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Tadesse BT, Svetlicic E, Zhao S, Berhane N, Jers C, Solem C, Mijakovic I. Bad to the bone? - Genomic analysis of Enterococcus isolates from diverse environments reveals that most are safe and display potential as food fermentation microorganisms. Microbiol Res 2024; 283:127702. [PMID: 38552381 DOI: 10.1016/j.micres.2024.127702] [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: 11/29/2023] [Revised: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
Enterococci comprise a group of lactic acid bacteria (LAB) with considerable potential to serve as food fermentation microorganisms. Unfortunately, enterococci have received a lot of negative attention, due to the occurrence of pathogenic and multidrug resistant strains. In this study, we used genomics to select safe candidates among the forty-four studied enterococcal isolates. The genomes of the forty-four strains were fully sequenced and assessed for presence of virulence and antibiotic resistance genes. Nineteen isolates belonging to the species Enterococcus lactis, Enterococcus faecium, Enterococcus durans, and Enterococcus thailandicus, were deemed safe from the genome analysis. The presence of secondary metabolite gene clusters for bacteriocins was assessed, and twelve candidates were found to secrete antimicrobial compounds effective against Listeria monocytogenes isolated from cheese and Staphylococcus aureus. Physiological characterization revealed nineteen industrial potentials; all strains grew well at 42 °C and acidified 1.5 hours faster than their mesophilic counterpart Lactococcus lactis, with which they share metabolism and flavor forming ability. We conclude that a large fraction of the examined enterococci were safe and could serve as excellent food fermentation microorganisms with inherent bioprotective abilities.
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Affiliation(s)
- Belay Tilahun Tadesse
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark; Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Ema Svetlicic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Shuangqing Zhao
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark
| | - Nega Berhane
- Institute of Biotechnology, University of Gondar, Ethiopia
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark.
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark; Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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Joshi AS, Bapat MV, Singh P, Mijakovic I. Viridibacillus culture derived silver nanoparticles exert potent anticancer action in 2D and 3D models of lung cancer via mitochondrial depolarization-mediated apoptosis. Mater Today Bio 2024; 25:100997. [PMID: 38379934 PMCID: PMC10876681 DOI: 10.1016/j.mtbio.2024.100997] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
Lung cancer is one of the most commonly occurring cancer types that accounts for almost 2 million cases per year. Its resistance to anticancer drugs, failure of new molecules in clinical trials, severe side-effects of current treatments, and its recurrence limit the success of anticancer therapies. Nanotherapeutic agents offer several advantages over conventional anticancer therapies, including improved retention in tumors, specificity, and anticancer effects at lower concentrations, hence reducing the side-effects. Here, we have explored the anticancer activity of silver nanoparticles synthesized in Viridibacillus sp. enriched culture medium for the first time. Such green nanoparticles, synthesized by biological systems, are superior to chemically synthesized ones in terms of their environmental footprint and production cost, and have one crucial advantage of excellent stability owing to their biological corona. To assess anticancer activity of these nanoparticles, we used conventional 2D cultured A549 cells as well as 3D spheroids of A549 cells. In both models of lung cancer, our silver nanoparticles diminished cell proliferation, arrested DNA synthesis, and showed a dose dependent cytotoxic effect. The nanoparticles damaged the DNA and mitochondrial structures in both A549 cells and A549 spheroids, leading to mitochondrial depolarization and increased cell permeability. Low lethal median doses (LD50) for 2D cultured A549 cells (1 μg/ml) and for A549 spheroids (13 μg/ml) suggest that our nanoparticles are potent anticancer agents. We also developed in vitro tumor progression model and in vitro tumor size model using 3D spheroids to test anticancer potential of our nanoparticles which otherwise would require longer experimental duration along with large number of animals and trained personnel. In these models, our nanoparticles showed strong dose dependent anticancer activity. In case of in vitro tumor progression model, the A549 cells failed to form tight spheroidal mass and showed increased dead cell fraction since day 1 as compared to control. On the other hand, in case of in vitro tumor size model, the 4 and 8 μg/ml nanoparticle treatment led to reduction in spheroid size from 615 ± 53 μm to 440 ± 45 μm and 612 ± 44 μm to 368 ± 62 μm respectively, within the time span of 3 days post treatment. We believe that use of such novel experimental models offers excellent and fast alternative to in vivo studies, and to the best of our knowledge, this is the first report that gives proof-of-concept for use of such novel in vitro cancer models to test anticancer agents such as Viridibacilli culture derived silver nanoparticles. Based on our results, we propose that these nanoparticles offer an interesting alternative for anticancer therapies, especially if they can be combined with classical anticancer drugs.
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Affiliation(s)
- Abhayraj S. Joshi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mugdha V. Bapat
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Priyanka Singh
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Sweden
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More PR, Shinde S, Cao Z, Zhang J, Pandit S, De Filippis A, Mijakovic I, Galdiero M. Antibacterial applications of biologically synthesized Pichia pastoris silver nanoparticles. Heliyon 2024; 10:e25664. [PMID: 38375309 PMCID: PMC10875387 DOI: 10.1016/j.heliyon.2024.e25664] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/05/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Objectives This article highlights the biological synthesis of silver nanoparticles (AgNPs) with their characteristic analysis, and it focuses on the application of synthesized NPs against multidrug resistance (MDR) bacteria. A cytotoxicity study was performed to assess the biocompatibility. Methods Silver nanoparticle (AgNPs) formation was confirmed by different characterization methods such as UV-Vis spectrophotometer, Dynamic light scattering (DLS)- Zeta, Fourier transform infrared (FTIR), and Transmission electron microscope (TEM). The antimicrobial activity of the AgNPs was checked against various bacterial strains of Staphylococcus aureus (S. aureus), Escherichia coli (E. coli), Enterococcus faecalis (E. faecalis), and Klebsiella pneumonia (K. pneumonia) by disc diffusion, minimum inhibition concentration test (MIC), and kinetic studies. The cytotoxicity of NPs against the Vero cell line was studied by cytotoxic assay. Results The primary analysis of the formation of nanoparticles (NPs) was made by UV-Vis spectrophotometric analysis at 400 nm. At the same time, the efficient capping checked by FTIR shows the presence of a functional group at different wavelengths 3284, 1641,1573,1388,1288, and 1068 cm-1. At the same time, the transmission electron microscopic analysis (TEM) and DLS show that the shape and size of the synthesized NPs possess an average size of around ∼10-30 nm with spherical morphology. Further, the zeta potential confirmed the stability of the NPs. While the yield of NPs formation from silver salt was determined by an online yield calculator with the EDX analysis results. Synthesized NPs showed bactericidal effects against all the selected MDR pathogens with nontoxic effects against mammalian cells. Conclusion Our findings indicate the remarkable antimicrobial activity of the biologically synthesized AgNPs, which can be an antimicrobial agent against multi-drug-resistant bacteria.
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Affiliation(s)
- Pragati Rajendra More
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania “L. Vanvitelli, ” Via De Crecchio, 7, 80138, Naples, Italy
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Bio Sustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Surbhi Shinde
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania “L. Vanvitelli, ” Via De Crecchio, 7, 80138, Naples, Italy
| | - Zhejiang Cao
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Jian Zhang
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Santosh Pandit
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Anna De Filippis
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania “L. Vanvitelli, ” Via De Crecchio, 7, 80138, Naples, Italy
| | - Ivan Mijakovic
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania “L. Vanvitelli, ” Via De Crecchio, 7, 80138, Naples, Italy
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, 41296, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Bio Sustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Massimiliano Galdiero
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania “L. Vanvitelli, ” Via De Crecchio, 7, 80138, Naples, Italy
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Zou G, Li T, Mijakovic I, Wei Y. Synthetic biology enables mushrooms to meet emerging sustainable challenges. Front Microbiol 2024; 15:1337398. [PMID: 38414763 PMCID: PMC10897037 DOI: 10.3389/fmicb.2024.1337398] [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: 11/13/2023] [Accepted: 02/02/2024] [Indexed: 02/29/2024] Open
Abstract
With the increasing sustainability challenges, synthetic biology is offering new possibilities for addressing the emerging problems through the cultivation and fermentation of mushrooms. In this perspective, we aim to provide an overview on the research and applications mushroom synthetic biology, emphasizing the need for increased attention and inclusion of this rapidly advancing field in future mushroom technology over China and other countries. By leveraging synthetic biology, mushrooms are expected to play a more versatile role in various area, including traditional fields like circular economy, human wellness and pharmaceutics, as well as emerging fields like vegan meat, mushroom-based materials and pollution abatement. We are confident that these efforts using synthetic biology strategies have the potential to strengthen our capacity to effectively address sustainable challenges, leading to the development of a more sustainable social economy and ecology.
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Affiliation(s)
- Gen Zou
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Southern Key Laboratory of Edible Fungus Resource Utilization, Ministry of Agriculture, National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Tian Li
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Food Laboratory of Zhongyuan, Zhengzhou University, Zhengzhou, China
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Food Laboratory of Zhongyuan, Zhengzhou University, Zhengzhou, China
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Balasubramanian S, Køhler JB, Jers C, Jensen PR, Mijakovic I. Exploring the secretome of Corynebacterium glutamicum ATCC 13032. Front Bioeng Biotechnol 2024; 12:1348184. [PMID: 38415189 PMCID: PMC10896948 DOI: 10.3389/fbioe.2024.1348184] [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: 12/02/2023] [Accepted: 01/22/2024] [Indexed: 02/29/2024] Open
Abstract
The demand for alternative sources of food proteins is increasing due to the limitations and challenges associated with conventional food production. Advances in biotechnology have enabled the production of proteins using microorganisms, thus prompting the exploration of attractive microbial hosts capable of producing functional proteins in high titers. Corynebacterium glutamicum is widely used in industry for the production of amino acids and has many advantages as a host organism for recombinant protein production. However, its performance in this area is limited by low yields of target proteins and high levels of native protein secretion. Despite representing a challenge for heterologous protein production, the C. glutamicum secretome has not been fully characterized. In this study, state-of-the-art mass spectrometry-based proteomics was used to identify and analyze the proteins secreted by C. glutamicum. Both the wild-type strain and a strain that produced and secreted a recombinant β-lactoglobulin protein were analyzed. A total of 427 proteins were identified in the culture supernatants, with 148 predicted to possess a secretion signal peptide. MS-based proteomics on the secretome enabled a comprehensive characterization and quantification (based on abundance) of the secreted proteins through label-free quantification (LFQ). The top 12 most abundant proteins accounted for almost 80% of the secretome. These are uncharacterized proteins of unknown function, resuscitation promoting factors, protein PS1, Porin B, ABC-type transporter protein and hypothetical membrane protein. The data can be leveraged for protein production by, e.g., utilizing the signal peptides of the most abundant proteins to improve secretion of heterologous proteins. In addition, secretory stress can potentially be alleviated by inactivating non-essential secreted proteins. Here we provide targets by identifying the most abundant, secreted proteins of which majority are of unknown function. The data from this study can thus provide valuable insight for researchers looking to improve protein secretion and optimize C. glutamicum as a host for secretory protein production.
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Affiliation(s)
- Suvasini Balasubramanian
- Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julie Bonne Køhler
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Ruhdal Jensen
- Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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6
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Lanai V, Chen Y, Naumovska E, Pandit S, Schröder E, Mijakovic I, Rahimi S. Differences in interaction of graphene/graphene oxide with bacterial and mammalian cell membranes. Nanoscale 2024; 16:1156-1166. [PMID: 38126749 DOI: 10.1039/d3nr05354g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Graphene, a single layer, hexagonally packed two-dimensional carbon sheet is an attractive candidate for diverse applications including antibacterial potential and drug delivery. One of the knowledge gaps in biomedical application of graphene is the interaction of these materials with the cells. To address this, we investigated the interaction between graphene materials (graphene and graphene oxide) and plasma membranes of cells (bacterial and mammalian cells). The interactions of four of the most abundant phospholipids in bacteria and mammalian plasma membranes with graphene materials were studied using density functional theory (DFT) at the atomic level. The calculations showed that the mammalian phospholipids have stronger bonding to each other compared to bacterial phospholipids. When the graphene/graphene oxide sheet is approaching the phospholipid pairs, the bacterial pairs exhibit less repulsive interactions, thereby a more stable system with the sheets was found. We also assembled bacterial and mammalian phospholipids into liposomes. We further observed that the bacterial liposomes and cells let the graphene flakes penetrate the membrane. The differential scanning calorimetry measurements of liposomes revealed that the bacterial liposomes have the lowest heat capacity; this strengthens the theoretical predictions of weaker interaction between the bacterial phospholipids compared to the mammalian phospholipids. We further demonstrated that graphene oxide could be internalized into the mammalian liposomes without disrupting the membrane integrity. The results suggest that the weak bonding among bacteria phospholipids and less repulsive force when graphene materials approach, result in graphene materials interacting differently with the bacteria compared to mammalian cells.
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Affiliation(s)
- Victor Lanai
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
- Quantum Device Physics Laboratory, Department of Microtechnology and Nanoscience-MC2, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Yanyan Chen
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
| | - Elena Naumovska
- Energy and Materials division, Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Santosh Pandit
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
| | - Elsebeth Schröder
- Quantum Device Physics Laboratory, Department of Microtechnology and Nanoscience-MC2, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
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Mijakovic I, Rahimi S. Learning by teaching efficiently enhances learning outcomes in molecular biology of the cell course. Biochem Molecular Bio Educ 2024; 52:15-24. [PMID: 37712513 DOI: 10.1002/bmb.21784] [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: 12/18/2022] [Revised: 08/11/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
To evaluate the impact of active learning approaches in a basic molecular and cell biology course for undergraduate students, we assessed the effect of learning by teaching and peer review on the learning outcomes. A literature seminar activity with peer review and feedback was organized as a compulsory activity for all students, covering about 25% of the course content. The remaining 75% of the course was delivered as classical lectures. The students collaborated in groups to present the content of a review article complemented with a research article. For each group of students, an opponent group was assigned to challenge the presenting group by questions and contribute to the evaluation of the presentation together with the teacher. Based on the feedback survey, the students reacted positively to this active learning exercise, and they strongly recommended keeping it in the future editions of the course. The students' exam scores strongly indicated that the learning outcomes from the learning by teaching part of the course were consistently higher than from the classical lecture part of the course. Further optimization of the active learning part of the course is outlined based on student feedback.
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Affiliation(s)
- Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
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8
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Ruan H, Bek M, Pandit S, Aulova A, Zhang J, Bjellheim P, Lovmar M, Mijakovic I, Kádár R. Biomimetic Antibacterial Gelatin Hydrogels with Multifunctional Properties for Biomedical Applications. ACS Appl Mater Interfaces 2023; 15:54249-54265. [PMID: 37975260 PMCID: PMC10694820 DOI: 10.1021/acsami.3c10477] [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: 07/18/2023] [Revised: 10/19/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
A facile novel approach of introducing dopamine and [2-(methacryloyloxy) ethyl] dimethyl-(3-sulfopropyl) ammonium hydroxide via dopamine-triggered in situ synthesis into gelatin hydrogels in the presence of ZnSO4 is presented in this study. Remarkably, the resulting hydrogels showed 99.99 and 100% antibacterial efficiency against Gram-positive and Gram-negative bacteria, respectively, making them the highest performing surfaces in their class. Furthermore, the hydrogels showed adhesive properties, self-healing ability, antifreeze properties, electrical conductivity, fatigue resistance, and mechanical stability from -100 to 80 °C. The added multifunctional performance overcomes several disadvantages of gelatin-based hydrogels such as poor mechanical properties and limited thermostability. Overall, the newly developed hydrogels show significant potential for numerous biomedical applications, such as wearable monitoring sensors and antibacterial coatings.
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Affiliation(s)
- Hengzhi Ruan
- Department
of Industrial and Materials Science, Chalmers
University of Technology, 412 96 Göteborg, Sweden
| | - Marko Bek
- Department
of Industrial and Materials Science, Chalmers
University of Technology, 412 96 Göteborg, Sweden
| | - Santosh Pandit
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96 Göteborg, Sweden
| | - Alexandra Aulova
- Department
of Industrial and Materials Science, Chalmers
University of Technology, 412 96 Göteborg, Sweden
| | - Jian Zhang
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96 Göteborg, Sweden
| | | | - Martin Lovmar
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96 Göteborg, Sweden
- Welspect
AB, 431 21 Mölndal, Sweden
| | - Ivan Mijakovic
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96 Göteborg, Sweden
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Roland Kádár
- Department
of Industrial and Materials Science, Chalmers
University of Technology, 412 96 Göteborg, Sweden
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Zhang X, Miao Q, Tang B, Mijakovic I, Ji XJ, Qu L, Wei Y. Discovery of novel alkaline-tolerant xylanases from fecal microbiota of dairy cows. Biotechnol Biofuels Bioprod 2023; 16:182. [PMID: 38012750 PMCID: PMC10683242 DOI: 10.1186/s13068-023-02435-8] [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] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Xylo-oligosaccharides (XOS) are considered as a promising type of prebiotics that can be used in foods, feeds, and healthcare products. Xylanases play a key role in the production of XOS from xylan. In this study, we conducted a metagenomic analysis of the fecal microbiota from dairy cows fed with different types of fodders. Despite the diversity in their diets, the main phyla observed in all fecal microbiota were Firmicutes and Bacteroidetes. At the genus level, one group of dairy cows that were fed probiotic fermented herbal mixture-containing fodders displayed decreased abundance of Methanobrevibacter and increased growth of beneficial Akkermansia bacteria. Additionally, this group exhibited a high microbial richness and diversity. Through our analysis, we obtained a comprehensive dataset comprising over 280,000 carbohydrate-active enzyme genes. Among these, we identified a total of 163 potential xylanase genes and subsequently expressed 34 of them in Escherichia coli. Out of the 34 expressed genes, two alkaline xylanases with excellent temperature stability and pH tolerance were obtained. Notably, CDW-xyl-8 exhibited xylanase activity of 96.1 ± 7.5 U/mg protein, with an optimal working temperature of 55 ℃ and optimal pH of 8.0. CDW-xyl-16 displayed an activity of 427.3 ± 9.1 U/mg protein with an optimal pH of 8.5 and an optimal temperature at 40 ℃. Bioinformatic analyses and structural modeling suggest that CDW-xyl-8 belongs to GH10 family xylanase, and CDW-xyl-16 is a GH11 family xylanase. Both enzymes have the ability to hydrolyze beechwood xylan and produce XOS. In conclusion, this metagenomic study provides valuable insights into the fecal microbiota composition of dairy cows fed different fodder types, revealing main microbial groups and demonstrating the abundance of xylanases. Furthermore, the characterization of two novel xylanases highlights their potential application in XOS production.
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Affiliation(s)
- Xiaoling Zhang
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Qin Miao
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Bingling Tang
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 41296, Sweden
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Xiao-Jun Ji
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Lingbo Qu
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450001, China.
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Aminian-Dehkordi J, Rahimi S, Golzar-Ahmadi M, Singh A, Lopez J, Ledesma-Amaro R, Mijakovic I. Synthetic biology tools for environmental protection. Biotechnol Adv 2023; 68:108239. [PMID: 37619824 DOI: 10.1016/j.biotechadv.2023.108239] [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: 04/15/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.
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Affiliation(s)
| | - Shadi Rahimi
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Mehdi Golzar-Ahmadi
- Norman B. Keevil Institute of Mining Engineering, University of British Columbia, Vancouver, Canada
| | - Amritpal Singh
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | - Javiera Lopez
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | | | - Ivan Mijakovic
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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Balusamy SR, Joshi AS, Perumalsamy H, Mijakovic I, Singh P. Advancing sustainable agriculture: a critical review of smart and eco-friendly nanomaterial applications. J Nanobiotechnology 2023; 21:372. [PMID: 37821961 PMCID: PMC10568898 DOI: 10.1186/s12951-023-02135-3] [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: 05/22/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
Undoubtedly, nanoparticles are one of the ideal choices for achieving challenges related to bio sensing, drug delivery, and biotechnological tools. After gaining success in biomedical research, scientists are exploring various types of nanoparticles for achieving sustainable agriculture. The active nanoparticles can be used as a direct source of micronutrients or as a delivery platform for delivering the bioactive agrochemicals to improve crop growth, crop yield, and crop quality. Till date, several reports have been published showing applications of nanotechnology in agriculture. For instance, several methods have been employed for application of nanoparticles; especially metal nanoparticles to improve agriculture. The physicochemical properties of nanoparticles such as core metal used to synthesize the nanoparticles, their size, shape, surface chemistry, and surface coatings affect crops, soil health, and crop-associated ecosystem. Therefore, selecting nanoparticles with appropriate physicochemical properties and applying them to agriculture via suitable method stands as smart option to achieve sustainable agriculture and improved plant performance. In presented review, we have compared various methods of nanoparticle application in plants and critically interpreted the significant differences to find out relatively safe and specific method for sustainable agricultural practice. Further, we have critically analyzed and discussed the different physicochemical properties of nanoparticles that have direct influence on plants in terms of nano safety and nanotoxicity. From literature review, we would like to point out that the implementation of smaller sized metal nanoparticles in low concentration via seed priming and foliar spray methods could be safer method for minimizing nanotoxicity, and for exhibiting better plant performance during stress and non-stressed conditions. Moreover, using nanomaterials for delivery of bioactive agrochemicals could pose as a smart alternative for conventional chemical fertilizers for achieving the safer and cleaner technology in sustainable agriculture. While reviewing all the available literature, we came across some serious drawbacks such as the lack of proper regulatory bodies to control the usage of nanomaterials and poor knowledge of the long-term impact on the ecosystem which need to be addressed in near future for comprehensive knowledge of applicability of green nanotechnology in agriculture.
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Affiliation(s)
- Sri Renukadevi Balusamy
- Department of Food Science and Biotechnology, Sejong University, Gwangjin-Gu, Seoul, 05006 Republic of Korea
| | - Abhayraj S. Joshi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Haribalan Perumalsamy
- Institute for Next Generation Material Design, Hanyang University, Seoul, Republic of Korea
- Center for Creative Convergence Education, Hanyang University, Seoul, Republic of Korea
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Priyanka Singh
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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12
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Ruan H, Aulova A, Ghai V, Pandit S, Lovmar M, Mijakovic I, Kádár R. Polysaccharide-based antibacterial coating technologies. Acta Biomater 2023; 168:42-77. [PMID: 37481193 DOI: 10.1016/j.actbio.2023.07.023] [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: 03/28/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023]
Abstract
To tackle antimicrobial resistance, a global threat identified by the United Nations, is a common cause of healthcare-associated infections (HAI) and is responsible for significant costs on healthcare systems, a substantial amount of research has been devoted to developing polysaccharide-based strategies that prevent bacterial attachment and biofilm formation on surfaces. Polysaccharides are essential building blocks for life and an abundant renewable resource that have attracted much attention due to their intrinsic remarkable biological potential antibacterial activities. If converted into efficient antibacterial coatings that could be applied to a broad range of surfaces and applications, polysaccharide-based coatings could have a significant potential global impact. However, the ultimate success of polysaccharide-based antibacterial materials will be determined by their potential for use in manufacturing processes that are scalable, versatile, and affordable. Therefore, in this review we focus on recent advances in polysaccharide-based antibacterial coatings from the perspective of fabrication methods. We first provide an overview of strategies for designing polysaccharide-based antimicrobial formulations and methods to assess the antibacterial properties of coatings. Recent advances on manufacturing polysaccharide-based coatings using some of the most common polysaccharides and fabrication methods are then detailed, followed by a critical comparative overview of associated challenges and opportunities for future developments. STATEMENT OF SIGNIFICANCE: Our review presents a timely perspective by being the first review in the field to focus on advances on polysaccharide-based antibacterial coatings from the perspective of fabrication methods along with an overview of strategies for designing polysaccharide-based antimicrobial formulations, methods to assess the antibacterial properties of coatings as well as a critical comparative overview of associated challenges and opportunities for future developments. Meanwhile this work is specifically targeted at an audience focused on featuring critical information and guidelines for developing polysaccharide-based coatings. Including such a complementary work in the journal could lead to further developments on polysaccharide antibacterial applications.
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Affiliation(s)
- Hengzhi Ruan
- Department of Industrial and Materials Science, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Alexandra Aulova
- Department of Industrial and Materials Science, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Viney Ghai
- Department of Industrial and Materials Science, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Santosh Pandit
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Martin Lovmar
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; Wellspect Healthcare AB, 431 21 Mölndal, Sweden
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Roland Kádár
- Department of Industrial and Materials Science, Chalmers University of Technology, 412 96 Göteborg, Sweden; Wallenberg Wood Science Centre (WWSC), Chalmers University of Technology, 412 96 Göteborg, Sweden.
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13
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Balusamy SR, Perumalsamy H, Huq MA, Yoon TH, Mijakovic I, Thangavelu L, Yang DC, Rahimi S. A comprehensive and systemic review of ginseng-based nanomaterials: Synthesis, targeted delivery, and biomedical applications. Med Res Rev 2023; 43:1374-1410. [PMID: 36939049 DOI: 10.1002/med.21953] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 11/22/2022] [Accepted: 02/26/2023] [Indexed: 03/21/2023]
Abstract
Among 17 Panax species identified across the world, Panax ginseng (Korean ginseng), Panax quinquefolius (American ginseng), and Panax notoginseng (Chinese ginseng) are highly recognized for the presence of bioactive compound, ginsenosides and their pharmacological effects. P. ginseng is widely used for synthesis of different types of nanoparticles compared to P. quinquefolius and P. notoginseng. The use of nano-ginseng could increase the oral bioavailability, membrane permeability, and thus provide effective delivery of ginsenosides to the target sites through transport system. In this review, we explore the synthesis of ginseng nanoparticles using plant extracts from various organs, microbes, and polymers, as well as their biomedical applications. Furthermore, we highlight transporters involved in transport of ginsenoside nanoparticles to the target sites. Size, zeta potential, temperature, and pH are also discussed as the critical parameters affecting the quality of ginseng nanoparticles synthesis.
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Affiliation(s)
- Sri Renukadevi Balusamy
- Department of Food Science and Biotechnology, Sejong University, Seoul, Gwangjin-gu, Republic of Korea
| | - Haribalan Perumalsamy
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul, Republic of Korea
- Institute for Next Generation Material Design, Hanyang University, Seoul, Republic of Korea
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Md Amdadul Huq
- Department of Food and Nutrition, Chung Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Tae Hyun Yoon
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul, Republic of Korea
- Institute for Next Generation Material Design, Hanyang University, Seoul, Republic of Korea
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lakshmi Thangavelu
- Department of Pharmacology, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, Tamilnadu, India
| | - Deok Chun Yang
- Graduate School of Biotechnology, Kyung Hee University, Yongin, Republic of Korea
- Department of Oriental Medicinal Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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14
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Khan F, Singh P, Joshi AS, Tabassum N, Jeong GJ, Bamunuarachchi NI, Mijakovic I, Kim YM. Multiple potential strategies for the application of nisin and derivatives. Crit Rev Microbiol 2023; 49:628-657. [PMID: 35997756 DOI: 10.1080/1040841x.2022.2112650] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 12/22/2022]
Abstract
Nisin is a naturally occurring bioactive small peptide produced by Lactococcus lactis subsp. lactis and belongs to the Type A (I) lantibiotics. Due to its potent antimicrobial activity, it has been broadly employed to preserve various food materials as well as to combat a variety of microbial pathogens. The present review discusses the antimicrobial properties of nisin and different types of their derivatives employed to treat microbial pathogens with a detailed underlying mechanism of action. Several alternative strategies such as combination, conjugation, and nanoformulations have been discussed in order to address several issues such as rapid degradation, instability, and reduced activity due to the various environmental factors that arise in the applications of nisin. Furthermore, the evolutionary relationship of many nisin genes from different nisin-producing bacterial species has been investigated. A detailed description of the natural and bioengineered nisin variants, as well as the underlying action mechanisms, has also been provided. The chemistry used to apply nisin in conjugation with natural or synthetic compounds as a synergetic mode of antimicrobial action has also been thoroughly discussed. The current review will be useful in learning about recent and past research that has been performed on nisin and its derivatives as antimicrobial agents.
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Affiliation(s)
- Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, Republic of Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, Republic of Korea
| | - Priyanka Singh
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Abhayraj S Joshi
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Nazia Tabassum
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, Republic of Korea
| | - Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
| | | | - Ivan Mijakovic
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Young-Mog Kim
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, Republic of Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, Republic of Korea
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
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15
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Joshi AS, Madhusudanan M, Mijakovic I. 3D printed inserts for reproducible high throughput screening of cell migration. Front Cell Dev Biol 2023; 11:1256250. [PMID: 37711850 PMCID: PMC10498783 DOI: 10.3389/fcell.2023.1256250] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/07/2023] [Indexed: 09/16/2023] Open
Abstract
Cell migration is a fundamental and complex phenomenon that occurs in normal physiology and in diseases like cancer. Hence, understanding cell migration is very important in the fields of developmental biology and biomedical sciences. Cell migration occurs in 3 dimensions (3D) and involves an interplay of migrating cell(s), neighboring cells, extracellular matrix, and signaling molecules. To understand this phenomenon, most of the currently available techniques still rely on 2-dimensional (2D) cell migration assay, also known as the scratch assay or the wound healing assay. These methods suffer from limited reproducibility in creating a cell-free region (a scratch or a wound). Mechanical/heat related stress to cells is another issue which hampers the applicability of these methods. To tackle these problems, we developed an alternative method based on 3D printed biocompatible cell inserts, for quantifying cell migration in 24-well plates. The inserts were successfully validated via a high throughput assay for following migration of lung cancer cell line (A549 cell line) in the presence of standard cell migration promoters and inhibitors. We also developed an accompanying image analysis pipeline which demonstrated that our method outperforms the state-of-the-art methodologies for assessing the cell migration in terms of reproducibility and simplicity.
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Affiliation(s)
- Abhayraj S. Joshi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mukil Madhusudanan
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
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16
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Zhang J, Neupane N, Dahal PR, Rahimi S, Cao Z, Pandit S, Mijakovic I. Antibiotic-Loaded Boron Nitride Nanoconjugate with Strong Performance against Planktonic Bacteria and Biofilms. ACS Appl Bio Mater 2023; 6:3131-3142. [PMID: 37473743 PMCID: PMC10445265 DOI: 10.1021/acsabm.3c00247] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
Protecting surfaces from biofilm formation presents a significant challenge in the biomedical field. The utilization of antimicrobial component-conjugated nanoparticles is becoming an attractive strategy against infectious biofilms. Boron nitride (BN) nanomaterials have a unique biomedical application value due to their excellent biocompatibility. Here, we developed antibiotic-loaded BN nanoconjugates to combat bacterial biofilms. Antibiofilm testing included two types of pathogens, Staphylococcus aureus and Escherichia coli. Gentamicin was loaded on polydopamine-modified BN nanoparticles (GPBN) to construct a nanoconjugate, which was very effective in killing E. coli and S. aureus planktonic cells. GPBN exhibited equally strong capacity for biofilm destruction, tested on preformed biofilms. A 24 h treatment with the nanoconjugate reduced cell viability by more than 90%. Our results suggest that GPBN adheres to the surface of the biofilm, penetrates inside the biofilm matrix, and finally deactivates the cells. Interestingly, the GPBN coatings also strongly inhibited the formation of bacterial biofilms. Based on these results, we suggest that GPBN could serve as an effective means for treating biofilm-associated infections and as coatings for biofilm prevention.
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Affiliation(s)
- Jian Zhang
- Systems
and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Nisha Neupane
- Systems
and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Department
of Microbiology, Tri-Chandra Multiple College, Tribhuvan University, 44600 Kathmandu, Nepal
| | - Puspa Raj Dahal
- Department
of Microbiology, Tri-Chandra Multiple College, Tribhuvan University, 44600 Kathmandu, Nepal
| | - Shadi Rahimi
- Systems
and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Zhejian Cao
- Systems
and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Santosh Pandit
- Systems
and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Ivan Mijakovic
- Systems
and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- The
Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, DK-2800 Kogens Lyngby, Denmark
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17
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Abujubara H, Hintzen JCJ, Rahimi S, Mijakovic I, Tietze D, Tietze AA. Substrate-derived Sortase A inhibitors: targeting an essential virulence factor of Gram-positive pathogenic bacteria. Chem Sci 2023; 14:6975-6985. [PMID: 37389257 PMCID: PMC10306101 DOI: 10.1039/d3sc01209c] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023] Open
Abstract
The bacterial transpeptidase Sortase A (SrtA) is a surface enzyme of Gram-positive pathogenic bacteria. It has been shown to be an essential virulence factor for the establishment of various bacterial infections, including septic arthritis. However, the development of potent Sortase A inhibitors remains an unmet challenge. Sortase A relies on a five amino acid sorting signal (LPXTG), by which it recognizes its natural target. We report the synthesis of a series of peptidomimetic inhibitors of Sortase A based on the sorting signal, supported by computational binding analysis. By employing a FRET-compatible substrate, our inhibitors were assayed in vitro. Among our panel, we identified several promising inhibitors with IC50 values below 200 μM, with our strongest inhibitor - LPRDSar - having an IC50 of 18.9 μM. Furthermore, it was discovered that three of our compounds show an effect on growth and biofilm inhibition of pathogenic Staphylococcus aureus, with the inclusion of a phenyl ring seemingly key to this effect. The most promising compound in our panel, BzLPRDSar, could inhibit biofilm formation at concentrations as low as 32 μg mL-1, manifesting it as a potential future drug lead. This could lead to treatments for MRSA infections in clinics and diseases such as septic arthritis, which has been directly linked with SrtA.
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Affiliation(s)
- Helal Abujubara
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg Kemigården 4 412 96 Göteborg Sweden
| | - Jordi C J Hintzen
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg Kemigården 4 412 96 Göteborg Sweden
| | - Shadi Rahimi
- Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology Kemivägen 10 412 96 Göteborg Sweden
| | - Ivan Mijakovic
- Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology Kemivägen 10 412 96 Göteborg Sweden
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark DK-2800 Kongens Lyngby Denmark
| | - Daniel Tietze
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg Kemigården 4 412 96 Göteborg Sweden
| | - Alesia A Tietze
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg Kemigården 4 412 96 Göteborg Sweden
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Pandit S, Jacquemin L, Zhang J, Gao Z, Nishina Y, Meyer RL, Mijakovic I, Bianco A, Pang C. Polymyxin B complexation enhances the antimicrobial potential of graphene oxide. Front Cell Infect Microbiol 2023; 13:1209563. [PMID: 37415828 PMCID: PMC10321305 DOI: 10.3389/fcimb.2023.1209563] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction The antibacterial activity of graphene oxide (GO) has been widely explored and tested against various pathogenic bacterial strains. Although antimicrobial activity of GO against planktonic bacterial cells was demonstrated, its bacteriostatic and bactericidal effect alone is not sufficient to damage sedentary and well protected bacterial cells inside biofilms. Thus, to be utilized as an effective antibacterial agent, it is necessary to improve the antibacterial activity of GO either by integration with other nanomaterials or by attachment of antimicrobial agents. In this study, antimicrobial peptide polymyxin B (PMB) was adsorbed onto the surface of pristine GO and GO functionalized with triethylene glycol. Methods The antibacterial effects of the resulting materials were examined by evaluating minimum inhibitory concentration, minimum bactericidal concentration, time kill assay, live/dead viability staining and scanning electron microscopy. Results and discussion PMB adsorption significantly enhanced the bacteriostatic and bactericidal activity of GO against both planktonic cells and bacterial cells in biofilms. Furthermore, the coatings of PMB-adsorbed GO applied to catheter tubes strongly mitigated biofilm formation, by preventing bacterial adhesion and killing the bacterial cells that managed to attach. The presented results suggest that antibacterial peptide absorption can significantly enhance the antibacterial activity of GO and the resulting material can be effectively used not only against planktonic bacteria but also against infectious biofilms.
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Affiliation(s)
- Santosh Pandit
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Lucas Jacquemin
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, University of Strasbourg, ISIS, Strasbourg, France
| | - Jian Zhang
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Zhengfeng Gao
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, University of Strasbourg, ISIS, Strasbourg, France
| | - Yuta Nishina
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alberto Bianco
- CNRS, Immunology, Immunopathology and Therapeutic Chemistry, UPR 3572, University of Strasbourg, ISIS, Strasbourg, France
| | - Chengfang Pang
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- The Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
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Rahimi S, Lovmar T, Aulova A, Pandit S, Lovmar M, Forsberg S, Svensson M, Kádár R, Mijakovic I. Automated Prediction of Bacterial Exclusion Areas on SEM Images of Graphene-Polymer Composites. Nanomaterials (Basel) 2023; 13:nano13101605. [PMID: 37242022 DOI: 10.3390/nano13101605] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023]
Abstract
To counter the rising threat of bacterial infections in the post-antibiotic age, intensive efforts are invested in engineering new materials with antibacterial properties. The key bottleneck in this initiative is the speed of evaluation of the antibacterial potential of new materials. To overcome this, we developed an automated pipeline for the prediction of antibacterial potential based on scanning electron microscopy images of engineered surfaces. We developed polymer composites containing graphite-oriented nanoplatelets (GNPs). The key property that the algorithm needs to consider is the density of sharp exposed edges of GNPs that kill bacteria on contact. The surface area of these sharp exposed edges of GNPs, accessible to bacteria, needs to be inferior to the diameter of a typical bacterial cell. To test this assumption, we prepared several composites with variable distribution of exposed edges of GNP. For each of them, the percentage of bacterial exclusion area was predicted by our algorithm and validated experimentally by measuring the loss of viability of the opportunistic pathogen Staphylococcus epidermidis. We observed a remarkable linear correlation between predicted bacterial exclusion area and measured loss of viability (R2 = 0.95). The algorithm parameters we used are not generally applicable to any antibacterial surface. For each surface, key mechanistic parameters must be defined for successful prediction.
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Affiliation(s)
- Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Teo Lovmar
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Alexandra Aulova
- Division of Engineering Materials, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Santosh Pandit
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Martin Lovmar
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Wellspect Healthcare, Aminogatan 1, 43121 Mölndal, Sweden
| | | | | | - Roland Kádár
- Division of Engineering Materials, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, 41296 Gothenburg, Sweden
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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20
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More PR, Pandit S, Filippis AD, Franci G, Mijakovic I, Galdiero M. Silver Nanoparticles: Bactericidal and Mechanistic Approach against Drug Resistant Pathogens. Microorganisms 2023; 11:microorganisms11020369. [PMID: 36838334 PMCID: PMC9961011 DOI: 10.3390/microorganisms11020369] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/11/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
This review highlights the different modes of synthesizing silver nanoparticles (AgNPs) from their elemental state to particle format and their mechanism of action against multidrug-resistant and biofilm-forming bacterial pathogens. Various studies have demonstrated that the AgNPs cause oxidative stress, protein dysfunction, membrane disruption, and DNA damage in bacteria, ultimately leading to bacterial death. AgNPs have also been found to alter the adhesion of bacterial cells to prevent biofilm formation. The benefits of using AgNPs in medicine are, to some extent, counter-weighted by their toxic effect on humans and the environment. In this review, we have compiled recent studies demonstrating the antibacterial activity of AgNPs, and we are discussing the known mechanisms of action of AgNPs against bacterial pathogens. Ongoing clinical trials involving AgNPs are briefly presented. A particular focus is placed on the mechanism of interaction of AgNPs with bacterial biofilms, which are a significant pathogenicity determinant. A brief overview of the use of AgNPs in other medical applications (e.g., diagnostics, promotion of wound healing) and the non-medical sectors is presented. Finally, current drawbacks and limitations of AgNPs use in medicine are discussed, and perspectives for the improved future use of functionalized AgNPs in medical applications are presented.
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Affiliation(s)
- Pragati Rajendra More
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania “L. Vanvitelli”, Via De Crecchio, 7, 80138 Naples, Italy
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Santosh Pandit
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Anna De Filippis
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania “L. Vanvitelli”, Via De Crecchio, 7, 80138 Naples, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84081 Baronissi, Italy
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Bio Sustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Correspondence: (I.M.); (M.G.)
| | - Massimiliano Galdiero
- Department of Experimental Medicine, Section of Microbiology and Clinical Microbiology, University of Campania “L. Vanvitelli”, Via De Crecchio, 7, 80138 Naples, Italy
- Correspondence: (I.M.); (M.G.)
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Rahimi S, van Leeuwen D, Roshanzamir F, Pandit S, Shi L, Sasanian N, Nielsen J, Esbjörner EK, Mijakovic I. Ginsenoside Rg3 Reduces the Toxicity of Graphene Oxide Used for pH-Responsive Delivery of Doxorubicin to Liver and Breast Cancer Cells. Pharmaceutics 2023; 15:pharmaceutics15020391. [PMID: 36839713 PMCID: PMC9965446 DOI: 10.3390/pharmaceutics15020391] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
Doxorubicin (DOX) is extensively used in chemotherapy, but it has serious side effects and is inefficient against some cancers, e.g., hepatocarcinoma. To ameliorate the delivery of DOX and reduce its side effects, we designed a pH-responsive delivery system based on graphene oxide (GO) that is capable of a targeted drug release in the acidic tumor microenvironment. GO itself disrupted glutathione biosynthesis and induced reactive oxygen species (ROS) accumulation in human cells. It induced IL17-directed JAK-STAT signaling and VEGF gene expression, leading to increased cell proliferation as an unwanted effect. To counter this, GO was conjugated with the antioxidant, ginsenoside Rg3, prior to loading with DOX. The conjugation of Rg3 to GO significantly reduced the toxicity of the GO carrier by abolishing ROS production. Furthermore, treatment of cells with GO-Rg3 did not induce IL17-directed JAK-STAT signaling and VEGF gene expression-nor cell proliferation-suggesting GO-Rg3 as a promising drug carrier. The anticancer activity of GO-Rg3-DOX conjugates was investigated against Huh7 hepatocarcinoma and MDA-MB-231 breast cancer cells. GO-Rg3-DOX conjugates significantly reduced cancer cell viability, primarily via downregulation of transcription regulatory genes and upregulation of apoptosis genes. GO-Rg3 is an effective, biocompatible, and pH responsive DOX carrier with potential to improve chemotherapy-at least against liver and breast cancers.
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Affiliation(s)
- Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Daniel van Leeuwen
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Fariba Roshanzamir
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Santosh Pandit
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Lei Shi
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Nima Sasanian
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Jens Nielsen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
- BioInnovation Institute, DK-2200 Copenhagen, Denmark
| | - Elin K. Esbjörner
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
- Correspondence:
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Garg A, Jers C, Hwang HJ, Kalantari A, Ventina I, Mijakovic I. Engineering Bacillus subtilis for production of 3-hydroxypropanoic acid. Front Bioeng Biotechnol 2023; 11:1101232. [PMID: 36726744 PMCID: PMC9885095 DOI: 10.3389/fbioe.2023.1101232] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/04/2023] [Indexed: 01/17/2023] Open
Abstract
3-Hydroxypropionic acid (3-HP) is a valuable platform chemical that is used as a precursor for several higher value-added chemical products. There is an increased interest in development of cell factories as a means for the synthesis of 3-HP and various other platform chemicals. For more than a decade, concentrated effort has been invested by the scientific community towards developing bio-based approaches for the production of 3-HP using primarily Escherichia coli and Klebsiella pneumoniae as production hosts. These hosts however might not be optimal for applications in e.g., food industry due primarily to endotoxin production and the pathogenic origin of particularly the K. pneumoniae. We have previously demonstrated that the generally recognized as safe organism Bacillus subtilis can be engineered to produce 3-HP using glycerol, an abundant by-product of the biodiesel industry, as substrate. For commercial exploitation, there is a need to substantially increase the titer. In the present study, we optimized the bioprocess conditions and further engineered the B. subtilis 3-HP production strain. Thereby, using glycerol as substrate, we were able to improve 3-HP production in a 1-L bioreactor to a final titer of 22.9 g/L 3-HP.
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Affiliation(s)
- Abhroop Garg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Hee Jin Hwang
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden,Department of Molecular Science and Technology, Ajou University, World cup-ro, Yeongtong-gu, Suwon-si, South Korea
| | - Aida Kalantari
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ildze Ventina
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden,*Correspondence: Ivan Mijakovic,
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Svetlicic E, Jaén-Luchoro D, Klobucar RS, Jers C, Kazazic S, Franjevic D, Klobucar G, Shelton BG, Mijakovic I. Genomic characterization and assessment of pathogenic potential of Legionella spp. isolates from environmental monitoring. Front Microbiol 2023; 13:1091964. [PMID: 36713227 PMCID: PMC9879626 DOI: 10.3389/fmicb.2022.1091964] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Several species in the genus Legionella are known to cause an acute pneumonia when the aerosols containing the bacteria from man-made water systems are inhaled. The disease is usually caused by Legionella pneumophila, but other species have been implicated in the infection. The disease is frequently manifested as an outbreak, which means several people are affected when exposed to the common source of Legionella contamination. Therefor environmental surveillance which includes isolation and identification of Legionella is performed routinely. However, usually no molecular or genome-based methods are employed in further characterization of the isolates during routine environmental monitoring. During several years of such monitoring, isolates from different geographical locations were collected and 39 of them were sequenced by hybrid de novo approach utilizing short and long sequencing reads. In addition, the isolates were typed by standard culture and MALDI-TOF method. The sequencing reads were assembled and annotated to produce high-quality genomes. By employing discriminatory genome typing, four potential new species in the Legionella genus were identified, which are yet to be biochemically and morphologically characterized. Moreover, functional annotations concerning virulence and antimicrobial resistance were performed on the sequenced genomes. The study contributes to the knowledge on little-known non-pneumophila species present in man-made water systems and establishes support for future genetic relatedness studies as well as understanding of their pathogenic potential.
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Affiliation(s)
- Ema Svetlicic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases (Sahlgrenska Academy) at the University of Gothenburg, Gothenburg, Sweden
| | | | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Snjezana Kazazic
- Laboratory for Mass Spectrometry and Functional Proteomics, Ruder Boskovic Institute, Zagreb, Croatia
| | - Damjan Franjevic
- Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Goran Klobucar
- Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden,*Correspondence: Ivan Mijakovic,
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24
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Ravikumar V, Mijakovic I, Pandit S. Antimicrobial Activity of Graphene Oxide Contributes to Alteration of Key Stress-Related and Membrane Bound Proteins. Int J Nanomedicine 2022; 17:6707-6721. [PMID: 36597432 PMCID: PMC9805717 DOI: 10.2147/ijn.s387590] [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: 09/06/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022] Open
Abstract
Introduction Antibacterial activity of graphene oxide (GO) has been extensively studied, wherein penetration of the bacterial cell membrane and oxidative stress are considered to play a major role in the bactericidal activity of GO. However, the specific mechanism responsible for the antibacterial activity of GO remains largely unknown. Hence, the goal of this study was to explore the mode of action of GO, via an in-depth proteomic analysis of the targeted bacteria. Methods Staphylococcus aureus was grown in the presence of GO and samples were collected at different growth phases to examine the cell viability and to analyze the changes in protein expression. Antimicrobial efficiency of GO was tested by assessing bacterial viability, live/dead staining and scanning electron microscopy. The intracellular reactive oxygen species (ROS) induced by GO treatment were examined by fluorescence microscopy. Label-free quantitative proteomics analysis was performed to examine the differentially regulated proteins in S. aureus after GO treatment. Results GO treatment was observed to reduce S. aureus viability, from 50 ± 17% after 4 h, to 93 ± 2% after 24 h. The live/dead staining confirmed this progressive antimicrobial effect of GO. SEM images revealed the wrapping of bacterial cells and their morphological disruption by means of pore formation due to GO insertion. GO treatment was observed to generate intracellular ROS, correlating to the loss of cell viability. The proteomics analysis revealed alteration in the expression of cell membrane, oxidative stress response, general stress response, and virulence-associated proteins in GO-treated bacterial cells. The time-dependent bactericidal activity of GO correlated with a higher number of differentially regulated proteins involved in the above.-mentioned processes. Conclusion The obtained results suggest that the time-dependent bactericidal effect of GO is attributed to its wrapping/trapping ability, ROS production and due to physical disruption of the cell membrane.
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Affiliation(s)
- Vaishnavi Ravikumar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark,Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, 41296, Sweden
| | - Santosh Pandit
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, 41296, Sweden,Correspondence: Santosh Pandit, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Göteborg, 41296, Sweden, Tel +46 729484011, Fax +46 317723801, Email
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Acet Ö, Dikici E, Acet BÖ, Odabaşı M, Mijakovic I, Pandit S. Inhibition of bacterial adhesion by epigallocatechin gallate attached polymeric membranes. Colloids Surf B Biointerfaces 2022; 221:113024. [DOI: 10.1016/j.colsurfb.2022.113024] [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: 08/20/2022] [Revised: 10/22/2022] [Accepted: 11/13/2022] [Indexed: 11/17/2022]
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26
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Khan F, Jeong GJ, Singh P, Tabassum N, Mijakovic I, Kim YM. Retrospective analysis of the key molecules involved in the green synthesis of nanoparticles. Nanoscale 2022; 14:14824-14857. [PMID: 36196971 DOI: 10.1039/d2nr03632k] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Emerging nanotechnology leads to success in synthesizing and applying nanoparticles (NPs) using the green-chemistry approach. NPs synthesized using naturally derived materials are a potential alternative to chemical and physical methods because they are simple, cost-effective, eco-friendly, and lower the possibility of hazardous residues being released into the environment. Furthermore, NPs synthesized using the green synthesis approach are stable and biocompatible. However, because natural extracts contain a diverse spectrum of bioactive components, it is difficult to pinpoint the specific component involved in NP formation. Furthermore, the bioactive component contained in the extract changes based on a number of environmental factors; therefore, several studies began with the synthesis of NPs using a pure compound isolated from diverse natural sources. Hence, the present review paper makes an effort to retrospectively analyze the key compounds of the extracts which are responsible for the synthesis of the NPs. The analysis was carried out based on the physicochemical characteristics and biological activities of NPs synthesized from either the extract or the pure compounds. These pure-compound-based NPs were studied for their antimicrobial, antibiofilm, anti-inflammatory, anticancer, and antioxidant properties. In addition, the present review also describes progress in the study of pure compound-based numerous biological activities and the underlying mechanisms of action.
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Affiliation(s)
- Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea.
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Priyanka Singh
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, DK-2800 Kogens Lyngby, Denmark
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea.
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Ivan Mijakovic
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, DK-2800 Kogens Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Young-Mog Kim
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea.
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea
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Rahimi S, Chen Y, Zareian M, Pandit S, Mijakovic I. Cellular and subcellular interactions of graphene-based materials with cancerous and non-cancerous cells. Adv Drug Deliv Rev 2022; 189:114467. [PMID: 35914588 DOI: 10.1016/j.addr.2022.114467] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 02/25/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 01/24/2023]
Abstract
Despite significant advances in early detection and personalized treatment, cancer is still among the leading causes of death globally. One of the possible anticancer approaches that is presently receiving a lot of attention is the development of nanocarriers capable of specific and efficient delivery of anticancer drugs. Graphene-based materials are promising nanocarriers in this respect, due to their high drug loading capacity and biocompatibility. In this review, we present an overview on the interactions of graphene-based materials with normal mammalian cells at the molecular level as well as cellular and subcellular levels, including plasma membrane, cytoskeleton, and membrane-bound organelles such as lysosomes, mitochondria, nucleus, endoplasmic reticulum, and peroxisome. In parallel, we assemble the knowledge about the interactions of graphene-based materials with cancerous cells, that are considered as the potential applications of these materials for cancer therapy including metastasis treatment, targeted drug delivery, and differentiation to non-cancer stem cells. We highlight the influence of key parameters, such as the size and surface chemistry of graphene-based materials that govern the efficiency of internalization and biocompatibility of these particles in vitro and in vivo. Finally, this review aims to correlate the key parameters of graphene-based nanomaterials specially graphene oxide, such as size and surface modifications, to their interactions with the cancerous and non-cancerous cells for designing and engineering them for bio-applications and especially for therapeutic purposes.
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Affiliation(s)
- Shadi Rahimi
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg 41296, Sweden.
| | - Yanyan Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg 41296, Sweden
| | - Mohsen Zareian
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg 41296, Sweden; State Key Laboratory of Bio-based Material and Green Paper-making, Qilu University of Technology, Jinan, China
| | - Santosh Pandit
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg 41296, Sweden
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg 41296, Sweden; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
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Eswaran M, Chokkiah B, Pandit S, Rahimi S, Dhanusuraman R, Aleem M, Mijakovic I. A Road Map toward Field-Effect Transistor Biosensor Technology for Early Stage Cancer Detection. Small Methods 2022; 6:e2200809. [PMID: 36068169 DOI: 10.1002/smtd.202200809] [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: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Field effect transistor (FET)-based nanoelectronic biosensor devices provide a viable route for specific and sensitive detection of cancer biomarkers, which can be used for early stage cancer detection, monitoring the progress of the disease, and evaluating the effectiveness of therapies. On the road to implementation of FET-based devices in cancer diagnostics, several key issues need to be addressed: sensitivity, selectivity, operational conditions, anti-interference, reusability, reproducibility, disposability, large-scale production, and economic viability. To address these well-known issues, significant research efforts have been made recently. An overview of these efforts is provided here, highlighting the approaches and strategies presently engaged at each developmental stage, from the design and fabrication of devices to performance evaluation and data analysis. Specifically, this review discusses the multistep fabrication of FETs, choice of bioreceptors for relevant biomarkers, operational conditions, measurement configuration, and outlines strategies to improve the sensing performance and reach the level required for clinical applications. Finally, this review outlines the expected progress to the future generation of FET-based diagnostic devices and discusses their potential for detection of cancer biomarkers as well as biomarkers of other noncommunicable and communicable diseases.
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Affiliation(s)
- Muthusankar Eswaran
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Göteborg, Sweden
| | - Bavatharani Chokkiah
- Nanoelectrochemistry Lab, Department of Chemistry, National Institute of Technology Puducherry, Karaikal, 609609, India
| | - Santosh Pandit
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Göteborg, Sweden
| | - Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Göteborg, Sweden
| | - Ragupathy Dhanusuraman
- Nanoelectrochemistry Lab, Department of Chemistry, National Institute of Technology Puducherry, Karaikal, 609609, India
| | - Mahaboobbatcha Aleem
- Department of Electrical Engineering, City College of New York, New York, 10031, USA
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Göteborg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
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Yang Y, Qu L, Mijakovic I, Wei Y. Advances in the human skin microbiota and its roles in cutaneous diseases. Microb Cell Fact 2022; 21:176. [PMID: 36038876 PMCID: PMC9422115 DOI: 10.1186/s12934-022-01901-6] [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: 05/04/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
Abstract
Skin is the largest organ in the human body, and the interplay between the environment factors and human skin leads to some skin diseases, such as acne, psoriasis, and atopic dermatitis. As the first line of human immune defense, skin plays significant roles in human health via preventing the invasion of pathogens that is heavily influenced by the skin microbiota. Despite being a challenging niche for microbes, human skin is colonized by diverse commensal microorganisms that shape the skin environment. The skin microbiota can affect human health, and its imbalance and dysbiosis contribute to the skin diseases. This review focuses on the advances in our understanding of skin microbiota and its interaction with human skin. Moreover, the potential roles of microbiota in skin health and diseases are described, and some key species are highlighted. The prevention, diagnosis and treatment strategies for microbe-related skin diseases, such as healthy diets, lifestyles, probiotics and prebiotics, are discussed. Strategies for modulation of skin microbiota using synthetic biology are discussed as an interesting venue for optimization of the skin-microbiota interactions. In summary, this review provides insights into human skin microbiota recovery, the interactions between human skin microbiota and diseases, and the strategies for engineering/rebuilding human skin microbiota.
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Affiliation(s)
- Yudie Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450051, China.,Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450051, China
| | - Lingbo Qu
- Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450051, China.,College of Chemistry, Zhengzhou University, Zhengzhou, China
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450051, China. .,Laboratory of Synthetic Biology, Zhengzhou University, Zhengzhou, 450051, China.
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Mijakovic I. Fantastic science and where to find it. PERIOD BIOL 2022. [DOI: 10.18054/pb.v123i1-2.16473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Not applicable, format is "letter to editor".
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Singh P, Mijakovic I. Green synthesis and antibacterial applications of gold and silver nanoparticles from Ligustrum vulgare berries. Sci Rep 2022; 12:7902. [PMID: 35551489 PMCID: PMC9098411 DOI: 10.1038/s41598-022-11811-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/21/2022] [Indexed: 12/03/2022] Open
Abstract
Increasing demand for green or biological nanoparticles has led to various green technologies and resources, which play a critical role in forming biocompatible or green nanoparticles. So far, numerous medicinal plants have been explored for this purpose, assuming that medicinal components from the plant's material will contribute to corona formation around nanoparticles and enhance their efficacy. Research is also extended to other green and waste resources to be utilized for this purpose. In the current study, we explored Ligustrum vulgare berries, also known as privet berries, to reduce gold and silver salts into nanoparticles. L. vulgare berries showed great potential to form these nanoparticles, as gold nanoparticles (LV-AuNPs) formed within 5 min at room temperature, and silver nanoparticles (LV-AgNPs) formed in 15 min at 90 °C. LV-AuNPs and LV-AgNPs were characterized by various analytical methods, including UV–Vis, SEM, EDX, TEM, DLS, sp-ICP-MS, TGA, FT-IR, and MALDI-TOF. The results demonstrate that the LV-AuNPs are polydisperse in appearance with a size range 50–200 nm. LV-AuNPs exhibit various shapes, including spherical, triangular, hexagonal, rod, cuboid, etc. In contrast, LV-AgNPs are quite monodisperse, 20–70 nm, and most of the population was spherical. The nanoparticles remain stable over long periods and exhibit high negative zeta potential values. The antimicrobial investigation of LV-AgNPs demonstrated that the nanoparticles exhibit antibacterial ability with an MBC value of 150 g/mL against P. aeruginosa and 100 g/mL against E. coli, as determined by plate assay, live and dead staining, and SEM cell morphology analysis.
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Affiliation(s)
- Priyanka Singh
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, 2800, Kogens Lyngby, Denmark.
| | - Ivan Mijakovic
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, 2800, Kogens Lyngby, Denmark. .,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
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Balusamy SR, Rahimi S, Sukweenadhi J, Sunderraj S, Shanmugam R, Thangavelu L, Mijakovic I, Perumalsamy H. Chitosan, chitosan nanoparticles and modified chitosan biomaterials, a potential tool to combat salinity stress in plants. Carbohydr Polym 2022; 284:119189. [DOI: 10.1016/j.carbpol.2022.119189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 11/02/2022]
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Neissi A, Rafiee G, Rahimi S, Farahmand H, Pandit S, Mijakovic I. Enriched microbial communities for ammonium and nitrite removal from recirculating aquaculture systems. Chemosphere 2022; 295:133811. [PMID: 35124092 DOI: 10.1016/j.chemosphere.2022.133811] [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: 11/22/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The aim of this study was the enrichment of high-performance microbial communities in biofilters for removal of ammonium and nitrite from aquaculture water. Ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) were enriched from different environmental water samples. The microbial communities with higher ammonium and nitrite removal activity were selected and adapted to different temperatures [9 °C, 15 °C, room temperature (25 °C), and 30 °C]. The expression of genes involved in nitrification including ammonia monooxygenase (AMO) and nitrite oxidoreductase (NXR) were measured in temperature-adapted AOB and NOB microbiomes. The microbial species present in the selected microbiomes were identified via 16s rRNA sequencing. The microbial communities containing Nitrosomonas oligotropha and Nitrobacter winogradskyi showed the highest ammonium and nitrite removal activity at all temperatures used for adaptation. Furthermore, the microbial communities do not contain any pathogenic bacteria. They also exhibited the highest expression of AMO and NXR genes. Using the enriched microbial communities, we achieved a 288% and 181% improvement in ammonium and nitrite removal over the commonly used communities in biofilters at 9 °C, respectively. These results suggest that the selected microbiomes allowed for a significant improvement of water quality in a recirculating aquaculture system (RAS).
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Affiliation(s)
- Alireza Neissi
- Nuclear Agricultural School, Nuclear Science and Technology Research Institute, 31465/1498, Karaj, Iran
| | - Gholamreza Rafiee
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, 331585-4314, Karaj, Iran.
| | - Shadi Rahimi
- Chalmers University of Technology, Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Kemivägen 10, 41296, Gothenburg, Sweden.
| | - Hamid Farahmand
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, 331585-4314, Karaj, Iran
| | - Santosh Pandit
- Chalmers University of Technology, Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Kemivägen 10, 41296, Gothenburg, Sweden
| | - Ivan Mijakovic
- Chalmers University of Technology, Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Kemivägen 10, 41296, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
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Singh P, Mijakovic I. Strong Antimicrobial Activity of Silver Nanoparticles Obtained by the Green Synthesis in Viridibacillus sp. Extracts. Front Microbiol 2022; 13:820048. [PMID: 35250934 PMCID: PMC8888960 DOI: 10.3389/fmicb.2022.820048] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 11/22/2021] [Accepted: 01/25/2022] [Indexed: 12/22/2022] Open
Abstract
Recently, green silver nanoparticles (G-AgNPs) have gained much attention in medical science due to their extraordinary effects against multidrug-resistant microorganisms. The strong antimicrobial nature of G-AgNPs corresponds to their unique physicochemical properties such as size, shape, surface charge, and active surface groups available to interact with the pathogens. The current study demonstrates a simple, environmentally friendly, and economical method to produce G-AgNPs from an environmental isolate of Viridibacillus sp. The produced G-AgNPs were characterized by various analytical methods, including UV-Vis spectroscopy, single-particle inductively coupled plasma-mass spectrometry (sp-ICP-MS), scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDX), elemental mapping, transmission electron microscopy (TEM), dynamic light scattering (DLS), Fourier-transform infrared spectroscopy (FTIR), and Thermogravimetric analysis (TGA). The reduction of Ag+ to Ag° was observed by UV-Vis spectroscopy, which demonstrated the formation of stable G-AgNPs with a Surface Plasmon Resonance (SPR) band at the maximum of 430 nm. TEM analysis demonstrated that the G-AgNPs were spherical with a 5–30 nm size range. The produced G-AgNPs were stable for more than 1 year in an aqueous solution at 4°C. Importantly, G-AgNPs showed remarkable antimicrobial activity against Gram-negative pathogens- E. coli and P. aeruginosa with MIC values of 0.1 and 4 μg/mL and MBC values of 1 and 8 μg/mL, respectively. This level of antimicrobial activity is superior to other AgNPs reported in the literature.
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Affiliation(s)
- Priyanka Singh
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Sun J, Rattanasawatesun T, Tang P, Bi Z, Pandit S, Lam L, Wasén C, Erlandsson M, Bokarewa M, Dong J, Ding F, Xiong F, Mijakovic I. Insights into the Mechanism for Vertical Graphene Growth by Plasma-Enhanced Chemical Vapor Deposition. ACS Appl Mater Interfaces 2022; 14:7152-7160. [PMID: 35005901 PMCID: PMC8832395 DOI: 10.1021/acsami.1c21640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/29/2021] [Indexed: 06/01/2023]
Abstract
Vertically oriented graphene (VG) has attracted attention for years, but the growth mechanism is still not fully revealed. The electric field may play a role, but the direct evidence and exactly what role it plays remains unclear. Here, we conduct a systematic study and find that in plasma-enhanced chemical vapor deposition, the VG growth preferably occurs at spots where the local field is stronger, for example, at GaN nanowire tips. On almost round-shaped nanoparticles, instead of being perpendicular to the substrate, the VG grows along the field direction, that is, perpendicular to the particles' local surfaces. Even more convincingly, the sheath field is screened to different degrees, and a direct correlation between the field strength and the VG growth is observed. Numerical calculation suggests that during the growth, the field helps accumulate charges on graphene, which eventually changes the cohesive graphene layers into separate three-dimensional VG flakes. Furthermore, the field helps attract charged precursors to places sticking out from the substrate and makes them even sharper and turn into VG. Finally, we demonstrate that the VG-covered nanoparticles are benign to human blood leukocytes and could be considered for drug delivery. Our research may serve as a starting point for further vertical two-dimensional material growth mechanism studies.
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Affiliation(s)
- Jie Sun
- National and Local
United Engineering Laboratory of Flat Panel Display Technology, College
of Physics and Information Engineering, Fuzhou University, and Fujian Science & Technology Innovation
Laboratory for Optoelectronic Information of China, Fuzhou 350116, China
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, Göteborg 41296, Sweden
| | - Tanupong Rattanasawatesun
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, Göteborg 41296, Sweden
| | - Penghao Tang
- Key Laboratory of Optoelectronics Technology,
College of Microelectronics, Beijing University
of Technology, Beijing 100124, China
| | - Zhaoxia Bi
- Division
of Solid State Physics and NanoLund, Department of Physics, Lund University, Box
118, S-22100 Lund, Sweden
| | - Santosh Pandit
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg 41296, Sweden
| | - Lisa Lam
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Göteborg 41346, Sweden
| | - Caroline Wasén
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Göteborg 41346, Sweden
| | - Malin Erlandsson
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Göteborg 41346, Sweden
| | - Maria Bokarewa
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Göteborg 41346, Sweden
| | - Jichen Dong
- Centre for Multidimensional Carbon Materials, Institute
for Basic Science, Ulsan National Institute
of Science and Technology, Ulsan 44919, Korea
| | - Feng Ding
- Centre for Multidimensional Carbon Materials, Institute
for Basic Science, Ulsan National Institute
of Science and Technology, Ulsan 44919, Korea
| | - Fangzhu Xiong
- Key Laboratory of Optoelectronics Technology,
College of Microelectronics, Beijing University
of Technology, Beijing 100124, China
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg 41296, Sweden
- The Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Singh P, Mijakovic I. Rowan Berries: A Potential Source for Green Synthesis of Extremely Monodisperse Gold and Silver Nanoparticles and Their Antimicrobial Property. Pharmaceutics 2021; 14:pharmaceutics14010082. [PMID: 35056978 PMCID: PMC8781835 DOI: 10.3390/pharmaceutics14010082] [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: 12/07/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 12/23/2022] Open
Abstract
Rowanberries (Sorbus aucuparia) are omnipresent in Europe. The medicinal importance of rowanberries is widely known and corresponds to the active ingredients present in the fruits, mainly polyphenols, carotenoids, and organic acids. In the current study, we explored rowanberries for the reduction of gold and silver salts into nanoparticles. Rowanberries-mediated gold nanoparticles (RB-AuNPs) formed within 5 s at room temperature, and silver nanoparticles (RB-AgNPs) formed in 20 min at 90 °C. The produced nanoparticles were thoroughly characterized by UV-Vis spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray (EDX), transmission electron microscopy (TEM), dynamic light scattering (DLS), single-particle inductively coupled plasma–mass spectrometry (sp-ICP-MS), thermogravimetric analysis (TGA), Fourier transform-infrared spectroscopy (FT-IR) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF). The characterization confirmed that the nanoparticles are highly monodisperse, spherical, stable over long periods, and exhibit a high negative zeta potential values. The produced RB-AuNPs and RB-AgNPs were 90–100 nm and 20–30 nm in size with a thick biological corona layer surrounding them, providing extreme stability but lowering the antimicrobial activity. The antimicrobials study of RB-AgNPs revealed that the nanoparticles have antimicrobial potential with an MBC value of 100 µg/mL against P. aeruginosa and 200 µg/mL against E. coli.
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Affiliation(s)
- Priyanka Singh
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, DK-2800 Kogens Lyngby, Denmark
- Correspondence: (P.S.); (I.M.)
| | - Ivan Mijakovic
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, DK-2800 Kogens Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Correspondence: (P.S.); (I.M.)
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Pandit S, Li M, Chen Y, Rahimi S, Mokkapati V, Merlo A, Yurgens A, Mijakovic I. Graphene-Based Sensor for Detection of Bacterial Pathogens. Sensors (Basel) 2021; 21:s21238085. [PMID: 34884089 PMCID: PMC8662450 DOI: 10.3390/s21238085] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 11/23/2022]
Abstract
Microbial colonization to biomedical surfaces and biofilm formation is one of the key challenges in the medical field. Recalcitrant biofilms on such surfaces cause serious infections which are difficult to treat using antimicrobial agents, due to their complex structure. Early detection of microbial colonization and monitoring of biofilm growth could turn the tide by providing timely guidance for treatment or replacement of biomedical devices. Hence, there is a need for sensors, which could generate rapid signals upon bacterial colonization. In this study, we developed a simple prototype sensor based on pristine, non-functionalized graphene. The detection principle is a change in electrical resistance of graphene upon exposure to bacterial cells. Without functionalization with specific receptors, such sensors cannot be expected to be selective to certain bacteria. However, we demonstrated that two different bacterial species can be detected and differentiated by our sensor due to their different growth dynamics, adherence pattern, density of adhered bacteria and microcolonies formation. These distinct behaviors of tested bacteria depicted distinguishable pattern of resistance change, resistance versus gate voltage plot and hysteresis effect. This sensor is simple to fabricate, can easily be miniaturized, and can be effective in cases when precise identification of species is not needed.
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Affiliation(s)
- Santosh Pandit
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
| | - Mengyue Li
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, 412 96 Göteborg, Sweden; (M.L.); (A.Y.)
| | - Yanyan Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
| | - Shadi Rahimi
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
| | - Vrss Mokkapati
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
| | - Alessandra Merlo
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
| | - August Yurgens
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, 412 96 Göteborg, Sweden; (M.L.); (A.Y.)
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; (S.P.); (Y.C.); (S.R.); (V.M.); (A.M.)
- Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Correspondence: ; Tel.: +46-(0)7-0982-8446
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Helalat SH, Jers C, Bebahani M, Mohabatkar H, Mijakovic I. Metabolic engineering of Deinococcus radiodurans for pinene production from glycerol. Microb Cell Fact 2021; 20:187. [PMID: 34565367 PMCID: PMC8474958 DOI: 10.1186/s12934-021-01674-4] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The objective of this work was to engineer Deinococcus radiodurans R1 as a microbial cell factory for the production of pinene, a monoterpene molecule prominently used for the production of fragrances, pharmaceutical products, and jet engine biofuels. Our objective was to produce pinene from glycerol, an abundant by-product of various industries. RESULTS To enable pinene production in D. radiodurans, we expressed the pinene synthase from Abies grandis, the geranyl pyrophosphate (GPP) synthase from Escherichia coli, and overexpressed the native 1-deoxy-D-xylulose 5-phosphate synthase. Further, we disrupted the deinoxanthin pathway competing for the substrate GPP by either inactivating the gene dr0862, encoding phytoene synthase, or substituting the native GPP synthase with that of E. coli. These manipulations resulted in a D. radiodurans strain capable of producing 3.2 ± 0.2 mg/L pinene in a minimal medium supplemented with glycerol, with a yield of 0.13 ± 0.04 mg/g glycerol in shake flask cultures. Additionally, our results indicated a higher tolerance of D. radiodurans towards pinene as compared to E. coli. CONCLUSIONS In this study, we successfully engineered the extremophile bacterium D. radiodurans to produce pinene. This is the first study demonstrating the use of D. radiodurans as a cell factory for the production of terpenoid molecules. Besides, its high resistance to pinene makes D. radiodurans a suitable host for further engineering efforts to increase pinene titer as well as a candidate for the production of the other terpenoid molecules.
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Affiliation(s)
- Seyed Hossein Helalat
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mandana Bebahani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Hassan Mohabatkar
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Affiliation(s)
- Priyanka Singh
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ivan Mijakovic
- The Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Pandit S, Rahimi S, Derouiche A, Boulaoued A, Mijakovic I. Sustained release of usnic acid from graphene coatings ensures long term antibiofilm protection. Sci Rep 2021; 11:9956. [PMID: 33976310 PMCID: PMC8113508 DOI: 10.1038/s41598-021-89452-5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/20/2021] [Indexed: 02/03/2023] Open
Abstract
Protecting surfaces from bacterial colonization and biofilm development is an important challenge for the medical sector, particularly when it comes to biomedical devices and implants that spend longer periods in contact with the human body. A particularly difficult challenge is ensuring long-term protection, which is usually attempted by ensuring sustained release of antibacterial compounds loaded onto various coatings. Graphene have a considerable potential to reversibly interact water insoluble molecules, which makes them promising cargo systems for sustained release of such compounds. In this study, we developed graphene coatings that act as carriers capable of sustained release of usnic acid (UA), and hence enable long-term protection of surfaces against colonization by bacterial pathogens Staphylococcus aureus and Staphylococcus epidermidis. Our coatings exhibited several features that made them particularly effective for antibiofilm protection: (i) UA was successfully integrated with the graphene material, (ii) a steady release of UA was documented, (iii) steady UA release ensured strong inhibition of bacterial biofilm formation. Interestingly, even after the initial burst release of UA, the second phase of steady release was sufficient to block bacterial colonization. Based on these results, we propose that graphene coatings loaded with UA can serve as effective antibiofilm protection of biomedical surfaces.
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Affiliation(s)
- Santosh Pandit
- grid.5371.00000 0001 0775 6028Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden
| | - Shadi Rahimi
- grid.5371.00000 0001 0775 6028Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden
| | - Abderahmane Derouiche
- grid.5371.00000 0001 0775 6028Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden
| | - Athmane Boulaoued
- grid.5371.00000 0001 0775 6028Department of Physics, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden
| | - Ivan Mijakovic
- grid.5371.00000 0001 0775 6028Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Göteborg, Sweden ,grid.5170.30000 0001 2181 8870Center for Biosustainability, Novo Nordisk Foundation, Technical University of Denmark, Kongens, Lyngby, Denmark
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Sultan A, Jers C, Ganief TA, Shi L, Senissar M, Køhler JB, Macek B, Mijakovic I. Phosphoproteome Study of Escherichia coli Devoid of Ser/Thr Kinase YeaG During the Metabolic Shift From Glucose to Malate. Front Microbiol 2021; 12:657562. [PMID: 33889145 PMCID: PMC8055822 DOI: 10.3389/fmicb.2021.657562] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 01/23/2021] [Accepted: 03/15/2021] [Indexed: 12/30/2022] Open
Abstract
Understanding phosphorylation-mediated regulation of metabolic enzymes, pathways, and cell phenotypes under metabolic shifts represents a major challenge. The kinases associated with most phosphorylation sites and the link between phosphorylation and enzyme activity remain unknown. In this study, we performed stable isotope labeling by amino acids in cell culture (SILAC)-based proteome and phosphoproteome analysis of Escherichia coli ΔyeaG, a strain lacking a poorly characterized serine/threonine kinase YeaG, to decipher kinase-substrate interactions and the effects on metabolic phenotype during shifts from glucose to malate. The starting point of our analysis was the identification of physiological conditions under which ΔyeaG exhibits a clear phenotype. By metabolic profiling, we discovered that ΔyeaG strain has a significantly shorter lag phase than the wild type during metabolic shift from glucose to malate. Under those conditions, our SILAC analysis revealed several proteins that were differentially phosphorylated in the ΔyeaG strain. By focusing on metabolic enzymes potentially involved in central carbon metabolism, we narrowed down our search for putative YeaG substrates and identified isocitrate lyase AceA as the direct substrate of YeaG. YeaG was capable of phosphorylating AceA in vitro only in the presence of malate, suggesting that this phosphorylation event is indeed relevant for glucose to malate shift. There is currently not enough evidence to firmly establish the exact mechanism of this newly observed regulatory phenomenon. However, our study clearly exemplifies the usefulness of SILAC-based approaches in identifying proteins kinase substrates, when applied in physiological conditions relevant for the activity of the protein kinase in question.
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Affiliation(s)
- Abida Sultan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tariq A Ganief
- Quantitative Proteomics and Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Meriem Senissar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julie Bonne Køhler
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Boris Macek
- Quantitative Proteomics and Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Shi L, Derouiche A, Pandit S, Rahimi S, Kalantari A, Futo M, Ravikumar V, Jers C, Mokkapati VRSS, Vlahoviček K, Mijakovic I. Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation. Mol Biol Evol 2021; 37:1667-1678. [PMID: 32061128 PMCID: PMC7426031 DOI: 10.1093/molbev/msaa035] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Indexed: 12/14/2022] Open
Abstract
Bacilli can form dormant, highly resistant, and metabolically inactive spores to cope with extreme environmental challenges. In this study, we examined the evolutionary age of Bacillus subtilis sporulation genes using the approach known as genomic phylostratigraphy. We found that B. subtilis sporulation genes cluster in several groups that emerged at distant evolutionary time-points, suggesting that the sporulation process underwent several stages of expansion. Next, we asked whether such evolutionary stratification of the genome could be used to predict involvement in sporulation of presently uncharacterized genes (y-genes). We individually inactivated a representative sample of uncharacterized genes that arose during the same evolutionary periods as the known sporulation genes and tested the resulting strains for sporulation phenotypes. Sporulation was significantly affected in 16 out of 37 (43%) tested strains. In addition to expanding the knowledge base on B. subtilis sporulation, our findings suggest that evolutionary age could be used to help with genome mining.
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Affiliation(s)
- Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Santosh Pandit
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Shadi Rahimi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Aida Kalantari
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Venkata R S S Mokkapati
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Kristian Vlahoviček
- Bioinformatics group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia.,School of Bioscience, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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Abstract
Biomedical application of graphene derivatives have been intensively studied in last decade. With the exceptional structural, thermal, electrical, and mechanical properties, these materials have attracted immense attention of biomedical scientists to utilize graphene derivatives in biomedical devices to improve their performance or to achieve desired functions. Surfaces of graphene derivatives including graphite, graphene, graphene oxide and reduce graphene oxide have been demonstrated to pave an excellent platform for antimicrobial behavior, enhanced biocompatibility, tissue engineering, biosensors and drug delivery. This review focuses on the recent advancement in the research of biomedical devices with the coatings or highly structured polymer nanocomposite surfaces of graphene derivatives for antimicrobial activity and sterile surfaces comprising an entirely new class of antibacterial materials. Overall, we aim to highlight on the potential of these materials, current understanding and knowledge gap in the antimicrobial behavior and biocompatibility to be utilized of their coatings to prevent the cross infections.
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Affiliation(s)
- Santosh Pandit
- Department of Biology and Biological EngineeringChalmers University of TechnologyKemivägen 10412 96GöteborgSweden
| | - Karolina Gaska
- Department of Industrial and Materials scienceChalmers University of Technology412 96GöteborgSweden
- Department of Aerospace EngineeringUniversity of BristolBS8 1TRBristolUK
| | - Roland Kádár
- Department of Industrial and Materials scienceChalmers University of Technology412 96GöteborgSweden
| | - Ivan Mijakovic
- Department of Biology and Biological EngineeringChalmers University of TechnologyKemivägen 10412 96GöteborgSweden
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kgs. LyngbyDenmark
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Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, Thorsell A, Lenuzzi M, Kifer D, Domazet-Lošo M, Vlahoviček K, Mijakovic I, Domazet-Lošo T. Embryo-Like Features in Developing Bacillus subtilis Biofilms. Mol Biol Evol 2021; 38:31-47. [PMID: 32871001 PMCID: PMC7783165 DOI: 10.1093/molbev/msaa217] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
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Affiliation(s)
- Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Luka Opašić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sara Koska
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Nina Čorak
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tin Široki
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Annika Thorsell
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maša Lenuzzi
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Domagoj Kifer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mirjana Domazet-Lošo
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- School of Biosciences, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Catholic University of Croatia, Zagreb, Croatia
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Motwalli O, Uludag M, Mijakovic I, Alazmi M, Bajic VB, Gojobori T, Gao X, Essack M. PATH cre8: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes. ACS Synth Biol 2020; 9:3217-3227. [PMID: 33198455 DOI: 10.1021/acssynbio.0c00058] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Developing computational tools that can facilitate the rational design of cell factories producing desired products at increased yields is challenging, as the tool needs to take into account that the preferred host organism usually has compounds that are consumed by competing reactions that reduce the yield of the desired product. On the other hand, the preferred host organisms may not have the native metabolic reactions needed to produce the compound of interest; thus, the computational tool needs to identify the metabolic reactions that will most efficiently produce the desired product. In this regard, we developed the generic tool PATHcre8 to facilitate an optimized search for heterologous biosynthetic pathway routes. PATHcre8 finds and ranks biosynthesis routes in a large number of organisms, including Cyanobacteria. The tool ranks the pathways based on feature scores that reflect reaction thermodynamics, the potentially toxic products in the pathway (compound toxicity), intermediate products in the pathway consumed by competing reactions (product consumption), and host-specific information such as enzyme copy number. A comparison with several other similar tools shows that PATHcre8 is more efficient in ranking functional pathways. To illustrate the effectiveness of PATHcre8, we further provide case studies focused on isoprene production and the biodegradation of cocaine. PATHcre8 is free for academic and nonprofit users and can be accessed at https://www.cbrc.kaust.edu.sa/pathcre8/.
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Affiliation(s)
- Olaa Motwalli
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Saudi Electronic University (SEU), College of Computing and Informatics, Madinah 41538-53307, Kingdom of Saudi Arabia
| | - Mahmut Uludag
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ivan Mijakovic
- Chalmers University of Technology, Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Kemivägen 10, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Meshari Alazmi
- Department of Information and Computer Science, College of Computer Science and Engineering, University of Ha’il, P.O. Box 2440, Ha’il 81411, Kingdom of Saudi Arabia
| | - Vladimir B. Bajic
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Takashi Gojobori
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
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Joshi AS, Singh P, Mijakovic I. Interactions of Gold and Silver Nanoparticles with Bacterial Biofilms: Molecular Interactions behind Inhibition and Resistance. Int J Mol Sci 2020; 21:E7658. [PMID: 33081366 PMCID: PMC7589962 DOI: 10.3390/ijms21207658] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Many bacteria have the capability to form a three-dimensional, strongly adherent network called 'biofilm'. Biofilms provide adherence, resourcing nutrients and offer protection to bacterial cells. They are involved in pathogenesis, disease progression and resistance to almost all classical antibiotics. The need for new antimicrobial therapies has led to exploring applications of gold and silver nanoparticles against bacterial biofilms. These nanoparticles and their respective ions exert antimicrobial action by damaging the biofilm structure, biofilm components and hampering bacterial metabolism via various mechanisms. While exerting the antimicrobial activity, these nanoparticles approach the biofilm, penetrate it, migrate internally and interact with key components of biofilm such as polysaccharides, proteins, nucleic acids and lipids via electrostatic, hydrophobic, hydrogen-bonding, Van der Waals and ionic interactions. Few bacterial biofilms also show resistance to these nanoparticles through similar interactions. The nature of these interactions and overall antimicrobial effect depend on the physicochemical properties of biofilm and nanoparticles. Hence, study of these interactions and participating molecular players is of prime importance, with which one can modulate properties of nanoparticles to get maximal antibacterial effects against a wide spectrum of bacterial pathogens. This article provides a comprehensive review of research specifically directed to understand the molecular interactions of gold and silver nanoparticles with various bacterial biofilms.
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Affiliation(s)
- Abhayraj S. Joshi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; (A.S.J.); (P.S.)
| | - Priyanka Singh
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; (A.S.J.); (P.S.)
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; (A.S.J.); (P.S.)
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
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Pandit S, Fazilati M, Gaska K, Derouiche A, Nypelö T, Mijakovic I, Kádár R. The Exo-Polysaccharide Component of Extracellular Matrix is Essential for the Viscoelastic Properties of Bacillus subtilis Biofilms. Int J Mol Sci 2020; 21:ijms21186755. [PMID: 32942569 PMCID: PMC7555405 DOI: 10.3390/ijms21186755] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/17/2022] Open
Abstract
Bacteria are known to form biofilms on various surfaces. Biofilms are multicellular aggregates, held together by an extracellular matrix, which is composed of biological polymers. Three principal components of the biofilm matrix are exopolysaccharides (EPS), proteins, and nucleic acids. The biofilm matrix is essential for biofilms to remain organized under mechanical stress. Thanks to their polymeric nature, biofilms exhibit both elastic and viscous mechanical characteristics; therefore, an accurate mechanical description needs to take into account their viscoelastic nature. Their viscoelastic properties, including during their growth dynamics, are crucial for biofilm survival in many environments, particularly during infection processes. How changes in the composition of the biofilm matrix affect viscoelasticity has not been thoroughly investigated. In this study, we used interfacial rheology to study the contribution of the EPS component of the matrix to viscoelasticity of Bacillus subtilis biofilms. Two strategies were used to specifically deplete the EPS component of the biofilm matrix, namely (i) treatment with sub-lethal doses of vitamin C and (ii) seamless inactivation of the eps operon responsible for biosynthesis of the EPS. In both cases, the obtained results suggest that the EPS component of the matrix is essential for maintaining the viscoelastic properties of bacterial biofilms during their growth. If the EPS component of the matrix is depleted, the mechanical stability of biofilms is compromised and the biofilms become more susceptible to eradication by mechanical stress.
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Affiliation(s)
- Santosh Pandit
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden; (S.P.); (A.D.)
| | - Mina Fazilati
- Department of Industrial and Materials Science, Chalmers University of Technology, 412 96 Göteborg, Sweden;
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden;
| | - Karolina Gaska
- Department of Aerospace Engineering, University of Bristol, Bristol BS8 1TR, UK;
| | - Abderahmane Derouiche
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden; (S.P.); (A.D.)
| | - Tiina Nypelö
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden;
- Wallenberg Wood Science Center, Chalmers, 412 96 Göteborg, Sweden
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden; (S.P.); (A.D.)
- Correspondence: (I.M.); (R.K.)
| | - Roland Kádár
- Department of Industrial and Materials Science, Chalmers University of Technology, 412 96 Göteborg, Sweden;
- Wallenberg Wood Science Center, Chalmers, 412 96 Göteborg, Sweden
- Correspondence: (I.M.); (R.K.)
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Neissi A, Rafiee G, Farahmand H, Rahimi S, Mijakovic I. Cold-Resistant Heterotrophic Ammonium and Nitrite-Removing Bacteria Improve Aquaculture Conditions of Rainbow Trout (Oncorhynchus mykiss). Microb Ecol 2020; 80:266-277. [PMID: 32162039 PMCID: PMC7371659 DOI: 10.1007/s00248-020-01498-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 12/01/2019] [Accepted: 02/19/2020] [Indexed: 05/31/2023]
Abstract
The aim of this study was isolation and characterization of heterotrophic bacteria capable of ammonium and nitrite removal at 15 °C (optimal temperature for growing rainbow trout Oncorhynchus mykiss). Environmental isolates were grown in liquid media containing ammonium or nitrite, and best strains in terms of growth and ammonium or nitrite removal were identified via 16S rRNA sequencing. Dyadobacter sp. (no. 68) and Janthinobacterium sp. (no. 100) were selected for optimal adaptation to growth at 15 °C and best ammonium and nitrite removal (P < 0.05), respectively. A heterotrophic ammonium and nitrite removal (HAN) microbial complex, containing selected strains, was prepared and applied in a trout culture system. After 10 days, the effect of microbial HAN complex was investigated in terms of ammonium and nitrite removal, as well as stress and immune indices present in the plasma of cultivated trout. Compared to a standard cultivation setup, addition of the HAN complex had a clear beneficial effect on keeping the un-ionized ammonia and nitrite level below prescribed standards (P < 0.05). This resulted in reduction of stress and immune reactions of cultivated fish (P < 0.05), leading to an augmentation of final weight and survival. Application of the selected microbial complex resulted in a significant improvement of the aquaculture ecosystem.
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Affiliation(s)
- Alireza Neissi
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, Karaj, 331585-4314, Iran
| | - Gholamreza Rafiee
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, Karaj, 331585-4314, Iran.
| | - Hamid Farahmand
- Department of Fisheries Sciences, Faculty of Natural Resources, University of Tehran, Karaj, 331585-4314, Iran
| | - Shadi Rahimi
- Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden
| | - Ivan Mijakovic
- Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
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Bonne Køhler J, Jers C, Senissar M, Shi L, Derouiche A, Mijakovic I. Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis. FEBS Lett 2020; 594:2339-2369. [PMID: 32337704 DOI: 10.1002/1873-3468.13797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 03/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation regulates a large variety of biological processes in all living cells. In pathogenic bacteria, the study of serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation has shed light on the course of infectious diseases, from adherence to host cells to pathogen virulence, replication, and persistence. Mass spectrometry (MS)-based phosphoproteomics has provided global maps of Ser/Thr/Tyr phosphosites in bacterial pathogens. Despite recent developments, a quantitative and dynamic view of phosphorylation events that occur during bacterial pathogenesis is currently lacking. Temporal, spatial, and subpopulation resolution of phosphorylation data is required to identify key regulatory nodes underlying bacterial pathogenesis. Herein, we discuss how technological improvements in sample handling, MS instrumentation, data processing, and machine learning should improve bacterial phosphoproteomic datasets and the information extracted from them. Such information is expected to significantly extend the current knowledge of Ser/Thr/Tyr phosphorylation in pathogenic bacteria and should ultimately contribute to the design of novel strategies to combat bacterial infections.
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Affiliation(s)
- Julie Bonne Køhler
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mériem Senissar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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