faculty of Basic Medicine, Guilin Medical University, Guilin, China
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207
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Falcón García C, Kretschmer M, Lozano-Andrade CN, Schönleitner M, Dragoŝ A, Kovács ÁT, Lieleg O. Metal ions weaken the hydrophobicity and antibiotic resistance of Bacillus subtilis NCIB 3610 biofilms. NPJ Biofilms Microbiomes 2020; 6:1. [PMID: 31908831 PMCID: PMC6941983 DOI: 10.1038/s41522-019-0111-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/03/2019] [Indexed: 02/06/2023] Open
Abstract
Surface superhydrophobicity makes bacterial biofilms very difficult to fight, and it is a combination of their matrix composition and complex surface roughness which synergistically protects these biomaterials from wetting. Although trying to eradicate biofilms with aqueous (antibiotic) solutions is common practice, this can be a futile approach if the biofilms have superhydrophobic properties. To date, there are not many options available to reduce the liquid repellency of biofilms or to prevent this material property from developing. Here, we present a solution to this challenge. We demonstrate how the addition of metal ions such as copper and zinc during or after biofilm formation can render the surface of otherwise superhydrophobic B. subtilis NCIB 3610 biofilms completely wettable. As a result of this procedure, these smoother, hydrophilic biofilms are more susceptible to aqueous antibiotics solutions. Our strategy proposes a scalable and widely applicable step in a multi-faceted approach to eradicate biofilms.
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Affiliation(s)
- Carolina Falcón García
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Martin Kretschmer
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Carlos N. Lozano-Andrade
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kongens Lyngby, Denmark
| | - Markus Schönleitner
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Anna Dragoŝ
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kongens Lyngby, Denmark
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kongens Lyngby, Denmark
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
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208
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Borzenkov M, Pallavicini P, Taglietti A, D’Alfonso L, Collini M, Chirico G. Photothermally active nanoparticles as a promising tool for eliminating bacteria and biofilms. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:1134-1146. [PMID: 32802716 PMCID: PMC7404213 DOI: 10.3762/bjnano.11.98] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/29/2020] [Indexed: 05/11/2023]
Abstract
Bacterial contamination is a severe issue that affects medical devices, hospital tools and surfaces. When microorganisms adhere to a surface (e.g., medical devices or implants) they can develop into a biofilm, thereby becoming more resistant to conventional biocides and disinfectants. Nanoparticles can be used as an antibacterial agent in medical instruments or as a protective coating in implantable devices. In particular, attention is being drawn to photothermally active nanoparticles that are capable of converting absorbed light into heat. These nanoparticles can efficiently eradicate bacteria and biofilms upon light activation (predominantly near the infrared to near-infrared spectral region) due a rapid and pronounced local temperature increase. By using this approach new, protective, antibacterial surfaces and materials can be developed that can be remotely activated on demand. In this review, we summarize the state-of-the art regarding the application of various photothermally active nanoparticles and their corresponding nanocomposites for the light-triggered eradication of bacteria and biofilms.
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Affiliation(s)
- Mykola Borzenkov
- Department of Medicine and Surgery, Nanomedicine Center, University of Milano-Bicocca, piazza dell’Ateneo Nuovo, 20126, Milan, Italy
| | | | - Angelo Taglietti
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100, Pavia, Italy
| | - Laura D’Alfonso
- Department of Physics, University of Milano-Bicocca, piazza dell’Ateneo Nuovo, 20126, Milan, Italy
| | - Maddalena Collini
- Department of Physics, University of Milano-Bicocca, piazza dell’Ateneo Nuovo, 20126, Milan, Italy
| | - Giuseppe Chirico
- Department of Physics, University of Milano-Bicocca, piazza dell’Ateneo Nuovo, 20126, Milan, Italy
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209
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Abstract
When protein/peptides aggregate, they usually form the amyloid state consisting of cross β-sheet structure built by repetitively stacked β-strands forming long fibrils. Amyloids are usually associated with disease including Alzheimer's. However, amyloid has many useful features. It efficiently transforms protein from the soluble to the insoluble state in an essentially two-state process, while its repetitive structure provides high stability and a robust prion-like replication mechanism. Accordingly, amyloid is used by nature in multifaceted and ingenious ways of life, ranging from bacteria and fungi to mammals. These include (1) Structure: Templating for small chemical molecules (Pmel17), biofilm formation in bacteria (curli), assisting aerial hyphae formation in streptomycetes (chaplins) or monolayer formation at a surface (hydrophobins). (2) Reservoirs: A storage state for peptide/proteins to protect them from their surroundings or vice versa (storage of peptide hormones in mammalian secretory granules or major basic protein in eosinophils). (3) Information carriers: The fungal immune system (HET-s prion in Podospora anserina, yeast prions) or long-term memory (e.g., mnemons in yeast, cytoplasmic polyadenylation element-binding protein in aplysia). Aggregation is also used to (4) "suppress" the function of the soluble protein (e.g., Cdc19 in yeast stress granules), or (5) "signaling" through formation of oligomers (e.g., HET-s prion, necroptosis-related proteins RIP1/RIP3). This review summarizes current knowledge on functional amyloids with a focus on the amyloid systems curli in bacteria, HET-s prion in P. anserina, and peptide hormone storage in mammals together with an attempt to highlight differences between functional and disease-associated amyloids.
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Affiliation(s)
- Daniel Otzen
- iNANO, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, CH-8093 Zürich, Switzerland
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210
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Huang Z, Wu L, Li X, Ma L, Borriss R, Gao X. Zn(II) suppresses biofilm formation in Bacillus amyloliquefaciens by inactivation of the Mn(II) uptake. Environ Microbiol 2019; 22:1547-1558. [PMID: 31715659 DOI: 10.1111/1462-2920.14859] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 11/29/2022]
Abstract
Biofilms are architecturally complex communities of microbial cells held together by a self-produced extracellular matrix. Considerable research has focused on the environmental signals that trigger or inhibit biofilm formation by affecting cellular signalling pathways; however, response to soil cues in plant-associated Bacillus has remained largely unaddressed. Therefore, we aimed to investigate the effect of Zn(II) ions in biofilm formation of Bacillus amyloliquefaciens FZB42. We demonstrated that the biofilm formation of B. amyloliquefaciens FZB42 was abolished by Zn(II) at non-deleterious concentrations. Moreover, Zn(II) blocked matrix exopolysaccharide and TasA accumulations. Furthermore, the presence of Zn(II) suppressed expression of the response regulator Spo0F but not of sensor histidine kinases KinA-D. Suppression of phosphorelay by excess Zn interferes with sinI induction under biofilm-inducing conditions, leading to repression of transcription of operons epsA-O and tapA-sigW-tasA. Addition of Zn(II) decreased the intracellular Mn(II) level by competing for binding to the solute-binding protein MntA during Mn(II) uptake. These results suggest that the metal ion Zn(II) has a negative effect on biofilm formation in the plant growth promoting and biocontrol bacterium B. amyloliquefaciens FZB42.
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Affiliation(s)
- Ziyang Huang
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Education, Nanjing, 210095, China
| | - Liming Wu
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Education, Nanjing, 210095, China
| | - Xi Li
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Education, Nanjing, 210095, China
| | - Liumin Ma
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Education, Nanjing, 210095, China
| | - Rainer Borriss
- Nord Reet UG, Greifswald, Germany.,Fachgebiet Phytomedizin, Institut für Agrar- und Gartenbauwissenschaften, Humboldt Universität, Berlin, Germany
| | - Xuewen Gao
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Education, Nanjing, 210095, China
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211
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Nanomechanical properties of steric zipper globular structures. Proc Natl Acad Sci U S A 2019; 116:22478-22484. [PMID: 31636220 DOI: 10.1073/pnas.1908782116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The term amyloid defines a group of proteins that aggregate into plaques or fibers. Amyloid fibers gained their fame mostly due to their relation with neurodegenerative diseases in humans. However, secreted by lower organisms, such as bacteria and fungi, amyloid fibers play a functional role: for example, when they serve as cement in the extracellular matrix of biofilms. Originating either in humans or in microorganisms, the sequence of amyloid proteins is decorated with hexapeptides with high propensity to form fibers, known as steric zippers. We have found that steric zippers form globular structures on route to making fibers and exhibit a characteristic force-distance (F-D) fingerprint when pulled with an atomic force microscope (AFM) tip. Particularly, the F-D pulling curves showed force plateau steps, suggesting that the globular structures were composed of chains that were unwound like a yarn ball. Force plateau analysis showed that the F-D characteristic parameters were sequence sensitive, representing differences in the packing of the hexapeptides within the globules. These unprecedented findings show that steric zippers exhibit a characteristic nanomechanical signature in solution in addition to previously observed characteristic crystallographic structure. Getting to the fundamental interactions that govern the unzipping of full-length amyloid fibers may initiate the development of antiamyloid methods that target the physical in addition to the structural properties of steric zippers.
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212
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Fulaz S, Vitale S, Quinn L, Casey E. Nanoparticle–Biofilm Interactions: The Role of the EPS Matrix. Trends Microbiol 2019; 27:915-926. [DOI: 10.1016/j.tim.2019.07.004] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/19/2019] [Accepted: 07/18/2019] [Indexed: 01/09/2023]
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213
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Kjeldgaard B, Listian SA, Ramaswamhi V, Richter A, Kiesewalter HT, Kovács ÁT. Fungal hyphae colonization by Bacillus subtilis relies on biofilm matrix components. Biofilm 2019; 1:100007. [PMID: 33447794 PMCID: PMC7798453 DOI: 10.1016/j.bioflm.2019.100007] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/15/2019] [Accepted: 10/19/2019] [Indexed: 02/07/2023] Open
Abstract
Bacteria interact with their environment including microbes and higher eukaryotes. The ability of bacteria and fungi to affect each other are defined by various chemical, physical and biological factors. During physical association, bacterial cells can directly attach and settle on the hyphae of various fungal species. Such colonization of mycelia was proposed to be dependent on biofilm formation by the bacteria, but the essentiality of the biofilm matrix was not represented before. Here, we demonstrate that secreted biofilm matrix components of the soil-dwelling bacterium, Bacillus subtilis are essential for the establishment of a dense bacterial population on the hyphae of the filamentous black mold fungus, Aspergillus niger and the basidiomycete mushroom, Agaricus bisporus. We further illustrate that these matrix components can be shared among various mutants highlighting the community shaping impact of biofilm formers on bacteria-fungi interactions.
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Affiliation(s)
- Bodil Kjeldgaard
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stevanus A Listian
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valliyammai Ramaswamhi
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Anne Richter
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Heiko T Kiesewalter
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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214
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Kobayashi K, Ikemoto Y. Biofilm-associated toxin and extracellular protease cooperatively suppress competitors in Bacillus subtilis biofilms. PLoS Genet 2019; 15:e1008232. [PMID: 31622331 PMCID: PMC6818787 DOI: 10.1371/journal.pgen.1008232] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/29/2019] [Accepted: 10/04/2019] [Indexed: 12/17/2022] Open
Abstract
In nature, most bacteria live in biofilms where they compete with their siblings and other species for space and nutrients. Some bacteria produce antibiotics in biofilms; however, since the diffusion of antibiotics is generally hindered in biofilms by extracellular polymeric substances, i.e., the biofilm matrix, their function remains unclear. The Bacillus subtilis yitPOM operon is a paralog of the sdpABC operon, which produces the secreted peptide toxin SDP. Unlike sdpABC, yitPOM is induced in biofilms by the DegS-DegU two-component regulatory system. High yitPOM expression leads to the production of a secreted toxin called YIT. Expression of yitQ, which lies upstream of yitPOM, confers resistance to the YIT toxin, suggesting that YitQ is an anti-toxin protein for the YIT toxin. The alternative sigma factor SigW also contributes to YIT toxin resistance. In a mutant lacking yitQ and sigW, the YIT toxin specifically inhibits biofilm formation, and the extracellular neutral protease NprB is required for this inhibition. The requirement for NprB is eliminated by Δeps and ΔbslA mutations, either of which impairs production of biofilm matrix polymers. Overexpression of biofilm matrix polymers prevents the action of the SDP toxin but not the YIT toxin. These results indicate that, unlike the SDP toxin and many conventional antibiotics, the YIT toxin can pass through layers of biofilm matrix polymers to attack cells within biofilms with assistance from NprB. When the wild-type strain and the YIT-sensitive mutant were grown together on a solid medium, the wild-type strain formed biofilms that excluded the YIT-sensitive mutant. This observation suggests that the YIT toxin protects B. subtilis biofilms against competitors. Several bacteria are known to produce antibiotics in biofilms. We propose that some bacteria including B. subtilis may have evolved specialized antibiotics that can function within biofilms. Biofilms are multicellular aggregates of bacteria that are formed on various living and non-living surfaces. Biofilms often cause serious problems, including food contamination and infectious diseases. Since bacteria in biofilms exhibit increased tolerance or resistance to antimicrobials, new agents and treatments for combating biofilm-related problems are required. In this study, we demonstrated that B. subtilis produces a secreted peptide antibiotic called the YIT toxin and its resistant proteins in biofilms. A mutant lacking the resistance genes was defective in biofilm formation. This effect resulted from the ability of the YIT toxin to pass through the biofilm defense barrier and to attack biofilm cells. Thus, unlike many conventional antibiotics, the YIT toxin can penetrate biofilms and suppress the growth of YIT toxin-sensitive cells within biofilms. Some bacteria produce antibiotics in biofilms, some of which can alter the bacterial composition in the biofilms. Taking these observations into consideration, our findings suggest that some bacteria produce special antibiotics that are effective against bacteria in biofilms, and these antibiotics might serve as anti-biofilm agents.
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Affiliation(s)
- Kazuo Kobayashi
- Division of Biological Science, Nara Institute of Science & Technology, Ikoma, Nara, Japan
- * E-mail:
| | - Yukako Ikemoto
- Division of Biological Science, Nara Institute of Science & Technology, Ikoma, Nara, Japan
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215
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Mohite BV, Koli SH, Rajput JD, Patil VS, Agarwal T, Patil SV. Production and characterization of multifacet exopolysaccharide from an agricultural isolate,Bacillus subtilis. Biotechnol Appl Biochem 2019; 66:1010-1023. [DOI: 10.1002/bab.1824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/16/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Bhavana V. Mohite
- School of Life SciencesKavayitri Bahinabai Chaudhari North Maharashtra University Jalgaon Maharashtra India
| | - Sunil H. Koli
- School of Life SciencesKavayitri Bahinabai Chaudhari North Maharashtra University Jalgaon Maharashtra India
| | - Jamatsing D. Rajput
- School of Life SciencesKavayitri Bahinabai Chaudhari North Maharashtra University Jalgaon Maharashtra India
| | - Vikas S. Patil
- University Institute of Chemical TechnologyKavayitri Bahinabai Chaudhari North Maharashtra University Jalgaon Maharashtra India
| | - Tarun Agarwal
- Department of BiotechnologyIndian Institute of Technology Kharagpur West Bengal India
| | - Satish V. Patil
- School of Life SciencesKavayitri Bahinabai Chaudhari North Maharashtra University Jalgaon Maharashtra India
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216
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Wang X, Kong Y, Zhao H, Yan X. Dependence of the
Bacillus subtilis
biofilm expansion rate on phenotypes and the morphology under different growing conditions. Dev Growth Differ 2019; 61:431-443. [DOI: 10.1111/dgd.12627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaoling Wang
- School of Mechanical Engineering University of Science and Technology Beijing Beijing China
- School of Engineering and Applied Sciences Harvard University Cambridge MA USA
| | - Yuhao Kong
- School of Mechanical Engineering University of Science and Technology Beijing Beijing China
| | - Hui Zhao
- State Key Laboratory of Computer Science Institute of Software Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Huairou China
| | - Xiaoqiang Yan
- School of Mechanical Engineering University of Science and Technology Beijing Beijing China
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217
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Iadanza MG, Jackson MP, Hewitt EW, Ranson NA, Radford SE. A new era for understanding amyloid structures and disease. Nat Rev Mol Cell Biol 2019; 19:755-773. [PMID: 30237470 DOI: 10.1038/s41580-018-0060-8] [Citation(s) in RCA: 580] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aggregation of proteins into amyloid fibrils and their deposition into plaques and intracellular inclusions is the hallmark of amyloid disease. The accumulation and deposition of amyloid fibrils, collectively known as amyloidosis, is associated with many pathological conditions that can be associated with ageing, such as Alzheimer disease, Parkinson disease, type II diabetes and dialysis-related amyloidosis. However, elucidation of the atomic structure of amyloid fibrils formed from their intact protein precursors and how fibril formation relates to disease has remained elusive. Recent advances in structural biology techniques, including cryo-electron microscopy and solid-state NMR spectroscopy, have finally broken this impasse. The first near-atomic-resolution structures of amyloid fibrils formed in vitro, seeded from plaque material and analysed directly ex vivo are now available. The results reveal cross-β structures that are far more intricate than anticipated. Here, we describe these structures, highlighting their similarities and differences, and the basis for their toxicity. We discuss how amyloid structure may affect the ability of fibrils to spread to different sites in the cell and between organisms in a prion-like manner, along with their roles in disease. These molecular insights will aid in understanding the development and spread of amyloid diseases and are inspiring new strategies for therapeutic intervention.
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Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Eric W Hewitt
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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218
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A Dual-Species Biofilm with Emergent Mechanical and Protective Properties. J Bacteriol 2019; 201:JB.00670-18. [PMID: 30833350 DOI: 10.1128/jb.00670-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/23/2019] [Indexed: 12/14/2022] Open
Abstract
Many microbes coexist within biofilms, or multispecies communities of cells encased in an extracellular matrix. However, little is known about the microbe-microbe interactions relevant for creating these structures. In this study, we explored a striking dual-species biofilm between Bacillus subtilis and Pantoea agglomerans that exhibited characteristics that were not predictable from previous work examining monoculture biofilms. Coculture wrinkle formation required a P. agglomerans exopolysaccharide as well as the B. subtilis amyloid-like protein TasA. Unexpectedly, other B. subtilis matrix components essential for monoculture biofilm formation were not necessary for coculture wrinkling (e.g., the exopolysaccharide EPS, the hydrophobin BslA, and cell chaining). In addition, B. subtilis cell chaining prevented coculture wrinkling, even though chaining was previously associated with more robust monoculture biofilms. We also observed that increasing the relative proportion of P. agglomerans (which forms completely featureless monoculture colonies) increased coculture wrinkling. Using microscopy and rheology, we observed that these two bacteria assemble into an organized layered structure that reflects the physical properties of both monocultures. This partitioning into distinct regions negatively affected the survival of P. agglomerans while also serving as a protective mechanism in the presence of antibiotic stress. Taken together, these data indicate that studying cocultures is a productive avenue to identify novel mechanisms that drive the formation of structured microbial communities.IMPORTANCE In the environment, many microbes form biofilms. However, the interspecies interactions underlying bacterial coexistence within these biofilms remain understudied. Here, we mimic environmentally relevant biofilms by studying a dual-species biofilm formed between Bacillus subtilis and Pantoea agglomerans and subjecting the coculture to chemical and physical stressors that it may experience in the natural world. We determined that both bacteria contribute structural elements to the coculture, which is reflected in its overall viscoelastic behavior. Existence within the coculture can be either beneficial or detrimental depending on the context. Many of the features and determinants of the coculture biofilm appear distinct from those identified in monoculture biofilm studies, highlighting the importance of characterizing multispecies consortia to understand naturally occurring bacterial interactions.
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219
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Mammeri NE, Hierrezuelo J, Tolchard J, Cámara‐Almirón J, Caro‐Astorga J, Álvarez‐Mena A, Dutour A, Berbon M, Shenoy J, Morvan E, Grélard A, Kauffmann B, Lecomte S, Vicente A, Habenstein B, Romero D, Loquet A. Molecular architecture of bacterial amyloids in
Bacillus
biofilms. FASEB J 2019; 33:12146-12163. [DOI: 10.1096/fj.201900831r] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Nadia El Mammeri
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | | | - James Tolchard
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | | | | | | | - Antoine Dutour
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Melanie Berbon
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Jayakrishna Shenoy
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Estelle Morvan
- Institut Européen de Chimie et Biologie (IECB)Unité Mixte de Service (UMS) 3033 Unité de Soutien (US) 001Centre National de la Recherche (CNRS)University of BordeauxPessacFrance
| | - Axelle Grélard
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie (IECB)Unité Mixte de Service (UMS) 3033 Unité de Soutien (US) 001Centre National de la Recherche (CNRS)University of BordeauxPessacFrance
| | - Sophie Lecomte
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Antonio Vicente
- Departamento de MicrobiologíaUniversidad de MálagaMálagaSpain
| | - Birgit Habenstein
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
| | - Diego Romero
- Departamento de MicrobiologíaUniversidad de MálagaMálagaSpain
| | - Antoine Loquet
- L'Institut de Chimie et Biologie des Membranes et des Nano‐Objets (CBMN)Unité Mixte de Recherche (UMR) 5248University of BordeauxPessacFrance
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220
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Ganin H, Kemper N, Meir S, Rogachev I, Ely S, Massalha H, Mandaby A, Shanzer A, Keren-Paz A, Meijler MM, Malitsky S, Aharoni A, Kolodkin-Gal I. Indole Derivatives Maintain the Status Quo Between Beneficial Biofilms and Their Plant Hosts. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1013-1025. [PMID: 30811315 DOI: 10.1094/mpmi-12-18-0327-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biofilms formed by bacteria on plant roots play an important role in maintaining an optimal rhizosphere environment that supports plant growth and fitness. Bacillus subtilis is a potent plant growth promoter, forming biofilms that play a key role in protecting the host from fungal and bacterial infections. In this work, we demonstrate that the development of B. subtilis biofilms is antagonized by specific indole derivatives that accumulate during symbiotic interactions with plant hosts. Indole derivatives are more potent signals when the plant polysaccharide xylan serves as a carbon source, a mechanism to sustain beneficial biofilms at a biomass that can be supported by the plant. Moreover, B. subtilis biofilms formed by mutants resistant to indole derivatives become deleterious to the plants due to their capacity to consume and recycle plant polysaccharides. These results demonstrate how a dynamic metabolite-based dialogue can promote homeostasis between plant hosts and their beneficial biofilm communities.
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Affiliation(s)
- Hadas Ganin
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Natalie Kemper
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sagit Meir
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Ilana Rogachev
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Shir Ely
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Hassan Massalha
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Aviad Mandaby
- 3Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Alona Keren-Paz
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael M Meijler
- 3Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Asaph Aharoni
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Ilana Kolodkin-Gal
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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221
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Varadi M, De Baets G, Vranken WF, Tompa P, Pancsa R. AmyPro: a database of proteins with validated amyloidogenic regions. Nucleic Acids Res 2019; 46:D387-D392. [PMID: 29040693 PMCID: PMC5753394 DOI: 10.1093/nar/gkx950] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/10/2017] [Indexed: 01/05/2023] Open
Abstract
Soluble functional proteins may transform into insoluble amyloid fibrils that deposit in a variety of tissues. Amyloid formation is a hallmark of age-related degenerative disorders. Perhaps surprisingly, amyloid fibrils can also be beneficial and are frequently exploited for diverse functional roles in organisms. Here we introduce AmyPro, an open-access database providing a comprehensive, carefully curated collection of validated amyloid fibril-forming proteins from all kingdoms of life classified into broad functional categories (http://amypro.net). In particular, AmyPro provides the boundaries of experimentally validated amyloidogenic sequence regions, short descriptions of the functional relevance of the proteins and their amyloid state, a list of the experimental techniques applied to study the amyloid state, important structural/functional/variation/mutation data transferred from UniProt, a list of relevant PDB structures categorized according to protein states, database cross-references and literature references. AmyPro greatly improves on similar currently available resources by incorporating both prions and functional amyloids in addition to pathogenic amyloids, and allows users to screen their sequences against the entire collection of validated amyloidogenic sequence fragments. By enabling further elucidation of the sequential determinants of amyloid fibril formation, we hope AmyPro will enhance the development of new methods for the precise prediction of amyloidogenic regions within proteins.
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Affiliation(s)
- Mihaly Varadi
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Greet De Baets
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium.,Interuniversity Institute of Bioinformatics in Brussels (IB) 2, ULB-VUB, Brussels, 1050, Belgium.,VIB Center for Structural Biology, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium
| | - Peter Tompa
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium.,VIB Center for Structural Biology, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium.,Institute of Enzymology, Research Centre for Natural Sciences of the HAS, Budapest, 1117, Hungary
| | - Rita Pancsa
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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222
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Alviz-Gazitua P, Fuentes-Alburquenque S, Rojas LA, Turner RJ, Guiliani N, Seeger M. The Response of Cupriavidus metallidurans CH34 to Cadmium Involves Inhibition of the Initiation of Biofilm Formation, Decrease in Intracellular c-di-GMP Levels, and a Novel Metal Regulated Phosphodiesterase. Front Microbiol 2019; 10:1499. [PMID: 31338076 PMCID: PMC6629876 DOI: 10.3389/fmicb.2019.01499] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 06/14/2019] [Indexed: 11/21/2022] Open
Abstract
Cadmium is a highly toxic heavy metal for biological systems. Cupriavidus metallidurans CH34 is a model strain to study heavy metal resistance and bioremediation as it is able to deal with high heavy metal concentrations. Biofilm formation by bacteria is mediated by the second messenger bis-(3′–5′)-cyclic dimeric guanosine monophosphate (c-di-GMP). The aim of this study was to characterize the response of C. metallidurans CH34 planktonic and biofilm cells to cadmium including their c-di-GMP regulatory pathway. Inhibition of the initiation of biofilm formation and EPS production by C. metallidurans CH34 correlates with increased concentration of cadmium. Planktonic and biofilm cells showed similar tolerance to cadmium. During exposure to cadmium an acute decrease of c-di-GMP levels in planktonic and biofilm cells was observed. Transcription analysis by RT-qPCR showed that cadmium exposure to planktonic and biofilm cells induced the expression of the urf2 gene and the mercuric reductase encoding merA gene, which belong to the Tn501/Tn21 mer operon. After exposure to cadmium, the cadA gene involved in cadmium resistance was equally upregulated in both lifestyles. Bioinformatic analysis and complementation assays indicated that the protein encoded by the urf2 gene is a functional phosphodiesterase (PDE) involved in the c-di-GMP metabolism. We propose to rename the urf2 gene as mrp gene for metal regulated PDE. An increase of the second messenger c-di-GMP content by the heterologous expression of the constitutively active diguanylate cyclase PleD correlated with an increase in biofilm formation and cadmium susceptibility. These results indicate that the response to cadmium in C. metallidurans CH34 inhibits the initiation of biofilm lifestyle and involves a decrease in c-di-GMP levels and a novel metal regulated PDE.
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Affiliation(s)
- Pablo Alviz-Gazitua
- Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile.,Ph.D. Program of Microbiology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Sebastián Fuentes-Alburquenque
- Microbial Ecology of Extreme Systems Laboratory, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
| | - Luis A Rojas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile.,Department of Chemistry, Universidad Catoìlica del Norte, Antofagasta, Chile
| | - Raymond J Turner
- Biofilm Research Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Nicolas Guiliani
- Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
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223
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Hengge R. Targeting Bacterial Biofilms by the Green Tea Polyphenol EGCG. Molecules 2019; 24:molecules24132403. [PMID: 31261858 PMCID: PMC6650844 DOI: 10.3390/molecules24132403] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 12/20/2022] Open
Abstract
Bacterial biofilms are multicellular aggregates in which cells are embedded in an extracellular matrix of self-produced biopolymers. Being refractory to antibiotic treatment and host immune systems, biofilms are involved in most chronic infections, and anti-biofilm agents are being searched for urgently. Epigallocatechin-3-gallate (EGCG) was recently shown to act against biofilms by strongly interfering with the assembly of amyloid fibres and the production of phosphoethanolamin-modified cellulose fibrils. Mechanistically, this includes a direct inhibition of the fibre assembly, but also triggers a cell envelope stress response that down-regulates the synthesis of these widely occurring biofilm matrix polymers. Based on its anti-amyloidogenic properties, EGCG seems useful against biofilms involved in cariogenesis or chronic wound infection. However, EGCG seems inefficient against or may even sometimes promote biofilms which rely on other types of matrix polymers, suggesting that searching for 'magic bullet' anti-biofilm agents is an unrealistic goal. Combining molecular and ecophysiological aspects in this review also illustrates why plants control the formation of biofilms on their surfaces by producing anti-amyloidogenic compounds such as EGCG. These agents are not only helpful in combating certain biofilms in chronic infections but even seem effective against the toxic amyloids associated with neuropathological diseases.
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Affiliation(s)
- Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10155 Berlin, Germany.
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224
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Abstract
Understanding the processes that underpin the mechanism of biofilm formation, dispersal, and inhibition is critical to allow exploitation and to understand how microbes thrive in the environment. Here, we reveal that the formation of an extracellular iron chelate restricts the expansion of a biofilm. The countering benefit to self-restriction of growth is protection of an environmental niche. These findings highlight the complex options and outcomes that bacteria need to balance to modulate their local environment to maximize colonization, and therefore survival. Biofilm formation by Bacillus subtilis is a communal process that culminates in the formation of architecturally complex multicellular communities. Here we reveal that the transition of the biofilm into a nonexpanding phase constitutes a distinct step in the process of biofilm development. Using genetic analysis we show that B. subtilis strains lacking the ability to synthesize pulcherriminic acid form biofilms that sustain the expansion phase, thereby linking pulcherriminic acid to growth arrest. However, production of pulcherriminic acid is not sufficient to block expansion of the biofilm. It needs to be secreted into the extracellular environment where it chelates Fe3+ from the growth medium in a nonenzymatic reaction. Utilizing mathematical modeling and a series of experimental methodologies we show that when the level of freely available iron in the environment drops below a critical threshold, expansion of the biofilm stops. Bioinformatics analysis allows us to identify the genes required for pulcherriminic acid synthesis in other Firmicutes but the patchwork presence both within and across closely related species suggests loss of these genes through multiple independent recombination events. The seemingly counterintuitive self-restriction of growth led us to explore if there were any benefits associated with pulcherriminic acid production. We identified that pulcherriminic acid producers can prevent invasion by neighboring communities through the generation of an “iron-free” zone, thereby addressing the paradox of pulcherriminic acid production by B. subtilis.
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225
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Malovichko YV, Nizhnikov AA, Antonets KS. Repertoire of the Bacillus thuringiensis Virulence Factors Unrelated to Major Classes of Protein Toxins and Its Role in Specificity of Host-Pathogen Interactions. Toxins (Basel) 2019; 11:E347. [PMID: 31212976 PMCID: PMC6628457 DOI: 10.3390/toxins11060347] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/21/2019] [Accepted: 06/10/2019] [Indexed: 12/28/2022] Open
Abstract
Bacillus thuringiensis (Bt) is a Gram-positive soil bacteria that infects invertebrates, predominantly of Arthropoda phylum. Due to its immense host range Bt has become a leading producer of biopesticides applied both in biotechnology and agriculture. Cytotoxic effect of Bt, as well as its host specificity, are commonly attributed either to proteinaceous crystal parasporal toxins (Cry and Cyt) produced by bacteria in a stationary phase or to soluble toxins of Vip and Sip families secreted by vegetative cells. At the same time, numerous non-toxin virulence factors of Bt have been discovered, including metalloproteases, chitinases, aminopolyol antibiotics and nucleotide-mimicking moieties. These agents act at each stage of the B. thuringiensis invasion and contribute to cytotoxic properties of Bt strains enhancing toxin activity, ensuring host immune response evasion and participating in extracellular matrix degeneration. In this review we attempt to classify Bt virulence factors unrelated to major groups of protein toxins and discuss their putative role in the establishment of Bt specificity to various groups of insects.
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Affiliation(s)
- Yury V Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg 196608, Russia.
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - Anton A Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg 196608, Russia.
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - Kirill S Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), St. Petersburg 196608, Russia.
- Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia.
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226
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Casciaro B, Lin Q, Afonin S, Loffredo MR, de Turris V, Middel V, Ulrich AS, Di YP, Mangoni ML. Inhibition of Pseudomonas aeruginosa biofilm formation and expression of virulence genes by selective epimerization in the peptide Esculentin-1a(1-21)NH 2. FEBS J 2019; 286:3874-3891. [PMID: 31144441 DOI: 10.1111/febs.14940] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/22/2019] [Accepted: 05/28/2019] [Indexed: 12/21/2022]
Abstract
Pseudomonas aeruginosa is a pathogenic bacterium known to cause serious human infections, especially in immune-compromised patients. This is due to its unique ability to transform from a drug-tolerant planktonic to a more dangerous and treatment-resistant sessile life form, called biofilm. Recently, two derivatives of the frog skin antimicrobial peptide esculentin-1a, i.e. Esc(1-21) and its D-amino acids containing diastereomer Esc(1-21)-1c, were characterized for their powerful anti-Pseudomonal activity against both forms. Prevention of biofilm formation already in its early stages could be even more advantageous for counteracting infections induced by this bacterium. In this work, we studied how the diastereomer Esc(1-21)-1c can inhibit Pseudomonas biofilm formation in comparison to the parent peptide and two clinically-used conventional antibiotics, i.e. colistin and aztreonam, when applied at dosages below the minimal growth inhibitory concentration. Biofilm prevention was correlated to the peptides' ability to inhibit Pseudomonas motility and to reduce the production of virulent metabolites, for example, pyoverdine and rhamnolipids. Furthermore, the molecular mechanism underlying these activities was evaluated by studying the peptides' effect on the expression of key genes involved in the virulence and motility of bacteria, as well as by monitoring the peptides' binding to the bacterial signaling nucleotide ppGpp. Our results demonstrate that the presence of only two D-amino acids in Esc(1-21)-1c is sufficient to downregulate ppGpp-mediated expression of biofilm-associated genes, presumably as a result of higher peptide stability and therefore prolonged interaction with the nucleotide. Overall, these studies should assist efficient design and optimization of new anti-infective agents with multiple pharmacologically beneficial properties.
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Affiliation(s)
- Bruno Casciaro
- Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, Italy.,Center for Life Nano Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Qiao Lin
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Maria Rosa Loffredo
- Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Valeria de Turris
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Volker Middel
- Institute of Toxicology and Genetics (ITG), KIT, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Organic Chemistry, KIT, Karlsruhe, Germany
| | - YuanPu Peter Di
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maria Luisa Mangoni
- Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, Italy
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227
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Shanmugam N, Baker MODG, Ball SR, Steain M, Pham CLL, Sunde M. Microbial functional amyloids serve diverse purposes for structure, adhesion and defence. Biophys Rev 2019; 11:287-302. [PMID: 31049855 PMCID: PMC6557962 DOI: 10.1007/s12551-019-00526-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
The functional amyloid state of proteins has in recent years garnered much attention for its role in serving crucial and diverse biological roles. Amyloid is a protein fold characterised by fibrillar morphology, binding of the amyloid-specific dyes Thioflavin T and Congo Red, insolubility and underlying cross-β structure. Amyloids were initially characterised as an aberrant protein fold associated with mammalian disease. However, in the last two decades, functional amyloids have been described in almost all biological systems, from viruses, to bacteria and archaea, to humans. Understanding the structure and role of these amyloids elucidates novel and potentially ancient mechanisms of protein function throughout nature. Many of these microbial functional amyloids are utilised by pathogens for invasion and maintenance of infection. As such, they offer novel avenues for therapies. This review examines the structure and mechanism of known microbial functional amyloids, with a particular focus on the pathogenicity conferred by the production of these structures and the strategies utilised by microbes to interfere with host amyloid structures. The biological importance of microbial amyloid assemblies is highlighted by their ubiquity and diverse functionality.
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Affiliation(s)
- Nirukshan Shanmugam
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Max O D G Baker
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Sarah R Ball
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Megan Steain
- Infectious Diseases and Immunology, Central Clinical School, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Chi L L Pham
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Margaret Sunde
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia.
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228
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Biofilm Formation and Synthesis of Antimicrobial Compounds by the Biocontrol Agent Bacillus velezensis QST713 in an Agaricus bisporus Compost Micromodel. Appl Environ Microbiol 2019; 85:AEM.00327-19. [PMID: 30979839 DOI: 10.1128/aem.00327-19] [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: 02/08/2019] [Accepted: 04/07/2019] [Indexed: 12/22/2022] Open
Abstract
Bacillus velezensis QST713 is widely used as a biological control agent for crop protection and disease suppression. This strain is used industrially in France for the protection of Agaricus bisporus against Trichoderma aggressivum f. europaeum, which causes green mold disease. The efficacy of this biocontrol process was evaluated in a previous study, yet the mode of its action has not been explored under production conditions. In order to decipher the underlying biocontrol mechanisms for effective biofilm formation by strain QST713 in the compost and for the involvement of antimicrobial compounds, we developed a simplified micromodel for the culture of A. bisporus during its early culture cycle. By using this micromodel system, we studied the transcriptional response of strain QST713 in the presence or absence of A. bisporus and/or T. aggressivum in axenic industrial compost. We report the overexpression of several genes of the biocontrol agent involved in biofilm formation in the compost compared to their expression during growth in broth compost extract either in the exponential growth phase (the epsC, blsA, and tapA genes) or in the stationary growth phase (the tapA gene), while a gene encoding a flagellar protein (hag) was underexpressed. We also report the overexpression of Bacillus velezensis QST713 genes related to surfactin (srfAA) and fengycin (fenA) production in the presence of the fungal pathogen in the compost.IMPORTANCE Biocontrol agents are increasingly used to replace chemical pesticides to prevent crop diseases. In the button mushroom field in France, the use of Bacillus velezensis QST713 as a biocontrol agent against the green mold Trichoderma aggressivum has been shown to be efficient. However, the biocontrol mechanisms effective in the Agaricus bisporus/Trichoderma aggressivum/Bacillus velezensis QST713 pathosystem are still unknown. Our paper focuses on the exploration of the bioprotection mechanisms of the biocontrol agent Bacillus velezensis QST713 during culture of the button mushroom (Agaricus bisporus) in a micromodel culture system to study the specific response of strain QST713 in the presence of T. aggressivum and/or A. bisporus.
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229
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Molina-Santiago C, Pearson JR, Navarro Y, Berlanga-Clavero MV, Caraballo-Rodriguez AM, Petras D, García-Martín ML, Lamon G, Haberstein B, Cazorla FM, de Vicente A, Loquet A, Dorrestein PC, Romero D. The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization. Nat Commun 2019; 10:1919. [PMID: 31015472 PMCID: PMC6478825 DOI: 10.1038/s41467-019-09944-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 04/05/2019] [Indexed: 12/15/2022] Open
Abstract
Bacteria of the genera Pseudomonas and Bacillus can promote plant growth and protect plants from pathogens. However, the interactions between these plant-beneficial bacteria are understudied. Here, we explore the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We show that the extracellular matrix protects B. subtilis colonies from infiltration by P. chlororaphis. The absence of extracellular matrix results in increased fluidity and loss of structure of the B. subtilis colony. The P. chlororaphis type VI secretion system (T6SS) is activated upon contact with B. subtilis cells, and stimulates B. subtilis sporulation. Furthermore, we find that B. subtilis sporulation observed prior to direct contact with P. chlororaphis is mediated by histidine kinases KinA and KinB. Finally, we demonstrate the importance of the extracellular matrix and the T6SS in modulating the coexistence of the two species on melon plant leaves and seeds. Pseudomonas and Bacillus can promote plant growth but their mutual interactions are unclear. Here, the authors show that the extracellular matrix protects Bacillus colonies from infiltration by Pseudomonas cells, while the Pseudomonas type VI secretion system stimulates Bacillus sporulation.
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Affiliation(s)
- Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - John R Pearson
- Nano-imaging Unit, Andalusian Centre for Nanomedicine and Biotechnology, BIONAND, 29071, Málaga, Spain
| | - Yurena Navarro
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - María Victoria Berlanga-Clavero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | | | - Daniel Petras
- University of California San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, CA, 92093, USA
| | - María Luisa García-Martín
- Nano-imaging Unit, Andalusian Centre for Nanomedicine and Biotechnology, BIONAND, 29071, Málaga, Spain
| | - Gaelle Lamon
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600, Pessac, France
| | - Birgit Haberstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600, Pessac, France
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600, Pessac, France
| | - Pieter C Dorrestein
- University of California San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, CA, 92093, USA
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain.
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230
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Upadhyay A. Structure of proteins: Evolution with unsolved mysteries. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 149:160-172. [PMID: 31014967 DOI: 10.1016/j.pbiomolbio.2019.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 02/07/2023]
Abstract
Evolution of macromolecules could be considered as a milestone in the history of life. Nucleic acids are the long stretches of nucleotides that contain all the possible codes and information of life. On the other hand, proteins are their actual translated outcomes, or reflections of modifications in their structure that have occurred at a slow, but steady rate over a very long period of evolution. Over the years of research, biophysicists, biochemists, molecular and structural biologists have unfurled several layers of the structural convolutions in these chemical molecules; however evolutionists look over their structures through a different prism, which may or may not coincide with others. There remains a need to outline several well-known, but less discussed features of protein structures, like intrinsically disordered states, degron signals and different types of ubiquitin chains providing degradation signals, which help the cellular proteolytic machinery to identify and target the proteins towards degradation pathways. There are several important factors, which are critical for folding of proteins into their native three-dimensional conformations by the cytoplasmic chaperones; but in real time how the chaperones fold the newly synthesized polypeptide sequences into a particular three-dimensional shape within a fraction of second is still a mystery for biologists as well as mathematicians. Multiple similar unsolved or unaddressed questions need to be addressed in detail so that future line of research can dig deeper into the finer details of these structures of the proteins.
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Affiliation(s)
- Arun Upadhyay
- Department of Biochemistry, Central University of Rajasthan, Ajmer, 305817, India.
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231
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Oelker A, Horger T, Kuttler C. From Staphylococcus aureus gene regulation to its pattern formation. J Math Biol 2019; 78:2207-2234. [PMID: 30949755 DOI: 10.1007/s00285-019-01340-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/31/2018] [Indexed: 11/25/2022]
Abstract
The focus of this paper is to develop a new partial differential equation model for the pattern formation of the human pathogen Staphylococcus aureus, starting from a newly developed model of selected gene regulation mechanisms. In our model, we do not only account for the bacteria densities and nutrient concentrations, but also for the quorum sensing and biofilm components, since they enable bacteria to coordinate their behavior and provide the environment in which the colony grows. To this end, we model the relevant gene regulation systems using ordinary differential equations and therefrom derive our evolution equations for quorum sensing and biofilm environment by time-scale arguments. Furthermore, we compare and validate our model and the corresponding simulation results with biological real data observations of Staphylococcus aureus mutant colony growth in the laboratory. We show that we are able to adequately display the qualitative biological features of pattern formation in selected mutants, using the parameter changes indicated by the gene regulation mechanisms.
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Affiliation(s)
- A Oelker
- Technische Universität München, Boltzmannstrasse 3, 85748, Garching bei München, Germany.
| | - T Horger
- Technische Universität München, Boltzmannstrasse 3, 85748, Garching bei München, Germany
| | - C Kuttler
- Technische Universität München, Boltzmannstrasse 3, 85748, Garching bei München, Germany
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232
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Adegbeye MJ, Elghandour MMMY, Barbabosa-Pliego A, Monroy JC, Mellado M, Ravi Kanth Reddy P, Salem AZM. Nanoparticles in Equine Nutrition: Mechanism of Action and Application as Feed Additives. J Equine Vet Sci 2019; 78:29-37. [PMID: 31203981 DOI: 10.1016/j.jevs.2019.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 03/31/2019] [Accepted: 04/01/2019] [Indexed: 12/29/2022]
Abstract
Several concerns exist regarding horse rearing such as environmental pollution, antibiotics resistance, digestive disorders, mycotoxins contamination of animal feed, gut health management, and improvement of feed efficiency. Nanoparticles have the potential to address these issues and thus could be used as feed additive. Citrate reduces and stabilizes gold nanoparticles, alongside biosynthesized silver nanoparticles have the potential to prolong and improve digestive enzyme activity, which would enhance starch digestibility in the stomach. Zinc oxide and selenium nanoparticles could be used to improve feed digestibility and volatile fatty acids production. Magnesium oxide, silver, and copper nanoparticles exhibit strong antimicrobial activity against gram-positive and gram-negative microbes and weaken the biofilm formation of the microbial community. Calcium, zinc, and silver nanoparticles could be used to prevent periodontal disease in horses. In addition, silver nanoparticles may be applied as antifasciolitics and potentially against other gastrointestinal parasites. Environmental concern of equines could be addressed by using cerium oxide, silver, and cobalt nanoparticles to reduce methane emission and zinc oxide could help to reduce fecal mineral output. Fullerol C60[OH]24, a honey-derived silver nanoparticle and zinc oxide nanoparticles exhibit attractive antibacterial properties because of increased specific surface area as the reduced particle enhance unit surface reactivity. Gut health management of equines could be solved with nanoparticles because of the ability of ferrous oxide and copper nanoparticles to improve microbial growth, whereas zinc oxide improves villus height, crypt depth, and villous surface area. It is required to explore in depth the beneficial effects of these nanoparticles as a novel area in the equine industry's both in vitro and in vivo before recommendation to equine owners.
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Affiliation(s)
- Moyosore J Adegbeye
- Department of Animal Science, College of Agriculture, Joseph Ayo Babalola University, Ilesha, Nigeria
| | - Mona M M Y Elghandour
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, México
| | | | - José Cedillo Monroy
- Centro Universitario UAEM-Temascaltepec, Universidad Autónoma del Estado de México, México
| | - Miguel Mellado
- Departamento de Nutrición Animal, Universidad Autónoma de Antonio Narro, Saltillo, México
| | | | - Abdelfattah Z M Salem
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, México.
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233
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Inactivation of cysL Inhibits Biofilm Formation by Activating the Disulfide Stress Regulator Spx in Bacillus subtilis. J Bacteriol 2019; 201:JB.00712-18. [PMID: 30718304 DOI: 10.1128/jb.00712-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/27/2019] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis forms biofilms in response to internal and external stimuli. I previously showed that the cysL deletion mutant was defective in biofilm formation, but the reason for this remains unidentified. CysL is a transcriptional activator of the cysJI operon, which encodes sulfite reductase, an enzyme involved in cysteine biosynthesis. Decreased production of sulfite reductase led to biofilm formation defects in the ΔcysL mutant. The ΔcysL mutation was suppressed by disrupting cysH operon genes, whose products function upstream of sulfite reductase in the cysteine biosynthesis pathway, indicating that defects in cysteine biosynthesis were not a direct cause for the defective biofilm formation observed in the ΔcysL mutant. The cysH gene encodes phosphoadenosine phosphosulfate reductase, which requires a reduced form of thioredoxin (TrxA) as an electron donor. High expression of trxA inhibited biofilm formation in the ΔcysL mutant but not in the wild-type strain. Northern blot analysis showed that trxA transcription was induced in the ΔcysL mutant in a disulfide stress-induced regulator Spx-dependent manner. On the basis of these results, I propose that the ΔcysL mutation causes phosphoadenosine phosphosulfate reductase to consume large amounts of reduced thioredoxin, inducing disulfide stress and activating Spx. The spx mutation restored biofilm formation to the ΔcysL mutant. The ΔcysL mutation reduced expression of the eps operon, which is required for exopolysaccharide production. Moreover, overexpression of the eps operon restored biofilm formation to the ΔcysL mutant. Taken together, these results suggest that the ΔcysL mutation activates Spx, which then inhibits biofilm formation through repression of the eps operon.IMPORTANCE Bacillus subtilis has been studied as a model organism for biofilm formation. In this study, I explored why the cysL deletion mutant was defective in biofilm formation. I demonstrated that the ΔcysL mutation activated the disulfide stress response regulator Spx, which inhibits biofilm formation by repressing biofilm matrix genes. Homologs of Spx are highly conserved among Gram-positive bacteria with low G+C contents. In some pathogens, Spx is also reported to inhibit biofilm formation by repressing biofilm matrix genes, even though these genes and their regulation are quite different from those of B. subtilis Thus, the negative regulation of biofilm formation by Spx is likely to be well conserved across species and may be an appropriate target for control of biofilm formation.
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234
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Seviour T, Derlon N, Dueholm MS, Flemming HC, Girbal-Neuhauser E, Horn H, Kjelleberg S, van Loosdrecht MCM, Lotti T, Malpei MF, Nerenberg R, Neu TR, Paul E, Yu H, Lin Y. Extracellular polymeric substances of biofilms: Suffering from an identity crisis. WATER RESEARCH 2019; 151:1-7. [PMID: 30557778 DOI: 10.1016/j.watres.2018.11.020] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/02/2018] [Accepted: 11/10/2018] [Indexed: 06/09/2023]
Abstract
Microbial biofilms can be both cause and cure to a range of emerging societal problems including antimicrobial tolerance, water sanitation, water scarcity and pollution. The identities of extracellular polymeric substances (EPS) responsible for the establishment and function of biofilms are poorly understood. The lack of information on the chemical and physical identities of EPS limits the potential to rationally engineer biofilm processes, and impedes progress within the water and wastewater sector towards a circular economy and resource recovery. Here, a multidisciplinary roadmap for addressing this EPS identity crisis is proposed. This involves improved EPS extraction and characterization methodologies, cross-referencing between model biofilms and full-scale biofilm systems, and functional description of isolated EPS with in situ techniques (e.g. microscopy) coupled with genomics, proteomics and glycomics. The current extraction and spectrophotometric characterization methods, often based on the principle not to compromise the integrity of the microbial cells, should be critically assessed, and more comprehensive methods for recovery and characterization of EPS need to be developed.
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Affiliation(s)
- Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore.
| | - Nicolas Derlon
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Department of Process Engineering, CH-8600, Dübendorf, Switzerland
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Hans-Curt Flemming
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; University of Duisburg-Essen, Faculty of Chemistry, Biofilm Centre, Essen, Germany
| | - Elisabeth Girbal-Neuhauser
- Laboratoire de Biotechnologies Agroalimentaire et Environmentale (LBAE), Universite Paul Sabatier, Toulouse, France
| | - Harald Horn
- Karlsruhe Institute of Technology (KIT), Engler-Bunte-Institut, Water Chemistry and Water Technology and DVGW Research Laboratories, Karlsruhe, Germany
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | | | - Tommaso Lotti
- Department of Civil and Environmental Engineering - DICEA, University of Florence, Florence, Italy
| | - M Francesca Malpei
- Dipartimento di Ingegneria Civile e Ambientale, Politecnico di Milano, Milan, Italy
| | - Robert Nerenberg
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Etienne Paul
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Toulouse, France
| | - Hanqing Yu
- Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Yuemei Lin
- Department of Biotechcnology, Delft University of Technology, Delft, the Netherlands.
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235
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Zhang P, Zhu J, Xu XY, Qing TP, Dai YZ, Feng B. Identification and function of extracellular protein in wastewater treatment using proteomic approaches: A minireview. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 233:24-29. [PMID: 30553123 DOI: 10.1016/j.jenvman.2018.12.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/04/2018] [Accepted: 12/09/2018] [Indexed: 06/09/2023]
Abstract
Microbial extracellular proteins serve as important functions in wastewater treatment process. Analysis of their compositions and properties is crucial to probe their specific functions. However, conventional analytical techniques cannot obtain interest protein information from complex proteins. Recently, the extracellular proteomics method has been applied to resolve the composition of extracellular proteins. In order to better understand the roles of extracellular protein in wastewater treatment process, this review provides the information on the proteomics methods and their application in investigating extracellular proteins involved in microbial attachment/aggregation, biodegradation of pollutants, and response to environmental stresses. Future work needs to exploit the full capability of the proteome.
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Affiliation(s)
- Peng Zhang
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China.
| | - Jing Zhu
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Xiao-Yan Xu
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Tai-Ping Qing
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - You-Zhi Dai
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Bo Feng
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
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Christensen LF, Jensen KF, Nielsen J, Vad BS, Christiansen G, Otzen DE. Reducing the Amyloidogenicity of Functional Amyloid Protein FapC Increases Its Ability To Inhibit α-Synuclein Fibrillation. ACS OMEGA 2019; 4:4029-4039. [PMID: 31459612 PMCID: PMC6647998 DOI: 10.1021/acsomega.8b03590] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/11/2019] [Indexed: 05/15/2023]
Abstract
Functional amyloid (FA) proteins have evolved to assemble into fibrils with a characteristic cross-β structure, which stabilizes biofilms and contributes to bacterial virulence. Some of the most studied bacterial FAs are the curli protein CsgA, expressed in a wide range of bacteria, and FapC, produced mainly by members of the Pseudomonas genus. Though unrelated, both CsgA and FapC contain imperfect repeats believed to drive the formation of amyloid fibrils. While much is known about CsgA biogenesis and fibrillation, the mechanism of FapC fibrillation remains less explored. Here, we show that removing the three imperfect repeats of FapC (FapC ΔR1R2R3) slows down the fibrillation but does not prevent it. The increased lag phase seen for FapC ΔR1R2R3 allows for disulfide bond formation, which further delays fibrillation. Remarkably, these disulfide-bonded species of FapC ΔR1R2R3 also significantly delay the fibrillation of human α-synuclein, a key protein in Parkinson's disease pathology. This attenuation of α-synuclein fibrillation was not seen for the reduced form of FapC ΔR1R2R3. The results presented here shed light on the FapC fibrillation mechanism and emphasize how unrelated fibrillation systems may share such common fibril formation mechanisms, allowing inhibitors of one fibrillating protein to affect a completely different protein.
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Affiliation(s)
- Line Friis
Bakmann Christensen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Kirstine Friis Jensen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Brian Stougaard Vad
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Gunna Christiansen
- Section
for Medical Microbiology and Immunology, Department of Biomedicine, Aarhus University, Vennelyst Boulevard 4, 8000 Aarhus C, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
- E-mail:
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237
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Chen D, Cao Y, Yu L, Tao Y, Zhou Y, Zhi Q, Lin H. Characteristics and influencing factors of amyloid fibers in S. mutans biofilm. AMB Express 2019; 9:31. [PMID: 30820691 PMCID: PMC6395465 DOI: 10.1186/s13568-019-0753-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/08/2019] [Indexed: 12/13/2022] Open
Abstract
There are signs that amyloid fibers exist in Streptococcus mutans biofilm recently. However, the characteristics of amyloid fibers and fibrillation influencing factors are unknown. In this study, we firstly used transmission electron microscopy (TEM) and atomic force microscopy (AFM) to observe the morphology of amyloid fibers in S. mutans. Then the extracted amyloid fibers from biofilm were studied for their characteristics. Further, the influencing factors, PH, temperature and eDNA, were investigated. Results showed there were mainly two morphologies of amyloid fibers in S. mutans, different in width. Amyloid fibers inhibitor-EGCG obviously destroyed biofilm at different stages, which is dose-dependent. The amount of amyloid fibers positively correlated with biofilm biomass in clinical isolates. Acidic pH and high temperature obviously accelerated amyloid fibrillation. During amyloid fibrillation, amyloid growth morphologies were observed by TEM and results showed two growth morphologies. Amyloid fibers formed complex with eDNA, which we call (a)eDNA. The molecular weight of (a)eDNA was similar to genomic DNA, greatly larger than that of eDNA in matrix. Combined use of DNase I and EGCG was more efficiently in inhibiting amyloid fibers and biofilm biomass. In conclusion, amyloid fibers are the crucial structures for S. mutans biofilm formation, showing two types of morphology. Acidic pH and temperature can obviously accelerate amyloid fibrillation. Amyloid fibers form complex with (a)eDNA and combined use of DNase and amyloid fiber inhibitor is more efficiently in inhibiting S. mutans biofilm formation.
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238
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Liu X, Xu J, Zhu J, Du P, Sun A. Combined Transcriptome and Proteome Analysis of RpoS Regulon Reveals Its Role in Spoilage Potential of Pseudomonas fluorescens. Front Microbiol 2019; 10:94. [PMID: 30787912 PMCID: PMC6372562 DOI: 10.3389/fmicb.2019.00094] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 01/16/2019] [Indexed: 12/23/2022] Open
Abstract
Microbial contamination is considered the main cause of food spoilage. Pseudomonas fluorescens is a typical spoilage bacterium contributing to a large extent to the spoilage process of proteinaceous foods. RpoS is known as an alternative sigma factor controlling stress resistance and virulence in many pathogens. Our previous work revealed that RpoS contributes to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. RNA-seq transcriptomics analysis combined with quantitative proteomics analysis based on multiplexed isobaric tandem mass tag (TMT) labeling was performed in the P. fluorescens wild-type strain UK4 and its derivative carrying an rpoS mutation. A total of 375 differentially expressed coding sequences (DECs) and 212 differentially expressed proteins (DEPs) were identified. The DECs were further verified by qRT-PCR. The combined transcriptome and proteome analyses revealed the involvement of this regulator in several cellular processes, mainly including polysaccharide metabolism, intracellular secretion, extracellular structures, cell wall biogenesis, stress responses, and amino acid and biogenic amine metabolism, which may contribute to the biofilm formation, stress resistance, and spoilage activities of P. fluorescens. Moreover, we indeed observed that RpoS contributed to the production of the macrocolony biofilm's matrix. Our results provide insights into the regulatory network of RpoS and expand the knowledge about the role of RpoS in the functioning of P. fluorescens in food spoilage.
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Affiliation(s)
- Xiaoxiang Liu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Jun Xu
- Hangzhou Lin'an District People's Hospital, Hangzhou, China
| | - Junli Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Peng Du
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Aihua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
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239
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Ching C, Yang B, Onwubueke C, Lazinski D, Camilli A, Godoy VG. Lon Protease Has Multifaceted Biological Functions in Acinetobacter baumannii. J Bacteriol 2019; 201:e00536-18. [PMID: 30348832 PMCID: PMC6304660 DOI: 10.1128/jb.00536-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/19/2018] [Indexed: 12/14/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative opportunistic pathogen that is known to survive harsh environmental conditions and is a leading cause of hospital-acquired infections. Specifically, multicellular communities (known as biofilms) of A. baumannii can withstand desiccation and survive on hospital surfaces and equipment. Biofilms are bacteria embedded in a self-produced extracellular matrix composed of proteins, sugars, and/or DNA. Bacteria in a biofilm are protected from environmental stresses, including antibiotics, which provides the bacteria with selective advantage for survival. Although some gene products are known to play roles in this developmental process in A. baumannii, mechanisms and signaling remain mostly unknown. Here, we find that Lon protease in A. baumannii affects biofilm development and has other important physiological roles, including motility and the cell envelope. Lon proteases are found in all domains of life, participating in regulatory processes and maintaining cellular homeostasis. These data reveal the importance of Lon protease in influencing key A. baumannii processes to survive stress and to maintain viability.IMPORTANCEAcinetobacter baumannii is an opportunistic pathogen and is a leading cause of hospital-acquired infections. A. baumannii is difficult to eradicate and to manage, because this bacterium is known to robustly survive desiccation and to quickly gain antibiotic resistance. We sought to investigate biofilm formation in A. baumannii, since much remains unknown about biofilm formation in this bacterium. Biofilms, which are multicellular communities of bacteria, are surface attached and difficult to eliminate from hospital equipment and implanted devices. Our research identifies multifaceted physiological roles for the conserved bacterial protease Lon in A. baumannii These roles include biofilm formation, motility, and viability. This work broadly affects and expands understanding of the biology of A. baumannii, which will permit us to find effective ways to eliminate the bacterium.
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Affiliation(s)
- Carly Ching
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Brendan Yang
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Chineme Onwubueke
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - David Lazinski
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
| | - Veronica G Godoy
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
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240
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Abstract
A wide range of bacterial pathogens have been shown to form biofilms, which significantly increase their resistance to environmental stresses, such as antibiotics, and are thus of central importance in the context of bacterial diseases. One of the major structural components of these bacterial biofilms are amyloid fibrils, yet the mechanism of fibril assembly and its importance for biofilm formation are currently not fully understood. By studying fibril formation in vitro, in a model system of two common but unrelated biofilm-forming proteins, FapC from Pseudomonas fluorescens and CsgA from Escherichia coli, we found that the two proteins have a common aggregation mechanism. In both systems, fibril formation proceeds via nucleated growth of linear fibrils exhibiting similar measured rates of elongation, with negligible fibril self-replication. These similarities between two unrelated systems suggest that convergent evolution plays a key role in tuning the assembly kinetics of functional amyloid fibrils and indicates that only a narrow window of mechanisms and assembly rates allows for successful biofilm formation. Thus, the amyloid assembly reaction is likely to represent a means for controlling biofilm formation, both by the organism and by possible inhibitory drugs.IMPORTANCE Biofilms are generated by bacteria, embedded in the formed extracellular matrix. The biofilm's function is to improve the survival of a bacterial colony through, for example, increased resistance to antibiotics or other environmental stresses. Proteins secreted by the bacteria act as a major structural component of this extracellular matrix, as they self-assemble into highly stable amyloid fibrils, making the biofilm very difficult to degrade by physical and chemical means once formed. By studying the self-assembly mechanism of the fibrils from their monomeric precursors in two unrelated bacteria, our experimental and theoretical approaches shed light on the mechanism of functional amyloid assembly in the context of biofilm formation. Our results suggest that fibril formation may be a rate-limiting step in biofilm formation, which in turn has implications on the protein self-assembly reaction as a target for potential antibiotic drugs.
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241
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Meisl G, Michaels TCT, Arosio P, Vendruscolo M, Dobson CM, Knowles TPJ. Dynamics and Control of Peptide Self-Assembly and Aggregation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:1-33. [DOI: 10.1007/978-981-13-9791-2_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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242
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243
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Bacterial Amyloids: Biogenesis and Biomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:113-159. [DOI: 10.1007/978-981-13-9791-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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244
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Klotz M, Kretschmer M, Goetz A, Ezendam S, Lieleg O, Opitz M. Importance of the biofilm matrix for the erosion stability of Bacillus subtilis NCIB 3610 biofilms. RSC Adv 2019; 9:11521-11529. [PMID: 35520264 PMCID: PMC9063333 DOI: 10.1039/c9ra01955c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/02/2019] [Indexed: 12/12/2022] Open
Abstract
Erosion of bacterial biofilms is dependent on the composition of the biofilm matrix and the surrounding chemical environment.
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Affiliation(s)
- M. Klotz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - M. Kretschmer
- Munich School of BioEngineering and Department of Mechanical Engineering
- Technische Universität München
- Garching
- Germany
| | - A. Goetz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - S. Ezendam
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
| | - O. Lieleg
- Munich School of BioEngineering and Department of Mechanical Engineering
- Technische Universität München
- Garching
- Germany
| | - M. Opitz
- Center for NanoScience
- Faculty of Physics
- Ludwig-Maximilians-Universität München
- Munich
- Germany
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245
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Abbasi R, Mousa R, Dekel N, Amartely H, Danieli T, Lebendiker M, Levi‐Kalisman Y, Shalev DE, Metanis N, Chai L. The Bacterial Extracellular Matrix Protein TapA Is a Two‐Domain Partially Disordered Protein. Chembiochem 2018; 20:355-359. [DOI: 10.1002/cbic.201800634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Razan Abbasi
- Institute of ChemistryThe Hebrew University of Jerusalem Jerusalem 91904 Israel
- The Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Reem Mousa
- Institute of ChemistryThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Noa Dekel
- Wolfson Centre for Applied Structural BiologyThe Hebrew University of Jerusalem Edmond J. Safra Jerusalem 91904 Israel
| | - Hadar Amartely
- Wolfson Centre for Applied Structural BiologyThe Hebrew University of Jerusalem Edmond J. Safra Jerusalem 91904 Israel
| | - Tsafi Danieli
- Wolfson Centre for Applied Structural BiologyThe Hebrew University of Jerusalem Edmond J. Safra Jerusalem 91904 Israel
| | - Mario Lebendiker
- Wolfson Centre for Applied Structural BiologyThe Hebrew University of Jerusalem Edmond J. Safra Jerusalem 91904 Israel
| | - Yael Levi‐Kalisman
- The Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
- Institute of Life SciencesThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Deborah E. Shalev
- Wolfson Centre for Applied Structural BiologyThe Hebrew University of Jerusalem Edmond J. Safra Jerusalem 91904 Israel
- Department of Pharmaceutical EngineeringAzrieli College of Engineering Jerusalem Jerusalem 9371207 Israel
| | - Norman Metanis
- Institute of ChemistryThe Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Liraz Chai
- Institute of ChemistryThe Hebrew University of Jerusalem Jerusalem 91904 Israel
- The Center for Nanoscience and NanotechnologyThe Hebrew University of Jerusalem Jerusalem 91904 Israel
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246
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Programmable and printable Bacillus subtilis biofilms as engineered living materials. Nat Chem Biol 2018; 15:34-41. [PMID: 30510190 DOI: 10.1038/s41589-018-0169-2] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022]
Abstract
Bacterial biofilms can be programmed to produce living materials with self-healing and evolvable functionalities. However, the wider use of artificial biofilms has been hindered by limitations on processability and functional protein secretion capacity. We describe a highly flexible and tunable living functional materials platform based on the TasA amyloid machinery of the bacterium Bacillus subtilis. We demonstrate that genetically programmable TasA fusion proteins harboring diverse functional proteins or domains can be secreted and can assemble into diverse extracellular nano-architectures with tunable physicochemical properties. Our engineered biofilms have the viscoelastic behaviors of hydrogels and can be precisely fabricated into microstructures having a diversity of three-dimensional (3D) shapes using 3D printing and microencapsulation techniques. Notably, these long-lasting and environmentally responsive fabricated living materials remain alive, self-regenerative, and functional. This new tunable platform offers previously unattainable properties for a variety of living functional materials having potential applications in biomaterials, biotechnology, and biomedicine.
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247
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Erskine E, Morris RJ, Schor M, Earl C, Gillespie RMC, Bromley KM, Sukhodub T, Clark L, Fyfe PK, Serpell LC, Stanley‐Wall NR, MacPhee CE. Formation of functional, non-amyloidogenic fibres by recombinant Bacillus subtilis TasA. Mol Microbiol 2018; 110:897-913. [PMID: 29802781 PMCID: PMC6334530 DOI: 10.1111/mmi.13985] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2018] [Indexed: 01/06/2023]
Abstract
Bacterial biofilms are communities of microbial cells encased within a self-produced polymeric matrix. In the Bacillus subtilis biofilm matrix, the extracellular fibres of TasA are essential. Here, a recombinant expression system allows interrogation of TasA, revealing that monomeric and fibre forms of TasA have identical secondary structure, suggesting that fibrous TasA is a linear assembly of globular units. Recombinant TasA fibres form spontaneously, and share the biological activity of TasA fibres extracted from B. subtilis, whereas a TasA variant restricted to a monomeric form is inactive and subjected to extracellular proteolysis. The biophysical properties of both native and recombinant TasA fibres indicate that they are not functional amyloid-like fibres. A gel formed by TasA fibres can recover after physical shear force, suggesting that the biofilm matrix is not static and that these properties may enable B. subtilis to remodel its local environment in response to external cues. Using recombinant fibres formed by TasA orthologues we uncover species variability in the ability of heterologous fibres to cross-complement the B. subtilis tasA deletion. These findings are indicative of specificity in the biophysical requirements of the TasA fibres across different species and/or reflect the precise molecular interactions needed for biofilm matrix assembly.
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Affiliation(s)
- Elliot Erskine
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Ryan J. Morris
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Marieke Schor
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Chris Earl
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Rachel M. C. Gillespie
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Keith M. Bromley
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Tetyana Sukhodub
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Lauren Clark
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
| | - Paul K. Fyfe
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | | | - Nicola R. Stanley‐Wall
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD1 4HNUK
| | - Cait E. MacPhee
- James Clerk Maxwell Building, School of Physics, and AstronomyUniversity of Edinburgh, The Kings Buildings, Peter Guthrie Tait RoadEdinburghEH9 3FDUK
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248
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Lin Y, Reino C, Carrera J, Pérez J, van Loosdrecht MCM. Glycosylated amyloid-like proteins in the structural extracellular polymers of aerobic granular sludge enriched with ammonium-oxidizing bacteria. Microbiologyopen 2018; 7:e00616. [PMID: 29604180 PMCID: PMC6291783 DOI: 10.1002/mbo3.616] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/20/2018] [Accepted: 02/10/2018] [Indexed: 12/31/2022] Open
Abstract
A new type of structural extracellular polymers (EPS) was extracted from aerobic granular sludge dominated by ammonium-oxidizing bacteria. It was analyzed by Raman and FTIR spectroscopy to characterize specific amino acids and protein secondary structure, and by SDS-PAGE with different stains to identify different glycoconjugates. Its intrinsic fluorescence was captured to visualize the location of the extracted EPS in the nitrifying granules, and its hydrogel-forming property was studied by rheometry. The extracted EPS is abundant with cross ß-sheet secondary structure, contains glycosylated proteins/polypeptides, and rich in tryptophan. It forms hydrogel with high mechanical strength. The extraction and discovery of glycosylated proteins and/or amyloids further shows that conventionally used extraction and characterization techniques are not adequate for the study of structural extracellular polymers in biofilms and/or granular sludge. Confirming amyloids secondary structure in such a complex sample is challengeable due to the possibility of amyloids glycosylation and self-assembly. A new definition of extracellular polymers components which includes glycosylated proteins and a better approach to studying them is required to stimulate biofilm research.
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Affiliation(s)
- Yuemei Lin
- Department of BiotechnologyFaculty of Applied SciencesDelft University of TechnologyDelftThe Netherlands
| | - Clara Reino
- GENOCOV Research GroupDepartment of Chemical, Biological and Environmental EngineeringSchool of EngineeringUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Julián Carrera
- GENOCOV Research GroupDepartment of Chemical, Biological and Environmental EngineeringSchool of EngineeringUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Julio Pérez
- Department of BiotechnologyFaculty of Applied SciencesDelft University of TechnologyDelftThe Netherlands
| | - Mark C. M. van Loosdrecht
- Department of BiotechnologyFaculty of Applied SciencesDelft University of TechnologyDelftThe Netherlands
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249
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Dragoš A, Lakshmanan N, Martin M, Horváth B, Maróti G, Falcón García C, Lieleg O, Kovács ÁT. Evolution of exploitative interactions during diversification in Bacillus subtilis biofilms. FEMS Microbiol Ecol 2018; 93:4604779. [PMID: 29126191 DOI: 10.1093/femsec/fix155] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022] Open
Abstract
Microbial biofilms are tightly packed, heterogeneous structures that serve as arenas for social interactions. Studies on Gram negative models reveal that during evolution in structured environments like biofilms, isogenic populations commonly diversify into phenotypically and genetically distinct variants. These variants can settle in alternative biofilm niches and develop new types of interactions that greatly influence population productivity. Here, we explore the evolutionary diversification of pellicle biofilms of the Gram positive, spore-forming bacterium Bacillus subtilis. We discovered that-similarly to other species-B. subtilis diversifies into distinct colony variants. These variants dramatically differ in biofilm formation abilities and expression of biofilm-related genes. In addition, using a quantitative approach, we reveal striking differences in surface complexity and hydrophobicity of the evolved colony types. Interestingly, one of the morphotypes completely lost the ability of independent biofilm formation and evolved to hitchhike with other morphotypes with improved biofilm forming abilities. Genome comparison suggests that major phenotypic transformations between the morphotypes can be triggered by subtle genetic differences. Our work demonstrates how positive complementarity effects and exploitative interactions intertwine during evolutionary diversification in biofilms.
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Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Nivedha Lakshmanan
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Marivic Martin
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
| | - Balázs Horváth
- Seqomics Biotechnology Ltd, Vállalkozók útja 7, Mórahalom 6782, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Carolina Falcón García
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstr. 11, Garching 85748, Germany
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstr. 11, Garching 85748, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej Building 301, Kgs Lyngby 2800, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 23, Jena 07743, Germany
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250
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Cámara-Almirón J, Caro-Astorga J, de Vicente A, Romero D. Beyond the expected: the structural and functional diversity of bacterial amyloids. Crit Rev Microbiol 2018; 44:653-666. [PMID: 30354913 DOI: 10.1080/1040841x.2018.1491527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intense research has confirmed the formerly theoretical distribution of amyloids in nature, and studies on different systems have illustrated the role of these proteins in microbial adaptation and in interactions with the environment. Two lines of research are expanding our knowledge on functional amyloids: (i) structural studies providing insights into the molecular machineries responsible for the transition from monomer to fibers and (ii) studies showing the way in which these proteins might participate in the microbial fitness in natural settings. Much is known about how amyloids play a role in the social behavior of bacteria, or biofilm formation, and in the adhesion of bacteria to surfaces; however, we are still in the initial stages of understanding a complementary involvement of amyloids in bacteria-host interactions. This review will cover the following two topics: first, the key aspects of the microbial platforms dedicated to the assembly of the fibers, and second, the mechanisms by which bacteria utilize the morphological and biochemical variability of amyloids to modulate the immunological response of the host, plants and humans, contributing to (i) infection, in the case of pathogenic bacteria or (ii) promotion of the health of the host, in the case of beneficial bacteria.
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Affiliation(s)
- Jesús Cámara-Almirón
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Joaquin Caro-Astorga
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Antonio de Vicente
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Diego Romero
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
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