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Loyez M, Fasseaux H, Lobry M, Wattiez R, Caucheteur C. Insulin biotrapping using plasmofluidic optical fiber chips: A benchmark. Biosens Bioelectron 2024; 254:116189. [PMID: 38507927 DOI: 10.1016/j.bios.2024.116189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
Plasmonic optical fiber-based biosensors are currently in their early stages of development as practical and integrated devices, gradually making their way towards the market. While the majority of these biosensors operate using white light and multimode optical fibers (OFs), our approach centers on single-mode OFs coupled with tilted fiber Bragg gratings (TFBGs) in the near-infrared wavelength range. Our objective is to enhance surface sensitivity and broaden sensing capabilities of OF-based sensors to develop in situ sensing with remote interrogation. In this study, we comprehensively assess their performance in comparison to the gold-standard plasmonic reference, a commercial device based on the Kretschmann-Raether prism configuration. We present their refractive index sensitivity and their capability for insulin sensing using a dedicated microfluidics approach. By optimizing a consistent surface biotrapping methodology, we elucidate the dynamic facets of both technologies and highlight their remarkable sensitivity to variations in bulk and surface properties. The one-to-one comparison between both technologies demonstrates the reliability of optical fiber-based measurements, showcasing similar experimental trends obtained with both the prismatic configuration and gold-coated TFBGs, with an even enhanced limit of detection for the latter. This study lays the foundation for the detection of punctual molecular interactions and opens the way towards the detection of spatially and temporally localized events on the surface of optical probes.
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Affiliation(s)
- Médéric Loyez
- Proteomics and Microbiology Department, University of Mons (UMONS), 7000, Belgium; Electromagnetism and Telecom. Department, University of Mons (UMONS), 7000, Belgium.
| | - Hadrien Fasseaux
- Electromagnetism and Telecom. Department, University of Mons (UMONS), 7000, Belgium
| | - Maxime Lobry
- Electromagnetism and Telecom. Department, University of Mons (UMONS), 7000, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons (UMONS), 7000, Belgium
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2
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Verbeelen T, Fernandez CA, Nguyen TH, Gupta S, Leroy B, Wattiez R, Vlaeminck SE, Leys N, Ganigué R, Mastroleo F. Radiotolerance of N-cycle bacteria and their transcriptomic response to low-dose space-analogue ionizing irradiation. iScience 2024; 27:109596. [PMID: 38638570 PMCID: PMC11024918 DOI: 10.1016/j.isci.2024.109596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/08/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
The advancement of regenerative life support systems (RLSS) is crucial to allow long-distance space travel. Within the Micro-Ecological Life Support System Alternative (MELiSSA), efficient nitrogen recovery from urine and other waste streams is vital to produce liquid fertilizer to feed food and oxygen production in subsequent photoautotrophic processes. This study explores the effects of ionizing radiation on nitrogen cycle bacteria that transform urea to nitrate. In particular, we assess the radiotolerance of Comamonas testosteroni, Nitrosomonas europaea, and Nitrobacter winogradskyi after exposure to acute γ-irradiation. Moreover, a comprehensive whole transcriptome analysis elucidates the effects of spaceflight-analogue low-dose ionizing radiation on the individual axenic strains and on their synthetic community o. This research sheds light on how the spaceflight environment could affect ureolysis and nitrification processes from a transcriptomic perspective.
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Affiliation(s)
- Tom Verbeelen
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Celia Alvarez Fernandez
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Thanh Huy Nguyen
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000 Mons, Belgium
| | - Surya Gupta
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
| | - Baptiste Leroy
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000 Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000 Mons, Belgium
| | - Siegfried E. Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium
| | - Natalie Leys
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium
| | - Felice Mastroleo
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
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Abdeljelil N, Ben Miloud Yahia N, Landoulsi A, Chatti A, Wattiez R, Gillan D, Van Houdt R. Proteomic and morphological insights into the exposure of Cupriavidus metallidurans CH34 planktonic cells and biofilms to aluminium. J Hazard Mater 2024; 465:133403. [PMID: 38215523 DOI: 10.1016/j.jhazmat.2023.133403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/15/2023] [Accepted: 12/27/2023] [Indexed: 01/14/2024]
Abstract
Aluminium (Al) is one of the most popular materials for industrial and domestic use. Nevertheless, research has proven that this metal can be toxic to most organisms. This light metal has no known biological function and to date very few aluminium-specific biological pathways have been identified. In addition, information about the impact of this metal on microbial life is scarce. Here, we aimed to study the effect of aluminium on the metal-resistant soil bacterium Cupriavidus metallidurans CH34 in different growth modes, i.e. planktonic cells, adhered cells and mature biofilms. Our results indicated that despite a significant tolerance to aluminium (minimal inhibitory concentration of 6.25 mM Al₂(SO₄)₃.18H₂O), the exposure of C. metallidurans to a sub-inhibitory dose (0.78 mM) caused early oxidative stress and an increase in hydrolytic activity. Changes in the outer membrane surface of planktonic cells were observed, in addition to a rapid disruption of mature biofilms. On protein level, aluminium exposure increased the expression of proteins involved in metabolic activity such as pyruvate kinase, formate dehydrogenase and poly(3-hydroxybutyrate) polymerase, whereas proteins involved in chemotaxis, and the production and transport of iron scavenging siderophores were significantly downregulated.
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Affiliation(s)
- Nissem Abdeljelil
- Proteomics and Microbiology Lab, Research Institute for Biosciences, Mons University, Mons, Belgium; Microbiology Unit, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium; Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, University of Carthage, Jarzouna, Tunisia
| | | | - Ahmed Landoulsi
- Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Abdelwaheb Chatti
- Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Ruddy Wattiez
- Proteomics and Microbiology Lab, Research Institute for Biosciences, Mons University, Mons, Belgium
| | - David Gillan
- Proteomics and Microbiology Lab, Research Institute for Biosciences, Mons University, Mons, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium.
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Matallana-Surget S, Geron A, Decroo C, Wattiez R. Diel Cycle Proteomics: Illuminating Molecular Dynamics in Purple Bacteria for Optimized Biotechnological Applications. Int J Mol Sci 2024; 25:2934. [PMID: 38474181 DOI: 10.3390/ijms25052934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Circadian rhythms, characterized by approximately 24 h cycles, play a pivotal role in enabling various organisms to synchronize their biological activities with daily variations. While ubiquitous in Eukaryotes, circadian clocks remain exclusively characterized in Cyanobacteria among Prokaryotes. These rhythms are regulated by a core oscillator, which is controlled by a cluster of three genes: kaiA, kaiB, and kaiC. Interestingly, recent studies revealed rhythmic activities, potentially tied to a circadian clock, in other Prokaryotes, including purple bacteria such as Rhodospirillum rubrum, known for its applications in fuel and plastic bioproduction. However, the pivotal question of how light and dark cycles influence protein dynamics and the expression of putative circadian clock genes remains unexplored in purple non-sulfur bacteria. Unraveling the regulation of these molecular clocks holds the key to unlocking optimal conditions for harnessing the biotechnological potential of R. rubrum. Understanding how its proteome responds to different light regimes-whether under continuous light or alternating light and dark cycles-could pave the way for precisely fine-tuning bioproduction processes. Here, we report for the first time the expressed proteome of R. rubrum grown under continuous light versus light and dark cycle conditions using a shotgun proteomic analysis. In addition, we measured the impact of light regimes on the expression of four putative circadian clock genes (kaiB1, kaiB2, kaiC1, kaiC2) at the transcriptional and translational levels using RT-qPCR and targeted proteomic (MRM-MS), respectively. The data revealed significant effects of light conditions on the overall differential regulation of the proteome, particularly during the early growth stages. Notably, several proteins were found to be differentially regulated during the light or dark period, thus impacting crucial biological processes such as energy conversion pathways and the general stress response. Furthermore, our study unveiled distinct regulation of the four kai genes at both the mRNA and protein levels in response to varying light conditions. Deciphering the impact of the diel cycle on purple bacteria not only enhances our understanding of their ecology but also holds promise for optimizing their applications in biotechnology, providing valuable insights into the origin and evolution of prokaryotic clock mechanisms.
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Affiliation(s)
- Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Augustin Geron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
- Proteomic and Microbiology Department, University of Mons, B-7000 Mons, Belgium
| | - Corentin Decroo
- Proteomic and Microbiology Department, University of Mons, B-7000 Mons, Belgium
| | - Ruddy Wattiez
- Proteomic and Microbiology Department, University of Mons, B-7000 Mons, Belgium
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Messer LF, Lee CE, Wattiez R, Matallana-Surget S. Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics. Microbiome 2024; 12:36. [PMID: 38389111 PMCID: PMC10882806 DOI: 10.1186/s40168-024-01751-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/03/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment. RESULTS For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community. CONCLUSION Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.
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Affiliation(s)
- Lauren F Messer
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland
| | - Charlotte E Lee
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Mons, 7000, Belgium
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland.
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Verbeelen T, Fernandez CA, Nguyen TH, Gupta S, Aarts R, Tabury K, Leroy B, Wattiez R, Vlaeminck SE, Leys N, Ganigué R, Mastroleo F. Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity. NPJ Microgravity 2024; 10:3. [PMID: 38200027 PMCID: PMC10781756 DOI: 10.1038/s41526-024-00345-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLifeTM PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.
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Affiliation(s)
- Tom Verbeelen
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Celia Alvarez Fernandez
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Thanh Huy Nguyen
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000, Mons, Belgium
| | - Surya Gupta
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Raf Aarts
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Kevin Tabury
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Baptiste Leroy
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000, Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000, Mons, Belgium
| | - Siegfried E Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052, Ghent, Belgium
| | - Natalie Leys
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052, Ghent, Belgium
| | - Felice Mastroleo
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium.
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Martinet B, Przybyla K, Decroo C, Wattiez R, Aron S. Proteomic differences in seminal fluid of social insects whose sperm differ in heat tolerance. R Soc Open Sci 2023; 10:231389. [PMID: 38026028 PMCID: PMC10645120 DOI: 10.1098/rsos.231389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
In the coming years, climate change is likely to increase the frequency and intensity of heatwaves. In many organisms, heat stress provokes physiological perturbations and can lead to decreased male fertility. Bumblebees are endo-heterothermic but display interspecific differences in thermotolerance that could have conservation implications. For the species of concern Bombus magnus, exposure to high temperatures can severely reduce sperm quality and, consequently, reproductive success. Such is not the case for B. terrestris, a ubiquitous species. To decipher the mechanisms at play, we characterized the seminal fluid proteomes of the two species. We quantified 1121 proteins, of which 522 were differentially expressed between B. terrestris and B. magnus. Several proteins with protective functions, such as proteases, antioxidant proteins and various heat-shock proteins, were present at higher levels in B. terrestris than in B. magnus under both control and heat-stress conditions. The same was true for proteins involved in cellular homeostasis, immunity, lipid/sugar metabolism and thermotolerance. Furthermore, proteins involved in the capture and elimination of reactive oxygen species also occurred at much high levels in B. terrestris. Overall, these results clearly indicate differences in the seminal proteome of the more thermotolerant B. terrestris versus B. magnus. The differences may contribute to explaining interspecific differences in sperm survival.
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Affiliation(s)
- Baptiste Martinet
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, Avenue Paul Héger - CP 160/12, 1000 Bruxelles, Belgium
| | | | - Corentin Decroo
- Department of Proteomics and Microbiology, Université de Mons, 7000 Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Université de Mons, 7000 Mons, Belgium
| | - Serge Aron
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, Avenue Paul Héger - CP 160/12, 1000 Bruxelles, Belgium
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Zhou Z, Wattiez R, Constant P, Marrakchi H, Soetaert K, Mathys V, Fontaine V, Zeng S. Telacebec Interferes with Virulence Lipid Biosynthesis Protein Expression and Sensitizes to Other Antibiotics. Microorganisms 2023; 11:2469. [PMID: 37894127 PMCID: PMC10609169 DOI: 10.3390/microorganisms11102469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a public health issue, particularly due to multi-drug-resistant Mtb. The bacillus is wrapped in a waxy envelope containing lipids acting as essential virulence factors, accounting for the natural antibiotic resistance of mycobacteria. Telacebec (previously known as Q203) is a promising new anti-TB agent inhibiting the cytochrome bc1 complex of a mycobacterial electron transport chain (ETC). Here, we show that the telacebec-challenged M. bovis BCG exhibited a reduced expression of proteins involved in the synthesis of phthiocerol dimycocerosates (PDIMs)/phenolic glycolipids (PGLs), lipid virulence factors associated with cell envelope impermeability. Consistently, telacebec, at concentrations lower than its MIC, downregulated the transcription of a PDIM/PGL-synthesizing operon, suggesting a metabolic vulnerability triggered by the drug. The drug was able to synergize on BCG with rifampicin or vancomycin, the latter being a drug exerting a marginal effect on PDIM-bearing bacilli. Telacebec at a concentration higher than its MIC had no detectable effect on cell wall PDIMs, as shown by TLC analysis, a finding potentially explained by the retaining of previously synthesized PDIMs due to the inhibition of growth. The study extends the potential of telacebec, demonstrating an effect on mycobacterial virulence lipids, allowing for the development of new anti-TB strategies.
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Affiliation(s)
- Zhiyu Zhou
- Microbiology, Bioorganic & Macromolecular Chemistry Research Unit, Faculté de Pharmacie, Université libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Patricia Constant
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31077 Toulouse, France
| | - Hedia Marrakchi
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier (UT3), 31077 Toulouse, France
| | - Karine Soetaert
- National Reference Laboratory "Mycobacterium", Sciensano, 1180 Uccle, Belgium
| | - Vanessa Mathys
- National Reference Laboratory "Mycobacterium", Sciensano, 1180 Uccle, Belgium
| | - Véronique Fontaine
- Microbiology, Bioorganic & Macromolecular Chemistry Research Unit, Faculté de Pharmacie, Université libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Sheng Zeng
- School of Nursing and Health, Nanfang College Guangzhou, Guangzhou 510970, China
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Géron A, Werner J, Wattiez R, Matallana-Surget S. Towards the discovery of novel molecular clocks in Prokaryotes. Crit Rev Microbiol 2023:1-13. [PMID: 37330701 DOI: 10.1080/1040841x.2023.2220789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/17/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
Diel cycle is of enormous biological importance as it imposes daily oscillation in environmental conditions, which temporally structures most ecosystems. Organisms developed biological time-keeping mechanisms - circadian clocks - that provide a significant fitness advantage over competitors by optimising the synchronisation of their biological activities. While circadian clocks are ubiquitous in Eukaryotes, they are so far only characterised in Cyanobacteria within Prokaryotes. However, growing evidence suggests that circadian clocks are widespread in the bacterial and archaeal domains. As Prokaryotes are at the heart of crucial environmental processes and are essential to human health, unravelling their time-keeping systems provides numerous applications in medical research, environmental sciences, and biotechnology. In this review, we elaborate on how novel circadian clocks in Prokaryotes offer research and development perspectives. We compare and contrast the different circadian systems in Cyanobacteria and discuss about their evolution and taxonomic distribution. We necessarily provide an updated phylogenetic analysis of bacterial and archaeal species that harbour homologs of the main cyanobacterial clock components. Finally, we elaborate on new potential clock-controlled microorganisms that represent opportunities of ecological and industrial relevance in prokaryotic groups such as anoxygenic photosynthetic bacteria, methanogenic archaea, methanotrophs or sulphate-reducing bacteria.
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Affiliation(s)
- Augustin Géron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), University of Tübingen, Tübingen, Germany
| | - Ruddy Wattiez
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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10
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Claverie E, Perini M, Onderwater RCA, Pianezze S, Larcher R, Roosa S, Yada B, Wattiez R. Multiple Technology Approach Based on Stable Isotope Ratio Analysis, Fourier Transform Infrared Spectrometry and Thermogravimetric Analysis to Ensure the Fungal Origin of the Chitosan. Molecules 2023; 28:molecules28114324. [PMID: 37298800 DOI: 10.3390/molecules28114324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Chitosan is a natural polysaccharide which has been authorized for oenological practices for the treatment of musts and wines. This authorization is limited to chitosan of fungal origin while that of crustacean origin is prohibited. To guarantee its origin, a method based on the measurement of the stable isotope ratios (SIR) of carbon δ13C, nitrogen δ15N, oxygen δ18O and hydrogen δ2H of chitosan has been recently proposed without indicating the threshold authenticity limits of these parameters which, for the first time, were estimated in this paper. In addition, on part of the samples analysed through SIR, Fourier transform infrared spectrometry (FTIR) and thermogravimetric analysis (TGA) were performed as simple and rapid discrimination methods due to limited technological resources. Samples having δ13C values above -14.2‱ and below -125.1‱ can be considered as authentic fungal chitosan without needing to analyse other parameters. If the δ13C value falls between -25.1‱ and -24.9‱, it is necessary to proceed further with the evaluation of the parameter δ15N, which must be above +2.7‱. Samples having δ18O values lower than +25.3‱ can be considered as authentic fungal chitosan. The combination of maximum degradation temperatures (obtained using TGA) and peak areas of Amide I and NH2/Amide II (obtained using FTIR) also allows the discrimination between the two origins of the polysaccharide. Hierarchical cluster analysis (HCA) and principal component analysis (PCA) based on TGA, FTIR and SIR data successfully distributed the tested samples into informative clusters. Therefore, we present the technologies described as part of a robust analytical strategy for the correct identification of chitosan samples from crustaceans or fungi.
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Affiliation(s)
- Elodie Claverie
- MateriaNova ASBL, Avenue Nicolas Copernic 3, 7000 Mons, Belgium
| | - Matteo Perini
- Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all'Adige, Italy
| | | | - Silvia Pianezze
- Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Roberto Larcher
- Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Stéphanie Roosa
- MateriaNova ASBL, Avenue Nicolas Copernic 3, 7000 Mons, Belgium
| | - Bopha Yada
- MateriaNova ASBL, Avenue Nicolas Copernic 3, 7000 Mons, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Avenue du Champ de Mars 6, 7000 Mons, Belgium
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11
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Delacuvellerie A, Brusselman A, Cyriaque V, Benali S, Moins S, Raquez JM, Gobert S, Wattiez R. Long-term immersion of compostable plastics in marine aquarium: Microbial biofilm evolution and polymer degradation. Mar Pollut Bull 2023; 189:114711. [PMID: 36807047 DOI: 10.1016/j.marpolbul.2023.114711] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
The best-selling compostable plastics, polylactic acid (PLA) and polybutylene adipate-co-terephthalate (PBAT), can accidentally end up in the marine environment due to plastic waste mismanagement. Their degradation and colonization by microbial communities are poorly documented in marine conditions. To better understand their degradation, as well as the dynamics of bacterial colonization after a long immersion time (99, 160, and 260 days), PBAT, semicrystalline, and amorphous PLA films were immersed in a marine aquarium. Sequencing and chemical analyses were used in parallel to characterize these samples. Despite the variation in the chemical intrinsic parameters of these plastics, their degradation remains very slow. Microbial community structure varied according to the immersion time with a high proportion of Archaea. Moreover, the plastisphere structure of PBAT was specific. A better understanding of compostable plastic degradability is crucial to evaluate their impact on ecosystems and to eco-design new recyclable plastics with optimal degradation properties.
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Affiliation(s)
- Alice Delacuvellerie
- Proteomics and Microbiology department, University of Mons, 20 place du parc, 7000 Mons, Belgium
| | - Axelle Brusselman
- Oceanology department, UR FOCUS, University of Liège, 11 Allée du 6 août, 4000 Liège, Belgium
| | - Valentine Cyriaque
- Proteomics and Microbiology department, University of Mons, 20 place du parc, 7000 Mons, Belgium; Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark
| | - Samira Benali
- Polymer and Composite Materials Department, University of Mons, 15 Avenue Maistriau, 7000 Mons, Belgium
| | - Sébastien Moins
- Polymer and Composite Materials Department, University of Mons, 15 Avenue Maistriau, 7000 Mons, Belgium
| | - Jean-Marie Raquez
- Polymer and Composite Materials Department, University of Mons, 15 Avenue Maistriau, 7000 Mons, Belgium
| | - Sylvie Gobert
- Oceanology department, UR FOCUS, University of Liège, 11 Allée du 6 août, 4000 Liège, Belgium; STARESO, Pointe Revellata, BP33, 20260 Corse, France
| | - Ruddy Wattiez
- Proteomics and Microbiology department, University of Mons, 20 place du parc, 7000 Mons, Belgium.
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12
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Correa JDS, Primo JDO, Balaba N, Pratsch C, Werner S, Toma HE, Anaissi FJ, Wattiez R, Zanette CM, Onderwater RCA, Bittencourt C. Copper(II) and Cobalt(II) Complexes Based on Abietate Ligands from Pinus Resin: Synthesis, Characterization and Their Antibacterial and Antiviral Activity against SARS-CoV-2. Nanomaterials (Basel) 2023; 13:1202. [PMID: 37049296 PMCID: PMC10096983 DOI: 10.3390/nano13071202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Co-abietate and Cu-abietate complexes were obtained by a low-cost and eco-friendly route. The synthesis process used Pinus elliottii resin and an aqueous solution of CuSO4/CoSO4 at a mild temperature (80 °C) without organic solvents. The obtained complexes are functional pigments for commercial architectural paints with antipathogenic activity. The pigments were characterized by Fourier-transform infrared spectroscopy (FTIR), mass spectrometry (MS), thermogravimetry (TG), near-edge X-ray absorption fine structure (NEXAFS), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), and colorimetric analysis. In addition, the antibacterial efficiency was evaluated using the minimum inhibitory concentration (MIC) test, and the antiviral tests followed an adaptation of the ISO 21702:2019 guideline. Finally, virus inactivation was measured using the RT-PCR protocol using 10% (w/w) of abietate complex in commercial white paint. The Co-abietate and Cu-abietate showed inactivation of >4 log against SARS-CoV-2 and a MIC value of 4.50 µg·mL-1 against both bacteria Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). The results suggest that the obtained Co-abietate and Cu-abietate complexes could be applied as pigments in architectural paints for healthcare centers, homes, and public places.
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Affiliation(s)
- Jamille de S. Correa
- Departament of Chemistry, Universidade Estadual do Centro-Oeste, UNICENTRO, Alameda Elio Antonio Dalla Vecchia, 838, Guarapuava 85040-167, PR, Brazil
| | - Julia de O. Primo
- Departament of Chemistry, Universidade Estadual do Centro-Oeste, UNICENTRO, Alameda Elio Antonio Dalla Vecchia, 838, Guarapuava 85040-167, PR, Brazil
| | - Nayara Balaba
- Departament of Chemistry, Universidade Estadual do Centro-Oeste, UNICENTRO, Alameda Elio Antonio Dalla Vecchia, 838, Guarapuava 85040-167, PR, Brazil
| | - Christoph Pratsch
- Department X-ray Microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Stephan Werner
- Department X-ray Microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Henrique E. Toma
- Institute of Chemistry, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Fauze J. Anaissi
- Departament of Chemistry, Universidade Estadual do Centro-Oeste, UNICENTRO, Alameda Elio Antonio Dalla Vecchia, 838, Guarapuava 85040-167, PR, Brazil
| | - Ruddy Wattiez
- Department of Chemistry, University of Mons, Place du Parc 23, 7000 Mons, Belgium;
| | - Cristina M. Zanette
- Department of Food Engineering, Universidade Estadual do Centro-Oeste, UNICENTRO, Alameda Elio Antonio Dalla Vecchia, 838, Guarapuava 85040-167, PR, Brazil
| | | | - Carla Bittencourt
- Department of Chemistry, University of Mons, Place du Parc 23, 7000 Mons, Belgium;
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13
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Cuellar-Bermudez SP, Bleus D, Mees MA, Struyf T, Lama S, Vandamme D, Adriaensens P, Scherrers R, Thielemans W, Van den Ende W, Wattiez R, Muylaert K. Isolation, purification, and metal-induced gelation of released polysaccharides from spent culture medium of Arthrospira. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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14
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Alloul A, Blansaer N, Cabecas Segura P, Wattiez R, Vlaeminck SE, Leroy B. Dehazing redox homeostasis to foster purple bacteria biotechnology. Trends Biotechnol 2023; 41:106-119. [PMID: 35843758 DOI: 10.1016/j.tibtech.2022.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 12/27/2022]
Abstract
Purple non-sulfur bacteria (PNSB) show great potential for environmental and industrial biotechnology, producing microbial protein, biohydrogen, polyhydroxyalkanoates (PHAs), pigments, etc. When grown photoheterotrophically, the carbon source is typically more reduced than the PNSB biomass, which leads to a redox imbalance. To mitigate the excess of electrons, PNSB can exhibit several 'electron sinking' strategies, such as CO2 fixation, N2 fixation, and H2 and PHA production. The lack of a comprehensive (over)view of these redox strategies is hindering the implementation of PNSB for biotechnology applications. This review aims to present the state of the art of redox homeostasis in phototrophically grown PNSB, presenting known and theoretically expected strategies, and discussing them from stoichiometric, thermodynamic, metabolic, and economic points of view.
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Affiliation(s)
- Abbas Alloul
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Antwerpen, Belgium.
| | - Naïm Blansaer
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Antwerpen, Belgium
| | | | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, University of Mons, Mons, Belgium
| | - Siegfried E Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Antwerpen, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, University of Mons, Mons, Belgium
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15
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Perez R, Benbachir M, Decroo C, Mascolo C, Wattiez R, Aron S. Cataglyphis desert ants use distinct behavioral and physiological adaptations to cope with extreme thermal conditions. J Therm Biol 2023; 111:103397. [PMID: 36585078 DOI: 10.1016/j.jtherbio.2022.103397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/25/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
Some ant species live in hot and arid environments, such as deserts and savannas. Worker polymorphism-variation in worker size and/or morphology within colonies-is adaptive in such ecosystems because it enhances resistance to heat stress and increases the efficiency of resource exploitation. However, species with small, monomorphic workers are also frequently found in these environments. How species with distinct worker size and degrees of polymorphism deal with such stressful environments remains poorly studied. We investigated the behavioral, physiological, and molecular adaptations that may enhance heat and desiccation tolerance in two sympatric species of Cataglyphis desert ants that differ dramatically in worker size and polymorphism: C. viatica is polymorphic, while C. cubica is small and monomorphic. We found that worker size, water content, water loss, and protein regulation play a key role in thermal resistance. (i) Large C. viatica workers better tolerated heat and desiccation stress than did small C. viatica or C. cubica workers. The former had greater water content and lost proportionally less water to evaporation under thermal stress. (ii) Despite their similar size distribution, workers of C. cubica are more heat tolerant than small C. viatica. This higher degree of tolerance likely stemmed from C. cubica workers having greater relative water content. (iii) Under thermal stress, small C. viatica workers metabolized larger quantities of fat and differentially expressed proteins involved in cellular homeostasis. In contrast, C. cubica downregulated the expression of numerous proteins involved in mitochondrial respiration likely reducing ROS accumulation. (iv) Consistent with these results, large C. viatica workers remained active throughout the day; C. cubica workers displayed a bimodal activity pattern, and small C. viatica remained poorly active outside the nest. Our study shows that ecologically similar ant species with different degrees of worker size polymorphism evolved distinct strategies for coping with extreme heat conditions.
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Affiliation(s)
- Rémy Perez
- Department of Evolutionary Biology & Ecology, Université Libre de Bruxelles, B-1050, Brussels, Belgium.
| | - Mohammed Benbachir
- Department of Evolutionary Biology & Ecology, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Corentin Decroo
- Department of Proteomics and Microbiology, Université de Mons, B-7000, Mons, Belgium
| | - Cyril Mascolo
- Department of Proteomics and Microbiology, Université de Mons, B-7000, Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Université de Mons, B-7000, Mons, Belgium
| | - Serge Aron
- Department of Evolutionary Biology & Ecology, Université Libre de Bruxelles, B-1050, Brussels, Belgium
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16
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Segura PC, Wattiez R, Vande Wouwer A, Leroy B, Dewasme L. Dynamic modeling of Rhodospirillum rubrum PHA production triggered by redox stress during VFA photoheterotrophic assimilations. J Biotechnol 2022; 360:45-54. [PMID: 36273668 DOI: 10.1016/j.jbiotec.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/29/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
Polyhydroxyalkanoates (PHA) represent an environmentally friendly alternative to petroleum based plastics for a broad range of applications from packaging to biomedical devices. In the prospect of an industrial PHA production, it is highly valuable to accurately control the incorporation of different repeating units into the polymer, to produce a polyester with specific material characteristics. In this study, we develop macroscopic dynamic models predicting the polymer production and composition when mixtures containing up to four volatile fatty acids (VFA) are used as substrates. These models successfully reproduce the sequential (and preferential) substrate consumption and polymer production/reconsumption patterns, experimentally observed during biomass growth, thanks to simple kinetic structures based on Monod and inhibition factors. These models can serve as a basis for numerical simulation and process analysis, as well as process intensification through model-based optimization and control.
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Affiliation(s)
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, University of Mons, 7000 Mons, Belgium
| | - Alain Vande Wouwer
- Systems, Estimation, Control and Optimization Group (SECO), University of Mons, 7000 Mons, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, University of Mons, 7000 Mons, Belgium
| | - Laurent Dewasme
- Systems, Estimation, Control and Optimization Group (SECO), University of Mons, 7000 Mons, Belgium.
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17
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Primo JDO, Correa JDS, Horsth DFL, Das A, Zając M, Umek P, Wattiez R, Anaissi FJ, Onderwater RCA, Bittencourt C. Antiviral Properties against SARS-CoV-2 of Nanostructured ZnO Obtained by Green Combustion Synthesis and Coated in Waterborne Acrylic Coatings. Nanomaterials (Basel) 2022; 12:4345. [PMID: 36500967 PMCID: PMC9740257 DOI: 10.3390/nano12234345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The COVID-19 pandemic has increased the need for developing disinfectant surfaces as well as reducing the spread of infections on contaminated surfaces and the contamination risk from the fomite route. The present work reports on the antiviral activity of coatings containing ZnO particles obtained by two simple synthesis routes using Aloe vera (ZnO-aloe) or cassava starch (ZnO-starch) as reaction fuel. After detailed characterization using XRD and NEXAFS, the obtained ZnO particles were dispersed in a proportion of 10% with two different waterborne acrylic coatings (binder and commercial white paint) and brushed on the surface of polycarbonates (PC). The cured ZnO/coatings were characterized by scanning electron microscopes (SEM) and energy-dispersive X-ray spectroscopy (EDS). Wettability tests were performed. The virucidal activity of the ZnO particles dispersed in the waterborne acrylic coating was compared to a reference control sample (PC plates). According to RT-PCR results, the ZnO-aloe/coating displays the highest outcome for antiviral activity against SARS-CoV-2 using the acrylic binder, inactivating >99% of the virus after 24 h of contact relative to reference control.
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Affiliation(s)
- Julia de O. Primo
- Departamento de Química, Universidade Estadual Do Centro-Oeste, Guarapuava 85-040-200, Brazil
- Chimie des Interactions Plasma-Surface (ChIPS), Research Institute for Materials Science and Engineering, University of Mons, 7000 Mons, Belgium
| | - Jamille de S. Correa
- Departamento de Química, Universidade Estadual Do Centro-Oeste, Guarapuava 85-040-200, Brazil
| | - Dienifer F. L. Horsth
- Departamento de Química, Universidade Estadual Do Centro-Oeste, Guarapuava 85-040-200, Brazil
- Chimie des Interactions Plasma-Surface (ChIPS), Research Institute for Materials Science and Engineering, University of Mons, 7000 Mons, Belgium
| | - Arkaprava Das
- Chimie des Interactions Plasma-Surface (ChIPS), Research Institute for Materials Science and Engineering, University of Mons, 7000 Mons, Belgium
| | - Marcin Zając
- National Synchrotron Radiation Centre Solaris, Jagiellonian University, 30-392 Kraków, Poland
| | - Polona Umek
- Solid State Physics Department, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, 7000 Mons, Belgium
| | - Fauze J. Anaissi
- Departamento de Química, Universidade Estadual Do Centro-Oeste, Guarapuava 85-040-200, Brazil
| | | | - Carla Bittencourt
- Chimie des Interactions Plasma-Surface (ChIPS), Research Institute for Materials Science and Engineering, University of Mons, 7000 Mons, Belgium
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18
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Bisconti M, Leroy B, Gallagher MT, Senet C, Martinet B, Arcolia V, Wattiez R, Kirkman-Brown JC, Simon JF, Hennebert E. The ribosome inhibitor chloramphenicol induces motility deficits in human spermatozoa: A proteomic approach identifies potentially involved proteins. Front Cell Dev Biol 2022; 10:965076. [PMID: 36120567 PMCID: PMC9478589 DOI: 10.3389/fcell.2022.965076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Mature spermatozoa are almost completely devoid of cytoplasm; as such it has long been believed that they do not contain ribosomes and are therefore not capable of synthesising proteins. However, since the 1950s, various studies have shown translational activity within spermatozoa, particularly during their in vitro capacitation. But the type of ribosomes involved (cytoplasmic or mitochondrial) is still debated. Here, we investigate the presence and activity of the two types of ribosomes in mature human spermatozoa. By targeting ribosomal RNAs and proteins, we show that both types of ribosomes are localized in the midpiece as well as in the neck and the base of the head of the spermatozoa. We assessed the impact of cycloheximide (CHX) and chloramphenicol (CP), inhibitors of cytoplasmic and mitochondrial ribosomes, respectively, on different sperm parameters. Neither CHX, nor CP impacted sperm vitality, mitochondrial activity (measured through the ATP content), or capacitation (measured through the content in phosphotyrosines). However, increasing CP concentrations induced a decrease in total and progressive motilities as well as on some kinematic parameters while no effect was observed with CHX. A quantitative proteomic analysis was performed by mass spectrometry in SWATH mode to compare the proteomes of spermatozoa capacitated in the absence or presence of the two ribosome inhibitors. Among the ∼700 proteins identified in the different tested conditions, 3, 3 and 25 proteins presented a modified abundance in the presence of 1 and 2 mg/ml of CHX, and 1 mg/ml of CP, respectively. The observed abundance variations of some CP-down regulated proteins were validated using Multiple-Reaction Monitoring (MRM). Taken together, our results are in favor of an activity of mitochondrial ribosomes. Their inhibition by CP results in a decrease in the abundance of several proteins, at least FUNDC2 and QRICH2, and consequently induces sperm motility deficits.
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Affiliation(s)
- Marie Bisconti
- Laboratory of Cell Biology, Research Institute for Biosciences, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, CISMa, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Meurig T. Gallagher
- Centre for Systems Modelling and Quantitative Biomedicine, University of Birmingham, Centre for Human Reproductive Science, Birmingham Women’s and Children’s National Health Service Foundation Trust, Birmingham, United Kingdom
| | - Coralie Senet
- Laboratory of Cell Biology, Research Institute for Biosciences, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
| | - Baptiste Martinet
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Vanessa Arcolia
- Clinique de Fertilité Régionale de Mons, CHU Ambroise Paré Hospital, Mons, Belgium
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, CISMa, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Jackson C. Kirkman-Brown
- Institute of Metabolism and Systems Research, University of Birmingham, Centre for Human Reproductive Science, Birmingham Women’s and Children’s National Health Service Foundation Trust, Birmingham, United Kingdom
| | - Jean-François Simon
- Clinique de Fertilité Régionale de Mons, CHU Ambroise Paré Hospital, Mons, Belgium
| | - Elise Hennebert
- Laboratory of Cell Biology, Research Institute for Biosciences, Research Institute for Health Sciences and Technology, University of Mons, Mons, Belgium
- *Correspondence: Elise Hennebert,
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19
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Algrain M, Hennebert E, Bertemes P, Wattiez R, Flammang P, Lengerer B. In the footsteps of sea stars: deciphering the catalogue of proteins involved in underwater temporary adhesion. Open Biol 2022; 12:220103. [PMID: 35975651 PMCID: PMC9382459 DOI: 10.1098/rsob.220103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Sea stars adhere strongly but temporarily to underwater substrata via the secretion of a blend of proteins, forming an adhesive footprint that they leave on the surface after detachment. Their tube feet enclose a duo-gland adhesive system comprising two types of adhesive cells, contributing different layers of the footprint and de-adhesive cells. In this study, we characterized the catalogue of sea star footprint proteins (Sfps) in the species Asterias rubens to gain insights in their potential function. We identified 16 Sfps and mapped their expression to type 1 and/or type 2 adhesive cells or to de-adhesive cells by double fluorescent in situ hybridization. Based on their cellular expression pattern and their conserved functional domains, we propose that the identified Sfps serve different functions during attachment, with two Sfps coupling to the surface, six providing cohesive strength and the rest forming a binding matrix. Immunolabelling of footprints with antibodies directed against one protein of each category confirmed these roles. A de-adhesive gland cell-specific astacin-like proteinase presumably weakens the bond between the adhesive material and the tube foot surface during detachment. Overall, we provide a model for temporary adhesion in sea stars, including a comprehensive list of the proteins involved.
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Affiliation(s)
- Morgane Algrain
- Laboratory of Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Elise Hennebert
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Philip Bertemes
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Technikerstr. 25, Innsbruck 6020, Austria
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Patrick Flammang
- Laboratory of Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Birgit Lengerer
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Technikerstr. 25, Innsbruck 6020, Austria
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20
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Cabecas Segura P, De Meur Q, Alloul A, Tanghe A, Onderwater R, Vlaeminck SE, Wouwer AV, Wattiez R, Dewasme L, Leroy B. Preferential photoassimilation of volatile fatty acids by purple non-sulfur bacteria: Experimental kinetics and dynamic modelling. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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21
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Delacuvellerie A, Ballerini T, Frère L, Matallana-Surget S, Dumontet B, Wattiez R. From rivers to marine environments: A constantly evolving microbial community within the plastisphere. Mar Pollut Bull 2022; 179:113660. [PMID: 35460946 DOI: 10.1016/j.marpolbul.2022.113660] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Plastics accumulate in the environment and the Mediterranean Sea is one of the most polluted sea in the world. The plastic surface is rapidly colonized by microorganisms, forming the plastisphere. Our unique sampling supplied 107 plastic pieces from 22 geographical sites from four aquatic ecosystems (river, estuary, harbor and inshore) in the south of France in order to better understand the parameters which influence biofilm composition. In parallel, 48 enrichment cultures were performed to investigate the presence of plastic degrading-bacteria in the plastisphere. In this context, we showed that the most important drivers of microbial community structure were the sampling site followed by the polymer chemical composition. The study of pathogenic genus distribution highlighted that only 11% of our plastic samples contained higher proportions of Vibrio compared to the natural environment. Finally, results of the enrichment cultures showed a selection of hydrocarbon-degrading microorganisms suggesting their potential role in the plastic degradation.
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Affiliation(s)
- Alice Delacuvellerie
- Proteomics and Microbiology department, University of Mons, 20 place du parc, 7000 Mons, Belgium
| | - Tosca Ballerini
- Expédition MED, 4 Allée des Avettes, 56230 Questembert, France
| | - Laura Frère
- Expédition MED, 4 Allée des Avettes, 56230 Questembert, France
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, Stirling University, United Kingdom
| | - Bruno Dumontet
- Expédition MED, 4 Allée des Avettes, 56230 Questembert, France
| | - Ruddy Wattiez
- Proteomics and Microbiology department, University of Mons, 20 place du parc, 7000 Mons, Belgium.
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22
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Van Camp C, Fraikin C, Claverie E, Onderwater R, Wattiez R. Capsular polysaccharides and exopolysaccharides from Gloeothece verrucosa under various nitrogen regimes and their potential plant defence stimulation activity. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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23
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Delacuvellerie A, Géron A, Gobert S, Wattiez R. New insights into the functioning and structure of the PE and PP plastispheres from the Mediterranean Sea. Environ Pollut 2022; 295:118678. [PMID: 34915097 DOI: 10.1016/j.envpol.2021.118678] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Plastic debris are accumulating in the marine environment and aggregate microorganisms that form a new ecosystem called the plastisphere. Better understanding the plastisphere is crucial as it has self-sufficient organization and carries pathogens or organisms that may be involved in the pollutant adsorption and/or plastic degradation. To date, the plastisphere is mainly described at the taxonomic level and the functioning of its microbial communities still remains poorly documented. In this work, metagenomic and metaproteomic analyzes were performed on the plastisphere of polypropylene and polyethylene plastic debris sampled on a pebble beach from the Mediterranean Sea. Our results confirmed that the plastisphere was organized as self-sufficient ecosystems containing highly active primary producers, heterotrophs and predators such as nematode. Interestingly, the chemical composition of the polymer did not impact the structure of the microbial communities but rather influenced the functions expressed. Despite the fact that the presence of hydrocarbon-degrading bacteria was observed in the metagenomes, polymer degradation metabolisms were not detected at the protein level. Finally, hydrocarbon degrader (i.e., Alcanivorax) and pathogenic bacteria (i.e., Vibrionaceae) were observed in the plastispheres but were not very active as no proteins involved in polymer degradation or pathogeny were detected. This work brings new insights into the functioning of the microbial plastisphere developed on plastic marine debris.
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Affiliation(s)
- A Delacuvellerie
- Proteomics and Microbiology Department, University of Mons, 20 Place du Parc, 7000, Mons, Belgium
| | - A Géron
- Proteomics and Microbiology Department, University of Mons, 20 Place du Parc, 7000, Mons, Belgium; University of Stirling, Division of Biological and Environmental Sciences, Faculty of Natural Sciences, FK9 4LA, Stirling, UK
| | - S Gobert
- Oceanology Department, University of Liège, 11 Allée du 6 Août, 4000, Liège, Belgium; STAtion de REcherches Sous-marines et Océanographiques (STARESO), Punta Revellata, BP33, 20260, Calvi, France
| | - R Wattiez
- Proteomics and Microbiology Department, University of Mons, 20 Place du Parc, 7000, Mons, Belgium.
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24
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Bonneel M, Hennebert E, Aranko AS, Hwang DS, Lefevre M, Pommier V, Wattiez R, Delroisse J, Flammang P. Molecular mechanisms mediating stiffening in the mechanically adaptable connective tissues of sea cucumbers. Matrix Biol 2022; 108:39-54. [DOI: 10.1016/j.matbio.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/24/2022] [Accepted: 02/23/2022] [Indexed: 11/25/2022]
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25
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Loyez M, DeRosa MC, Caucheteur C, Wattiez R. Overview and emerging trends in optical fiber aptasensing. Biosens Bioelectron 2022; 196:113694. [PMID: 34637994 DOI: 10.1016/j.bios.2021.113694] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 12/16/2022]
Abstract
Optical fiber biosensors have attracted growing interest over the last decade and quickly became a key enabling technology, especially for the detection of biomarkers at extremely low concentrations and in small volumes. Among the many and recent fiber-optic sensing amenities, aptamers-based sensors have shown unequalled performances in terms of ease of production, specificity, and sensitivity. The immobilization of small and highly stable bioreceptors such as DNA has bolstered their use for the most varied applications e.g., medical diagnosis, food safety and environmental monitoring. This review highlights the recent advances in aptamer-based optical fiber biosensors. An in-depth analysis of the literature summarizes different fiber-optic structures and biochemical strategies for molecular detection and immobilization of receptors over diverse surfaces. In this review, we analyze the features offered by those sensors and discuss about the next challenges to be addressed. This overview investigates both biochemical and optical parameters, drawing the guiding lines for forthcoming innovations and prospects in this ever-growing field of research.
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Affiliation(s)
- Médéric Loyez
- Proteomics and Microbiology Department, University of Mons, Avenue du Champ de Mars 6, 7000, Mons, Belgium; Electromagnetism and Telecommunication Department, University of Mons, Bld. Dolez 31, 7000, Mons, Belgium.
| | - Maria C DeRosa
- Department of Chemistry, 203 Steacie Building, Carleton University, 1125, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Christophe Caucheteur
- Electromagnetism and Telecommunication Department, University of Mons, Bld. Dolez 31, 7000, Mons, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Avenue du Champ de Mars 6, 7000, Mons, Belgium
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26
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Lozano C, Lee C, Wattiez R, Lebaron P, Matallana-Surget S. Unraveling the molecular effects of oxybenzone on the proteome of an environmentally relevant marine bacterium. Sci Total Environ 2021; 793:148431. [PMID: 34182435 DOI: 10.1016/j.scitotenv.2021.148431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/13/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
The use of Benzophenone-3 (BP3), also known as oxybenzone, a common UV filter, is a growing environmental concern in regard to its toxicity on aquatic organisms. Our previous work stressed that BP3 is toxic to Epibacterium mobile, an environmentally relevant marine α-proteobacterium. In this study, we implemented a label-free quantitative proteomics workflow to decipher the effects of BP3 on the E. mobile proteome. Furthermore, the effect of DMSO, one of the most common solvents used to vehicle low concentrations of lipophilic chemicals, was assessed to emphasize the importance of limiting solvent concentration in ecotoxicological studies. Data-independent analysis proteomics highlighted that BP3 induced changes in the regulation of 56 proteins involved in xenobiotic export, detoxification, oxidative stress response, motility, and fatty acid, iron and amino acid metabolisms. Our results also outlined that the use of DMSO at 0.046% caused regulation changes in proteins related to transport, iron uptake and metabolism, and housekeeping functions, underlining the need to reduce the concentration of solvents in ecotoxicological studies.
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Affiliation(s)
- Clément Lozano
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650 Banyuls-sur-mer, France; Division of Biological and Environmental Sciences, Faculty of Natural Sciences, Stirling University, United Kingdom
| | - Charlotte Lee
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, Stirling University, United Kingdom
| | - Ruddy Wattiez
- Department of Proteomic and Microbiology, University of Mons, Mons, Belgium
| | - Philippe Lebaron
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650 Banyuls-sur-mer, France
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, Stirling University, United Kingdom.
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27
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Carette X, Mincheva R, Herbin M, Cabecas Segura P, Wattiez R, Noirfalise X, Thai C, Leclere P, Godfroid T, Boudifa M, Kerdjoudj H, Jolois O, Raquez JM. Microwave Atmospheric Plasma: A Versatile and Fast Way to Confer Antimicrobial Activity toward Direct Chitosan Immobilization onto Poly(lactic acid) Substrate. ACS Appl Bio Mater 2021; 4:7445-7455. [DOI: 10.1021/acsabm.1c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xavier Carette
- Laboratory of Polymeric and Composite Materials (LPCM), University of Mons, Place du Parc, 23, B-7000, Mons, Belgium
| | - Rosica Mincheva
- Laboratory of Polymeric and Composite Materials (LPCM), University of Mons, Place du Parc, 23, B-7000, Mons, Belgium
| | - Morgane Herbin
- Laboratory of chemistry of plasma-surface interaction (ChIPS), University of Mons, 23 Place du Parc, B-7000 Mons, Belgium
- Materia-Nova Research Center, Parc Initialis, B-7000 Mons, Belgium
| | - Paloma Cabecas Segura
- Department of Proteomics and Microbiology, University of Mons, 23 Place du Parc, B-7000 Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, 23 Place du Parc, B-7000 Mons, Belgium
| | - Xavier Noirfalise
- Laboratory of chemistry of plasma-surface interaction (ChIPS), University of Mons, 23 Place du Parc, B-7000 Mons, Belgium
- Materia-Nova Research Center, Parc Initialis, B-7000 Mons, Belgium
| | - Cuong Thai
- Laboratory for Chemistry of Novel Materials (CMN), University of Mons, Place du Parc 20, B-7000 Mons, Belgium
| | - Philippe Leclere
- Laboratory for Chemistry of Novel Materials (CMN), University of Mons, Place du Parc 20, B-7000 Mons, Belgium
| | - Thomas Godfroid
- Laboratory of chemistry of plasma-surface interaction (ChIPS), University of Mons, 23 Place du Parc, B-7000 Mons, Belgium
| | - Mohamed Boudifa
- Centre du textile Belge (CENTEXBEL), 4460 Grâce-Hollogne, Belgium
- CRITT-MDTS, 08000 Charleville-Mézières, France
| | - Halima Kerdjoudj
- Laboratory for Chemistry of Novel Materials (CMN), University of Mons, Place du Parc 20, B-7000 Mons, Belgium
| | - Olivier Jolois
- EA 4691 Biomatériaux et Inflammation en Site Osseux (BIOS), SFR CAP Santé (FED4231), Université de Reims Champagne-Ardenne, 51097 Reims, France
| | - Jean-Marie Raquez
- Laboratory of Polymeric and Composite Materials (LPCM), University of Mons, Place du Parc, 23, B-7000, Mons, Belgium
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Delacuvellerie A, Benali S, Cyriaque V, Moins S, Raquez JM, Gobert S, Wattiez R. Microbial biofilm composition and polymer degradation of compostable and non-compostable plastics immersed in the marine environment. J Hazard Mater 2021; 419:126526. [PMID: 34328083 DOI: 10.1016/j.jhazmat.2021.126526] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 05/21/2023]
Abstract
Different plastic types considered as compostable are found on the market such as petro-based (e.g., polybutylene adipate terephthalate (PBAT)) or bio-based plastics (e.g., polylactic acid, (PLA)). Even if their degradation has been confirmed in industrial compost conditions, investigation of their degradation in natural marine environment has been limited. To better understand biodegradation into natural marine environment, commercial compostable (PBAT, semi-crystalline and amorphous PLA) and non-compostable polymers (low density polyethylene, polystyrene, polyethylene terephthalate, polyvinyl chloride) were submerged in situ on the sediment and in the water column in the Mediterranean Sea. These samples were studied by chemical and microbiological approaches. After 82 days of immersion, no significant bacterial degradation of the different polymers was observed, except some abiotic alterations of PBAT and LDPE probably due to a photooxidation process. However, after 80 days in an enrichment culture containing plastic films as a main carbon source, Marinomonas genus was specifically selected on the PBAT and a weight loss of 12% was highlighted. A better understanding of the bacterial community colonizing these plastics is essential for an eco-design of new biodegradable polymers to allow a rapid degradation in aquatic environment.
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Affiliation(s)
- Alice Delacuvellerie
- Proteomics and Microbiology Department, University of Mons, 20 place du parc, 7000 Mons, Belgium.
| | - Samira Benali
- Polymer and Composite Materials Department, University of Mons, 15 Avenue Maistriau, 7000 Mons, Belgium
| | - Valentine Cyriaque
- Proteomics and Microbiology Department, University of Mons, 20 place du parc, 7000 Mons, Belgium
| | - Sébastien Moins
- Polymer and Composite Materials Department, University of Mons, 15 Avenue Maistriau, 7000 Mons, Belgium
| | - Jean-Marie Raquez
- Polymer and Composite Materials Department, University of Mons, 15 Avenue Maistriau, 7000 Mons, Belgium
| | - Sylvie Gobert
- Oceanology Department, University of Liège, 11 Allée du 6 août, 4000 Liège, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, 20 place du parc, 7000 Mons, Belgium
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29
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Lefevre M, Ederth T, Masai T, Wattiez R, Leclère P, Flammang P, Hennebert E. Disentangling the Roles of Functional Domains in the Aggregation and Adsorption of the Multimodular Sea Star Adhesive Protein Sfp1. Mar Biotechnol (NY) 2021; 23:724-735. [PMID: 34528162 DOI: 10.1007/s10126-021-10059-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Sea stars can adhere to various underwater substrata using an adhesive secretion of which Sfp1 is a major component. Sfp1 is a multimodular protein composed of four subunits (Sfp1 Alpha, Beta, Delta, and Gamma) displaying different functional domains. We recombinantly produced two fragments of Sfp1 comprising most of its functional domains: the C-terminal part of the Beta subunit (rSfp1 Beta C-term) and the Delta subunit (rSfp1 Delta). Surface plasmon resonance analyses of protein adsorption onto different model surfaces showed that rSfp1 Beta C-term exhibits a significantly higher adsorption than the fibrinogen control on hydrophobic, hydrophilic protein-resistant, and charged self-assembled monolayers, while rSfp1 Delta adsorbed more on negatively charged and on protein-resistant surfaces compared to fibrinogen. Truncated recombinant rSfp1 Beta C-term proteins were produced in order to investigate the role of the different functional domains in the adsorption of this protein. The analysis of their adsorption capacities on glass showed that two mechanisms are involved in rSfp1 Beta C-term adsorption: (1) one mediated by the EGF-like domain and involving Ca2+ and Mg2+ ions, and (2) one mediated by the sequence of Sfp1 Beta with no homology with known functional domain in databases, in the presence of Na+, Ca2+ and Mg2+ ions.
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Affiliation(s)
- Mathilde Lefevre
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000, Mons, Belgium
- Laboratory for Chemistry of Novel Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), Research Institute for Materials, University of Mons, 7000, Mons, Belgium
| | - Thomas Ederth
- Division of Biophysics and Bioengineering, Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Thibault Masai
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000, Mons, Belgium
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, 7000, Mons, Belgium
| | - Philippe Leclère
- Laboratory for Chemistry of Novel Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), Research Institute for Materials, University of Mons, 7000, Mons, Belgium
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, 7000, Mons, Belgium
| | - Elise Hennebert
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000, Mons, Belgium.
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30
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Cabecas Segura P, De Meur Q, Tanghe A, Onderwater R, Dewasme L, Wattiez R, Leroy B. Effects of Mixing Volatile Fatty Acids as Carbon Sources on Rhodospirillum rubrum Carbon Metabolism and Redox Balance Mechanisms. Microorganisms 2021; 9:1996. [PMID: 34576891 PMCID: PMC8471276 DOI: 10.3390/microorganisms9091996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Rhodospirillum rubrum has a versatile metabolism, and as such can assimilate a broad range of carbon sources, including volatile fatty acids. These carbon sources are gaining increasing interest for biotechnological processes, since they reduce the production costs for numerous value-added compounds and contribute to the development of a more circular economy. Usually, studies characterizing carbon metabolism are performed by supplying a single carbon source; however, in both environmental and engineered conditions, cells would rather grow on mixtures of volatile fatty acids (VFAs) generated via anaerobic fermentation. In this study, we show that the use of a mixture of VFAs as carbon source appears to have a synergy effect on growth phenotype. In addition, while propionate and butyrate assimilation in Rs. rubrum is known to require an excess of bicarbonate in the culture medium, mixing them reduces the requirement for bicarbonate supplementation. The fixation of CO2 is one of the main electron sinks in purple bacteria; therefore, this observation suggests an adaptation of both metabolic pathways used for the assimilation of these VFAs and redox homeostasis mechanism. Based on proteomic data, modification of the propionate assimilation pathway seems to occur with a switch from a methylmalonyl-CoA intermediate to the methylcitrate cycle. Moreover, it seems that the presence of a mixture of VFAs switches electron sinking from CO2 fixation to H2 and isoleucine production.
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Affiliation(s)
- Paloma Cabecas Segura
- Laboratory of Proteomics and Microbiology, University of Mons, 7000 Mons, Belgium; (P.C.S.); (Q.D.M.); (R.W.)
| | - Quentin De Meur
- Laboratory of Proteomics and Microbiology, University of Mons, 7000 Mons, Belgium; (P.C.S.); (Q.D.M.); (R.W.)
| | - Audrey Tanghe
- Materia Nova ASBL, Parc Initialis, Avenue Copernic 3, 7000 Mons, Belgium; (A.T.); (R.O.)
| | - Rob Onderwater
- Materia Nova ASBL, Parc Initialis, Avenue Copernic 3, 7000 Mons, Belgium; (A.T.); (R.O.)
| | - Laurent Dewasme
- Systems, Estimation, Control and Optimization Group, University of Mons, 7000 Mons, Belgium;
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, University of Mons, 7000 Mons, Belgium; (P.C.S.); (Q.D.M.); (R.W.)
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, University of Mons, 7000 Mons, Belgium; (P.C.S.); (Q.D.M.); (R.W.)
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31
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Bayon-Vicente G, Marchand E, Ducrotois J, Dufrasne FE, Hallez R, Wattiez R, Leroy B. Analysis of the Involvement of the Isoleucine Biosynthesis Pathway in Photoheterotrophic Metabolism of Rhodospirillum rubrum. Front Microbiol 2021; 12:731976. [PMID: 34621257 PMCID: PMC8490811 DOI: 10.3389/fmicb.2021.731976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/26/2021] [Indexed: 12/05/2022] Open
Abstract
Purple non-sulfur bacteria (PNSB) are recognized as a highly versatile group of bacteria that assimilate a broad range of carbon sources. Growing heterotrophically, PNSB such as Rhodospirillum rubrum (Rs. rubrum) generate reduced equivalents that are used for biomass production. However, under photoheterotrophic conditions, more reduced electron carriers than required to produce biomass are generated. The excess of reduced equivalents still needs to be oxidized for the metabolism to optimally operate. These metabolic reactions are known as electron sinks. Most PNSB rely on the CO2-fixing Calvin cycle and H2 production to oxidize these reduced equivalents. In addition to these well-described electron sinks, the involvement of some pathways, such as polyhydroxyalkanoate (PHA) biosynthesis, in redox poise is still controversial and requires further studies. Among them, isoleucine biosynthesis has been recently highlighted as one of these potential pathways. Here, we explore the role of isoleucine biosynthesis in Rs. rubrum. Our results demonstrate that the isoleucine content is higher under illuminated conditions and that submitting Rs. rubrum to light stress further increases this phenomenon. Moreover, we explore the production of (p)ppGpp in Rs. rubrum and its potential link with light stress. We further demonstrate that a fully functional isoleucine biosynthesis pathway could be an important feature for the onset of Rs. rubrum growth under photoheterotrophic conditions even in the presence of an exogenous isoleucine source. Altogether, our data suggest that isoleucine biosynthesis could play a key role in redox homeostasis.
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Affiliation(s)
- Guillaume Bayon-Vicente
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Elie Marchand
- Bacterial Cell Cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur, Namur, Belgium
| | - Jeson Ducrotois
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - François E. Dufrasne
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Regis Hallez
- Bacterial Cell Cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur, Namur, Belgium
- Namur Research College (NARC), University of Namur, Namur, Belgium
- WELBIO, University of Namur, Namur, Belgium
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
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Baumans F, Hanozin E, Baiwir D, Decroo C, Wattiez R, De Pauw E, Eppe G, Mazzucchelli G. Liquid chromatography setup-dependent artefactual methionine oxidation of peptides: The importance of an adapted quality control process. J Chromatogr A 2021; 1654:462449. [PMID: 34399143 DOI: 10.1016/j.chroma.2021.462449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/26/2022]
Abstract
In both biologics quality control experiments and protein post-translational modification studies, the analytical system used is not supposed to bring any artefactual modifications which could impair the results. In this work, we investigated oxidation of methionine-containing peptides during reversed-phase (RP) chromatographic separation. We first used a synthetic methionine-containing peptide to evaluate this artefactual phenomenon and then considered more complex samples (i.e., plasma and HeLa protein digests). The methionine oxidation levels of the peptides were systematically assessed and compared for the long-term use of the analytical column, the sample trapping time, the gradient length, the sample load and the nature of the stationary phase (HSS T3 from Waters, YMC Triart C18 from YMC Europe GmbH and BEH130 C18 from Waters). In addition to the oxidation of methionine in solution, we observed on the HSS T3 and the BEH130 stationary phases an additional broad peak corresponding to an on-column oxidized species. Considering the HSS T3 phase, our results highlight that the on-column oxidation level significantly increases with the age of the analytical column and the gradient length and reaches 56 % when a 1-year-old column set is used with a 180 min-long LC method. These levels go to 0 % and 18 % for the YMC Triart C18 and the BEH130 C18 phases respectively. Interestingly, the on-column oxidation proportion decreases as the injected sample load increases suggesting the presence of a discrete number of oxidation sites within the stationary phase of the analytical column. Those findings observed in different laboratories using distinct set of columns, albeit to varying degrees, strengthen the need for a standard of methionine-containing peptide that could be used as a quality control to appraise the status of the liquid chromatographic columns.
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Affiliation(s)
- France Baumans
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Emeline Hanozin
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Dominique Baiwir
- GIGA Proteomics Facility, University of Liege, Liege 4000, Belgium
| | - Corentin Decroo
- Proteomics and Microbiology Laboratory, University of Mons, Mons 7000, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, University of Mons, Mons 7000, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium.
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Loyez M, Wells M, Hambÿe S, Hubinon F, Blankert B, Wattiez R, Caucheteur C. PfHRP2 detection using plasmonic optrodes: performance analysis. Malar J 2021; 20:332. [PMID: 34320995 PMCID: PMC8320217 DOI: 10.1186/s12936-021-03863-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Background Early malaria diagnosis and its profiling require the development of new sensing platforms enabling rapid and early analysis of parasites in blood or saliva, aside the widespread rapid diagnostic tests (RDTs). Methods This study shows the performance of a cost-effective optical fiber-based solution to target the presence of Plasmodium falciparum histidine-rich protein 2 (PfHRP2). Unclad multimode optical fiber probes are coated with a thin gold film to excite Surface Plasmon Resonance (SPR) yielding high sensitivity to bio-interactions between targets and bioreceptors grafted on the metal surface. Results Their performances are presented in laboratory conditions using PBS spiked with growing concentrations of purified target proteins and within in vitro cultures. Two probe configurations are studied through label-free detection and amplification using secondary antibodies to show the possibility to lower the intrisic limit of detection. Conclusions As malaria hits millions of people worldwide, the improvement and multiplexing of this optical fiber technique can be of great interest, especially for a future purpose of using multiple receptors on the fiber surface or several coated-nanoparticles as amplifiers. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03863-3.
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Affiliation(s)
- Médéric Loyez
- Proteomics and Microbiology Department, University of Mons, Champ de Mars 6, 7000, Mons, Belgium. .,Electromagnetism and Telecommunications Department, University of Mons, Bld. Dolez 31, 7000, Mons, Belgium.
| | - Mathilde Wells
- Laboratory of Pharmaceutical Analysis, University of Mons, Avenue Maistriau 15, 7000, Mons, Belgium
| | - Stéphanie Hambÿe
- Laboratory of Pharmaceutical Analysis, University of Mons, Avenue Maistriau 15, 7000, Mons, Belgium
| | - François Hubinon
- Electromagnetism and Telecommunications Department, University of Mons, Bld. Dolez 31, 7000, Mons, Belgium
| | - Bertrand Blankert
- Laboratory of Pharmaceutical Analysis, University of Mons, Avenue Maistriau 15, 7000, Mons, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Champ de Mars 6, 7000, Mons, Belgium
| | - Christophe Caucheteur
- Electromagnetism and Telecommunications Department, University of Mons, Bld. Dolez 31, 7000, Mons, Belgium
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Cyriaque V, Madsen JS, Fievez L, Leroy B, Hansen LH, Bureau F, Sørensen SJ, Wattiez R. Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community. Front Microbiol 2021; 12:655903. [PMID: 34122370 PMCID: PMC8195591 DOI: 10.3389/fmicb.2021.655903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/06/2021] [Indexed: 01/01/2023] Open
Abstract
Plasmids carrying metal resistance genes (MRGs) have been suggested to be key ecological players in the adaptation of metal-impacted microbial communities, making them promising drivers of bio-remediation processes. However, the impact of metals on plasmid-mediated spread of MRGs through selection, plasmid loss, and transfer is far from being fully understood. In the present study, we used two-member bacterial communities to test the impact of lead on the dispersal of the IncP plasmid pKJK5 from a Pseudomonas putida KT2440 plasmid donor and two distinct recipients, Variovorax paradoxus B4 or Delftia acidovorans SPH-1 after 4 and 10 days of mating. Two versions of the plasmid were used, carrying or not carrying the lead resistance pbrTRABCD operon, to assess the importance of fitness benefit and conjugative potential for the dispersal of the plasmid. The spread dynamics of metal resistance conveyed by the conjugative plasmid were dependent on the recipient and the lead concentration: For V. paradoxus, the pbr operon did not facilitate neither lead resistance nor variation in plasmid spread. The growth gain brought by the pbr operon to D. acidovorans SPH-1 and P. putida KT2440 at 1 mM Pb enhanced the spread of the plasmid. At 1.5 mM Pb after 4 days, the proteomics results revealed an oxidative stress response and an increased abundance of pKJK5-encoded conjugation and partitioning proteins, which most likely increased the transfer of the control plasmid to D. acidovorans SPH-1 and ensured plasmid maintenance. As a consequence, we observed an increased spread of pKJK5-gfp. Conversely, the pbr operon reduced the oxidative stress response and impeded the rise of conjugation- and partitioning-associated proteins, which slowed down the spread of the pbr carrying plasmid. Ultimately, when a fitness gain was recorded in the recipient strain, the spread of MRG-carrying plasmids was facilitated through positive selection at an intermediate metal concentration, while a high lead concentration induced oxidative stress with positive impacts on proteins encoding plasmid conjugation and partitioning.
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Affiliation(s)
- Valentine Cyriaque
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium.,Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Stenløkke Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laurence Fievez
- Cellular and Molecular Immunology Service, GIGA Research, University of Liège (ULG), Liège, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Lars H Hansen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Fabrice Bureau
- Cellular and Molecular Immunology Service, GIGA Research, University of Liège (ULG), Liège, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
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Cyriaque V, Géron A, Billon G, Nesme J, Werner J, Gillan DC, Sørensen SJ, Wattiez R. Metal-induced bacterial interactions promote diversity in river-sediment microbiomes. FEMS Microbiol Ecol 2020; 96:5826176. [PMID: 32343356 DOI: 10.1093/femsec/fiaa076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023] Open
Abstract
Anthropogenic metal contamination results in long-term environmental selective pressure with unclear impacts on bacterial communities, which comprise key players in ecosystem functioning. Since metal contamination poses serious toxicity and bioaccumulation issues, assessing their impact on environmental microbiomes is important to respond to current environmental and health issues. Despite elevated metal concentrations, the river sedimentary microbiome near the MetalEurop foundry (France) shows unexpected higher diversity compared with the upstream control site. In this work, a follow-up of the microbial community assembly during a metal contamination event was performed in microcosms with periodic renewal of the supernatant river water. Sediments of the control site were gradually exposed to a mixture of metals (Cd, Cu, Pb and Zn) in order to reach similar concentrations to MetalEurop sediments. Illumina sequencing of 16S rRNA gene amplicons was performed. Metal-resistant genes, czcA and pbrA, as well as IncP plasmid content, were assessed by quantitative PCR. The outcomes of this study support previous in situ observations showing that metals act as community assembly managers, increasing diversity. This work revealed progressive adaptation of the sediment microbiome through the selection of different metal-resistant mechanisms and cross-species interactions involving public good-providing bacteria co-occurring with the rest of the community.
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Affiliation(s)
- Valentine Cyriaque
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Augustin Géron
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium.,Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling,FK9 4LA, UK
| | - Gabriel Billon
- Univ. Lille, CNRS, UMR 8516 - LASIRE - LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, F-59000 Lille, France
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, D-18119 Rostock, Germany
| | - David C Gillan
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
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36
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Chang RL, Stanley JA, Robinson MC, Sher JW, Li Z, Chan YA, Omdahl AR, Wattiez R, Godzik A, Matallana-Surget S. Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage. EMBO J 2020; 39:e104523. [PMID: 33073387 PMCID: PMC7705453 DOI: 10.15252/embj.2020104523] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 02/05/2023] Open
Abstract
Oxidative stress alters cell viability, from microorganism irradiation sensitivity to human aging and neurodegeneration. Deleterious effects of protein carbonylation by reactive oxygen species (ROS) make understanding molecular properties determining ROS susceptibility essential. The radiation‐resistant bacterium Deinococcus radiodurans accumulates less carbonylation than sensitive organisms, making it a key model for deciphering properties governing oxidative stress resistance. We integrated shotgun redox proteomics, structural systems biology, and machine learning to resolve properties determining protein damage by γ‐irradiation in Escherichia coli and D. radiodurans at multiple scales. Local accessibility, charge, and lysine enrichment accurately predict ROS susceptibility. Lysine, methionine, and cysteine usage also contribute to ROS resistance of the D. radiodurans proteome. Our model predicts proteome maintenance machinery, and proteins protecting against ROS are more resistant in D. radiodurans. Our findings substantiate that protein‐intrinsic protection impacts oxidative stress resistance, identifying causal molecular properties.
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Affiliation(s)
- Roger L Chang
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Julian A Stanley
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Matthew C Robinson
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Joel W Sher
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Zhanwen Li
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Yujia A Chan
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ashton R Omdahl
- Department of Systems Biology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Adam Godzik
- Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, CA, USA
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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37
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Lobry M, Loyez M, Chah K, Hassan EM, Goormaghtigh E, DeRosa MC, Wattiez R, Caucheteur C. HER2 biosensing through SPR-envelope tracking in plasmonic optical fiber gratings. Biomed Opt Express 2020; 11:4862-4871. [PMID: 33014586 PMCID: PMC7510885 DOI: 10.1364/boe.401200] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 05/22/2023]
Abstract
In the biomedical detection context, plasmonic tilted fiber Bragg gratings (TFBGs) have been demonstrated to be a very accurate and sensitive sensing tool, especially well-adapted for biochemical detection. In this work, we have developed an aptasensor following a triple strategy to improve the overall sensing performances and robustness. Single polarization fiber (SPF) is used as biosensor substrate while the demodulation is based on tracking a peculiar feature of the lower envelope of the cladding mode resonances spectrum. This method is highly sensitive and yields wavelength shifts several tens of times higher than the ones reported so far based on the tracking of individual modes of the spectrum. An amplification of the response is further performed through a sandwich assay by the use of specific antibodies. These improvements have been achieved on a biosensor developed for the detection of the HER2 (Human Epidermal Growth Factor Receptor-2) protein, a relevant breast cancer biomarker. These advanced developments can be very interesting for point-of-care biomedical measurements in a convenient practical way.
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Affiliation(s)
- Maxime Lobry
- Electromagnetism and Telecommunication Department, University of Mons, 31 Bld Dolez, 7000 Mons, Belgium
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Bld du Triomphe 2,1050 Brussels, Belgium
| | - Médéric Loyez
- Proteomics and Microbiology Department, University of Mons, 6 Av. du Champ de Mars, 7000 Mons, Belgium
| | - Karima Chah
- Electromagnetism and Telecommunication Department, University of Mons, 31 Bld Dolez, 7000 Mons, Belgium
| | - Eman M. Hassan
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
- Metrology Research Centre, National Research Council Canada, Ottawa, Ontario, K1A0R6, Canada
| | - Erik Goormaghtigh
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Bld du Triomphe 2,1050 Brussels, Belgium
| | - Maria C. DeRosa
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, 6 Av. du Champ de Mars, 7000 Mons, Belgium
| | - Christophe Caucheteur
- Electromagnetism and Telecommunication Department, University of Mons, 31 Bld Dolez, 7000 Mons, Belgium
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38
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Lefevre M, Flammang P, Aranko AS, Linder MB, Scheibel T, Humenik M, Leclercq M, Surin M, Tafforeau L, Wattiez R, Leclère P, Hennebert E. Sea star-inspired recombinant adhesive proteins self-assemble and adsorb on surfaces in aqueous environments to form cytocompatible coatings. Acta Biomater 2020; 112:62-74. [PMID: 32502634 DOI: 10.1016/j.actbio.2020.05.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022]
Abstract
Sea stars adhere to various underwater substrata using an efficient protein-based adhesive secretion. The protein Sfp1 is a major component of this secretion. In the natural glue, it is cleaved into four subunits (Sfp1 Alpha, Beta, Delta and Gamma) displaying specific domains which mediate protein-protein or protein-carbohydrate interactions. In this study, we used the bacterium E. coli to produce recombinantly two fragments of Sfp1 comprising most of its functional domains: the C-terminal part of the Beta subunit (rSfp1 Beta C-term) and the Delta subunit (rSfp1 Delta). Using native polyacrylamide gel electrophoresis and size exclusion chromatography, we show that the proteins self-assemble and form oligomers and aggregates in the presence of NaCl. Moreover, they adsorb onto glass and polystyrene upon addition of Na+ and/or Ca2+ ions, forming homogeneous coatings or irregular meshworks, depending on the cation species and concentration. We show that coatings made of each of the two proteins have no cytotoxic effects on HeLa cells and even increase their proliferation. We propose that the Sfp1 recombinant protein coatings are valuable new materials with potential for cell culture or biomedical applications. STATEMENT OF SIGNIFICANCE: Biological adhesives offer impressive performance in their natural context and, therewith, the potential to inspire the development of advanced biomaterials for an increasing variety of applications in medicine or in material sciences. To date, most marine adhesive proteins that have been produced recombinantly in order to develop bio-inspired adhesives are small proteins from mussels and barnacles. Here, we produced two multi-modular proteins based on the sequence of Sfp1, a major protein from sea star adhesive secretion. These two proteins comprise most of Sfp1 functional domains which mediate protein-protein and protein-carbohydrate interactions. We characterized the two recombinant proteins with an emphasis on functional characteristics such as self-assembly, adsorption and cytocompatibility. We discuss their potential as biomaterials.
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Affiliation(s)
- Mathilde Lefevre
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium; Laboratory for Chemistry of Novel Materials, Research Institute for Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - A Sesilja Aranko
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-02150 Espoo, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-02150 Espoo, Finland
| | - Thomas Scheibel
- Department of Biomaterials, Faculty of Engineering Science, University of Bayreuth, Prof.-Rüdiger-Bormann Str.1, 95447 Bayreuth, Germany
| | - Martin Humenik
- Department of Biomaterials, Faculty of Engineering Science, University of Bayreuth, Prof.-Rüdiger-Bormann Str.1, 95447 Bayreuth, Germany
| | - Maxime Leclercq
- Laboratory for Chemistry of Novel Materials, Research Institute for Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Research Institute for Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Lionel Tafforeau
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Philippe Leclère
- Laboratory for Chemistry of Novel Materials, Research Institute for Materials, Center for Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Elise Hennebert
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium.
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Loyez M, Lobry M, Hassan EM, DeRosa MC, Caucheteur C, Wattiez R. HER2 breast cancer biomarker detection using a sandwich optical fiber assay. Talanta 2020; 221:121452. [PMID: 33076075 DOI: 10.1016/j.talanta.2020.121452] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/17/2022]
Abstract
Optical fiber-based surface plasmon resonance (OF-SPR) sensors have demonstrated high versatility and performances over the last years, which propelled the technique to the heart of numerous and original biosensing concepts. In this work, we contribute to this effort and present our recent findings about the detection of breast cancer HER2 biomarkers through OF-SPR optrodes. 1 cm-long sections of 400 μm core-diameter optical fibers were covered with a sputtered gold film, yielding enhanced sensitivity to surface refractive index changes. Studying the impacts of the gold film thickness on the plasmonic spectral response, we improved the quality and reproducibility of the sensors. These achievements were correlated in two ways, using both the central wavelengths of the plasmon resonance and its influence on the bulk refractive index sensitivity. Our dataset was fed by additional biosensing experiments with a direct and indirect approach, relying on aptamers and antibodies specifically implemented in a sandwich layout. HER2 biomarkers were specifically detected at 0.6 μg/mL (5.16 nM) in label-free while the amplification with HER2-antibodies provided a nearly hundredfold signal magnification, reaching 9.3 ng/mL (77.4 pM). We believe that these results harbinger the way for their further use in biomedical samples.
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Affiliation(s)
- Médéric Loyez
- Proteomics and Microbiology Department, University of Mons, Place Du Parc 20, 7000, Mons, Belgium.
| | - Maxime Lobry
- Electromagnetism and Telecommunications Department, University of Mons, Bld. Dolez 31, 7000, Mons, Belgium
| | - Eman M Hassan
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada; Metrology Research Centre, National Research Council Canada, Ottawa, Ontario, K1A 0R6, Canada
| | - Maria C DeRosa
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Christophe Caucheteur
- Electromagnetism and Telecommunications Department, University of Mons, Bld. Dolez 31, 7000, Mons, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Place Du Parc 20, 7000, Mons, Belgium
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40
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Cai S, Pan H, González-Vila Á, Guo T, Gillan DC, Wattiez R, Caucheteur C. Selective detection of cadmium ions using plasmonic optical fiber gratings functionalized with bacteria. Opt Express 2020; 28:19740-19749. [PMID: 32672244 DOI: 10.1364/oe.397505] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Environmental monitoring and potable water control are key applications where optical fiber sensing solutions can outperform other technologies. In this work, we report a highly sensitive plasmonic fiber-optic probe that has been developed to determine the concentration of cadmium ions (Cd2+) in solution. This original sensor was fabricated by immobilizing the Acinetobacter sp. around gold-coated tilted fiber Bragg gratings (TFBGs). To this aim, the immobilization conditions of bacteria on the gold-coated optical fiber surface were first experimentally determined. Then, the coated sensors were tested in vitro. The relative intensity of the sensor response experienced a change of 1.1 dB for a Cd2+ concentration increase from 0.1 to 1000 ppb. According to our test procedure, we estimate the experimental limit of detection to be close to 1 ppb. Cadmium ions strongly bind to the sensing surface, so the sensor exhibits a much higher sensitivity to Cd2+ than to other heavy metal ions such as Pb2+, Zn2+ and CrO42- found in contaminated water, which ensures a good selectivity.
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Abstract
Limpets (Patella vulgata L.) are renowned for their powerful attachments to rocks on wave-swept seashores. Unlike adult barnacles and mussels, limpets do not adhere permanently; instead, they repeatedly transition between long-term adhesion and locomotive adhesion depending on the tide. Recent studies on the adhesive secretions (bio-adhesives) of marine invertebrates have expanded our knowledge on the composition and function of temporary and permanent bio-adhesives. In comparison, our understanding of the limpets' transitory adhesion remains limited. In this study, we demonstrate that suction is not the primary attachment mechanism in P. vulgata; rather, they secrete specialized pedal mucus for glue-like adhesion. Through combined transcriptomics and proteomics, we identified 171 protein sequences from the pedal mucus. Several of these proteins contain conserved domains found in temporary bio-adhesives from sea stars, sea urchins, marine flatworms and sea anemones. Many of these proteins share homology with fibrous gel-forming glycoproteins, including fibrillin, hemolectin and SCO-spondin. Moreover, proteins with potential protein- and glycan-degrading domains could have an immune defence role or assist degrading adhesive mucus to facilitate the transition from stationary to locomotive states. We also discovered glycosylation patterns unique to the pedal mucus, indicating that specific sugars may be involved in transitory adhesion. Our findings elucidate the mechanisms underlying P. vulgata adhesion and provide opportunities for future studies on bio-adhesives that form strong attachments and resist degradation until necessary for locomotion.
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Affiliation(s)
- Victor Kang
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Birgit Lengerer
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Mons 7000, Belgium.,Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons 7000, Belgium
| | - Patrick Flammang
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Mons 7000, Belgium
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42
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Bayon-Vicente G, Wattiez R, Leroy B. Global Proteomic Analysis Reveals High Light Intensity Adaptation Strategies and Polyhydroxyalkanoate Production in Rhodospirillum rubrum Cultivated With Acetate as Carbon Source. Front Microbiol 2020; 11:464. [PMID: 32269553 PMCID: PMC7109303 DOI: 10.3389/fmicb.2020.00464] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/04/2020] [Indexed: 11/25/2022] Open
Abstract
Purple non-sulfur bacteria (PNSBs) are well known for their metabolic versatility. Among them, Rhodospirillum rubrum can assimilate a broad range of carbon sources, including volatile fatty acids (VFAs), such as acetate, propionate or butyrate. These carbon sources are gaining increasing interest in bioindustrial processes since they allow reduction of the production costs. Recently, our lab discovered that, after long term cultivation with acetate as unique carbon source, Rs. rubrum got acclimated to this carbon source which resulted in a drastic reduction of the lag phase. This acclimation was characterized by the amplification of the genomic region containing, among others, genes belonging to the ethylmalonyl-CoA (EMC) pathway, which has been demonstrated to be required for acetate assimilation in Rs. rubrum. In this paper, we combined bacterial growth analysis with proteomic (SWATH -Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra-processing) investigation to better understand the bacterial response to a sudden increase of the light intensity. We compared the impact of suddenly increasing light intensity on the WT strain to that on the newly described acetate-competent strain in the presence of acetate. Contrary to what was observed with the WT strain, we observed that the acetate-competent strain was tolerant to the light stress. Proteomic analysis revealed that increasing light intensity had a significant impact on the photosynthetic apparatus, especially in the wild-type strain cultivated in the presence of acetate and low concentration of HCO3–. This phenomenon was accompanied by a relatively higher abundance of certain stress related proteins. Our results suggested that the production of PHA, but also potentially of branched chain amino acids synthesis, could be part of the mechanism used by Rs. rubrum to adapt to the light stress and the redox imbalance it triggered.
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Affiliation(s)
- Guillaume Bayon-Vicente
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
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43
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Lobry M, Loyez M, Hassan EM, Chah K, DeRosa MC, Goormaghtigh E, Wattiez R, Caucheteur C. Multimodal plasmonic optical fiber grating aptasensor. Opt Express 2020; 28:7539-7551. [PMID: 32225979 DOI: 10.1364/oe.385747] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/16/2020] [Indexed: 05/22/2023]
Abstract
Tilted fiber Bragg gratings (TFBGs) are now a well-established technology in the scientific literature, bringing numerous advantages, especially for biodetection. Significant sensitivity improvements are achieved by exciting plasmon waves on their metal-coated surface. Nowadays, a large part of advances in this topic relies on new strategies aimed at providing sensitivity enhancements. In this work, TFBGs are produced in both single-mode and multimode telecommunication-grade optical fibers, and their relative performances are evaluated for refractometry and biosensing purposes. TFBGs are biofunctionalized with aptamers oriented against HER2 (Human Epidermal Growth Factor Receptor-2), a relevant protein biomarker for breast cancer diagnosis. In vitro assays confirm that the sensing performances of TFBGs in multimode fiber are higher or identical to those of their counterparts in single-mode fiber, respectively, when bulk refractometry or surface biosensing is considered. These observations are confirmed by numerical simulations. TFBGs in multimode fiber bring valuable practical assets, featuring a reduced spectral bandwidth for improved multiplexing possibilities enabling the detection of several biomarkers.
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44
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Loyez M, Hassan EM, Lobry M, Liu F, Caucheteur C, Wattiez R, DeRosa MC, Willmore WG, Albert J. Rapid Detection of Circulating Breast Cancer Cells Using a Multiresonant Optical Fiber Aptasensor with Plasmonic Amplification. ACS Sens 2020; 5:454-463. [PMID: 31967461 DOI: 10.1021/acssensors.9b02155] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The detection of circulating tumor cells (CTCs), which are responsible for metastasis in several forms of cancer, represents an important goal in oncological diagnosis and treatment. These cells remain extremely challenging to detect, despite numerous previous studies, due to their low concentration (1-10 cells/mL of blood). In this work, an all-fiber plasmonic aptasensor featuring multiple narrowband resonances in the near-infrared wavelength range was developed to detect metastatic breast cancer cells. To this aim, specific aptamers against mammaglobin-A were selected and immobilized as receptors on the sensor surface. In vitro assays confirm that the label-free and real-time detection of cancer cells [limit of detection (LOD) of 49 cells/mL] occurs within 5 min, while the additional use of functionalized gold nanoparticles allows a 2-fold amplification of the biosensor response. Differential measurements on selected optical resonances were used to process the sensor response, and results were confirmed by microscopy. The detection of only 10 cancer cells/mL was achieved with relevant specificity against control cells and with quick response time.
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Affiliation(s)
- Médéric Loyez
- Proteomics and Microbiology Department, University of Mons, Champ de Mars 6, 7000 Mons, Belgium
| | - Eman M. Hassan
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Maxime Lobry
- Electromagnetism and Telecommunications Department, University of Mons, Boulevard Dolez 31, 7000 Mons, Belgium
| | - Fu Liu
- Department of Electronics, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Christophe Caucheteur
- Electromagnetism and Telecommunications Department, University of Mons, Boulevard Dolez 31, 7000 Mons, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Champ de Mars 6, 7000 Mons, Belgium
| | - Maria C. DeRosa
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - William G. Willmore
- Institute of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Jacques Albert
- Department of Electronics, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
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45
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Cyriaque V, Jacquiod S, Riber L, Abu Al-Soud W, Gillan DC, Sørensen SJ, Wattiez R. Selection and propagation of IncP conjugative plasmids following long-term anthropogenic metal pollution in river sediments. J Hazard Mater 2020; 382:121173. [PMID: 31563088 DOI: 10.1016/j.jhazmat.2019.121173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/14/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
For a century, the MetalEurop foundry released metals into the river "La Deûle". Previous work revealed higher microbial diversity in metal impacted sediments, and horizontal gene transfer mediated by conjugative plasmids was suggested to drive the community adaptation to metals. We used an integrative state-of-the-art molecular approach coupling quantitative PCR, conjugation assays, flow cytometry, fluorescence activated cell sorting and 16S rRNA gene amplicon sequencing to investigate the presence of conjugative plasmids and their propagation patterns in sediment microbiomes. We highlighted the existence of a native broad-host range IncP conjugative plasmid population in polluted sediments, confirming their ecological importance for microbial adaptation. However, despite incompatibilities and decreased transfer frequencies with our own alien IncP plasmid, we evidenced that a wide diversity of bacterial members was still prone to uptake the plasmid, indicating that sediment microbial communities are still inclined to receive conjugative plasmids from the same group. We observed that metal pollution favoured exogenous plasmid transfer to specific metal-selected bacteria, which are likely coming from upstream sources (e.g. wastewater treatment plant, farms…). Altogether, our results suggest that MetalEurop sediments are hotspots for gene transfer via plasmids, acting as an "environmental reservoir" for microbes and mobile elements released by human activities.
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Affiliation(s)
- Valentine Cyriaque
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 place du parc, Mons, Belgium; Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark; Agroécologie, UMR 1347, INRA Centre Dijon, Dijon, France
| | - Leise Riber
- Section of Functional Genomics, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 Copenhagen N, Denmark
| | - Waleed Abu Al-Soud
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark; Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Jouf University, Qurayyat, Saudi Arabia
| | - David C Gillan
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 place du parc, Mons, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 place du parc, Mons, Belgium
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Delacuvellerie A, Cyriaque V, Gobert S, Benali S, Wattiez R. The plastisphere in marine ecosystem hosts potential specific microbial degraders including Alcanivorax borkumensis as a key player for the low-density polyethylene degradation. J Hazard Mater 2019; 380:120899. [PMID: 31326835 DOI: 10.1016/j.jhazmat.2019.120899] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 05/20/2023]
Abstract
Most plastics are released to the environment in landfills and around 32% end up in the sea, inducing large ecological and health impacts. The plastics constitute a physical substrate and potential carbon source for microorganisms. The present study compares the structures of bacterial communities from floating plastics, sediment-associated plastics and sediments from the Mediterranean Sea. The 16S rRNA microbiome profiles of surface and sediment plastic-associated microbial biofilms from the same geographic location differ significantly, with the omnipresence of Bacteroidetes and Gammaproteobacteria. Our research confirmed that plastisphere hosts microbial communities were environmental distinct niche. In parallel, this study used environmental samples to investigate the enrichment of potential plastic-degrading bacteria with Low Density PolyEthylene (LDPE), PolyEthylene Terephthalate (PET) and PolyStyrene (PS) plastics as the sole carbon source. In this context, we showed that the bacterial community composition is clearly plastic nature dependent. Hydrocarbon-degrading bacteria such as Alcanivorax, Marinobacter and Arenibacter genera are enriched with LDPE and PET, implying that these bacteria are potential players in plastic degradation. Finally, our data showed for the first time the ability of Alcanivorax borkumensis to form thick biofilms specifically on LDPE and to degrade this petroleum-based plastic.
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Affiliation(s)
- Alice Delacuvellerie
- Proteomics and Microbiology Department, University of Mons, 20 place du Parc, 7000 Mons, Belgium
| | - Valentine Cyriaque
- Proteomics and Microbiology Department, University of Mons, 20 place du Parc, 7000 Mons, Belgium
| | - Sylvie Gobert
- Oceanology Department, University of Liège, 11 Allée du 6 août, 4000 Liège, Belgium
| | - Samira Benali
- Polymer and Composite Materials Department, University of Mons, 15 Avenue Maistriau, 7000 Mons, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, 20 place du Parc, 7000 Mons, Belgium.
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Géron A, Werner J, Wattiez R, Lebaron P, Matallana-Surget S. Deciphering the Functioning of Microbial Communities: Shedding Light on the Critical Steps in Metaproteomics. Front Microbiol 2019; 10:2395. [PMID: 31708885 PMCID: PMC6821674 DOI: 10.3389/fmicb.2019.02395] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/03/2019] [Indexed: 11/13/2022] Open
Abstract
Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Despite its rapid development, this technology has faced many technical challenges that still hamper its potential power. How to maximize the number of protein identification, improve quality of protein annotation, and provide reliable ecological interpretation are questions of immediate urgency. In our study, we used a robust metaproteomic workflow combining two protein fractionation approaches (gel-based versus gel-free) and four protein search databases derived from the same metagenome to analyze the same seawater sample. The resulting eight metaproteomes provided different outcomes in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. The characterization and/or representativeness of numerous proteins from ecologically relevant taxa such as Pelagibacterales, Rhodobacterales, and Synechococcales, as well as crucial environmental processes, such as nutrient uptake, nitrogen assimilation, light harvesting, and oxidative stress response, were found to be particularly affected by the methodology. Our results provide clear evidences that the use of different protein search databases significantly alters the biological conclusions in both gel-free and gel-based approaches. Our findings emphasize the importance of diversifying the experimental workflow for a comprehensive metaproteomic study.
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Affiliation(s)
- Augustin Géron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- Department of Proteomic and Microbiology, University of Mons, Mons, Belgium
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Ruddy Wattiez
- Department of Proteomic and Microbiology, University of Mons, Mons, Belgium
| | - Philippe Lebaron
- Sorbonne Universités, UPMC Université Paris 06, USR 3579, LBBM, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
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48
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Raes B, Horemans B, Rentsch D, T'Syen J, Ghequire MGK, De Mot R, Wattiez R, Kohler HPE, Springael D. Aminobacter sp. MSH1 Mineralizes the Groundwater Micropollutant 2,6-Dichlorobenzamide through a Unique Chlorobenzoate Catabolic Pathway. Environ Sci Technol 2019; 53:10146-10156. [PMID: 31386350 DOI: 10.1021/acs.est.9b02021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
2,6-Dichlorobenzamide (BAM) is a major groundwater micropollutant posing problems for drinking water treatment plants (DWTPs) that depend on groundwater intake. Aminobacter sp. MSH1 uses BAM as the sole source of carbon, nitrogen, and energy and is considered a prime biocatalyst for groundwater bioremediation in DWTPs. Its use in bioremediation requires knowledge of its BAM-catabolic pathway, which is currently restricted to the amidase BbdA converting BAM into 2,6-dichlorobenzoic acid (2,6-DCBA) and the monooxygenase BbdD transforming 2,6-DCBA into 2,6-dichloro-3-hydroxybenzoic acid. Here, we show that the 2,6-DCBA catabolic pathway is unique and differs substantially from catabolism of other chlorobenzoates. BbdD catalyzes a second hydroxylation, forming 2,6-dichloro-3,5-dihydroxybenzoic acid. Subsequently, glutathione-dependent dehalogenases (BbdI and BbdE) catalyze the thiolytic removal of the first chlorine. The remaining chlorine is then removed hydrolytically by a dehalogenase of the α/β hydrolase superfamily (BbdC). BbdC is the first enzyme in that superfamily associated with dehalogenation of chlorinated aromatics and appears to represent a new subtype within the α/β hydrolase dehalogenases. The activity of BbdC yields a unique trihydroxylated aromatic intermediate for ring cleavage that is performed by an extradiol dioxygenase (BbdF) producing 2,4,6-trioxoheptanedioic acid, which is likely converted to Krebs cycle intermediates by BbdG.
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Affiliation(s)
| | | | - Daniel Rentsch
- Laboratory for Functional Polymers , Empa, Swiss Federal Laboratories for Materials Science and Technology , Dübendorf 8600 , Switzerland
| | | | | | | | - Ruddy Wattiez
- Department of Proteomics and Microbiology , University of Mons , Mons 7000 , Belgium
| | - Hans-Peter E Kohler
- Department of Environmental Microbiology , Eawag, Swiss Federal Institute of Aquatic Science and Technology , Dübendorf 8600 , Switzerland
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Zeng S, Constant P, Yang D, Baulard A, Lefèvre P, Daffé M, Wattiez R, Fontaine V. Cpn60.1 (GroEL1) Contributes to Mycobacterial Crabtree Effect: Implications for Biofilm Formation. Front Microbiol 2019; 10:1149. [PMID: 31244785 PMCID: PMC6579834 DOI: 10.3389/fmicb.2019.01149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/06/2019] [Indexed: 12/18/2022] Open
Abstract
Biofilm formation is a survival strategy for microorganisms facing a hostile environment. Under biofilm, bacteria are better protected against antibacterial drugs and the immune response, increasing treatment difficulty, as persistent populations recalcitrant to chemotherapy are promoted. Deciphering mechanisms leading to biofilms could, thus, be beneficial to obtain new antibacterial drug candidates. Here, we show that mycobacterial biofilm formation is linked to excess glycerol adaptation and the concomitant establishment of the Crabtree effect. This effect is characterized by respiratory reprogramming, ATP downregulation, and secretion of various metabolites including pyruvate, acetate, succinate, and glutamate. Interestingly, the Crabtree effect was abnormal in a mycobacterial strain deficient for Cpn60.1 (GroEL1). Indeed, this mutant strain had a compromised ability to downregulate ATP and secreted more pyruvate, acetate, succinate, and glutamate in the culture medium. Importantly, the mutant strain had higher intracellular pyruvate and produced more toxic methylglyoxal, suggesting a glycolytic stress leading to growth stasis and consequently biofilm failure. This study demonstrates, for the first time, the link between mycobacterial biofilm formation and the Crabtree effect.
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Affiliation(s)
- Sheng Zeng
- Microbiology, Bioorganic and Macromolecular Chemistry Research Unit, Faculté de Pharmacie, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Patricia Constant
- Department of Tuberculosis and Infection Biology, Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Dong Yang
- Microbiology, Bioorganic and Macromolecular Chemistry Research Unit, Faculté de Pharmacie, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Alain Baulard
- Institut Pasteur de Lille, Université de Lille, CNRS, INSERM, CHU Lille, U1019-UMR 8204, Center for Infection and Immunity of Lille, Lille, France
| | - Philippe Lefèvre
- Microbiology, Bioorganic and Macromolecular Chemistry Research Unit, Faculté de Pharmacie, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mamadou Daffé
- Department of Tuberculosis and Infection Biology, Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, Mons, Belgium
| | - Véronique Fontaine
- Microbiology, Bioorganic and Macromolecular Chemistry Research Unit, Faculté de Pharmacie, Université Libre de Bruxelles (ULB), Brussels, Belgium
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50
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Cuellar-Bermudez SP, Kilimtzidi E, Devaere J, Goiris K, Gonzalez-Fernandez C, Wattiez R, Muylaert K. Harvesting of Arthrospira platensis with helicoidal and straight trichomes using filtration and centrifugation. SEP SCI TECHNOL 2019. [DOI: 10.1080/01496395.2019.1624573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Sara P. Cuellar-Bermudez
- KU Leuven Campus Kortrijk, Laboratory Aquatic Biology, Kortrijk, Belgium
- Department of Proteomic and Microbiology, Research Institute for Biosciences, Mons, Belgium
| | | | - Jolien Devaere
- KU Leuven Technology Campus Ghent, Laboratory of Enzyme, Fermentation and Brewing Technology, Ghent, Belgium
| | - Koen Goiris
- KU Leuven Technology Campus Ghent, Laboratory of Enzyme, Fermentation and Brewing Technology, Ghent, Belgium
| | | | - Ruddy Wattiez
- Department of Proteomic and Microbiology, Research Institute for Biosciences, Mons, Belgium
| | - Koenraad Muylaert
- KU Leuven Campus Kortrijk, Laboratory Aquatic Biology, Kortrijk, Belgium
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