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Zlitni A, Yang S, Achterberg FB, Gowrishankar G, Steinberg I, Azevedo C, Gambhir SS, Valdez TA. Bridging the Translation of ICG-1-Maltotriose: A Multimodal Sensor for Monitoring and Detecting Bacterial Infections. ACS Sens 2024; 9:2806-2814. [PMID: 38810251 DOI: 10.1021/acssensors.3c02005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Bacterial infections lack reliable, specific, and quick detection methods, which incur substantial costs to patients and caretakers. Our team conjugated the FDA-approved fluorescent dye indocyanine green (ICG) with a maltotriose sugar, resulting in two highly specific imaging agents (ICG-DBCO-1-Maltotriose and ICG-Amide-1-Maltotriose) for detecting bacterial infections. We then evaluated the two derivatives using fluorescence imaging (FLI), bioluminescence imaging (BLI), and photoacoustic imaging (PAI) in bacterial infection murine models. Our findings indicate that both imaging agents can correlate with and reliably detect the infection site using FLI and PAI for both Gram-negative and Gram-positive strains, with various bacterial loads. Furthermore, the differences in pharmacokinetic (PK) properties between the two agents allow for one to be used for immediate imaging (2-4 h postinjection), while the other is more effective for longitudinal studies (18-40 h postinjection).
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Affiliation(s)
- Aimen Zlitni
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Stella Yang
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, California 94304, United States
| | - Friso B Achterberg
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Gayatri Gowrishankar
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Idan Steinberg
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Carmen Azevedo
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Sanjiv S Gambhir
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Tulio A Valdez
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, California 94304, United States
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2
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Munan S, Chang YT, Samanta A. Chronological development of functional fluorophores for bio-imaging. Chem Commun (Camb) 2024; 60:501-521. [PMID: 38095135 DOI: 10.1039/d3cc04895k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Functional fluorophores represent an emerging research field, distinguished by their diverse applications, especially in sensing and cellular imaging. After the discovery of quinine sulfate and subsequent elucidation of the fluorescence mechanism by Sir George Stokes, research in the field of fluorescence gained momentum. Over the past few decades, advancements in sophisticated instruments, including super-resolution microscopy, have further promoted cellular imaging using traditional fluorophores. These advancements include deciphering sensing mechanisms via photochemical reactions and scrutinizing the applications of fluorescent probes that specifically target organelles. This approach elucidates molecular interactions with biomolecules. Despite the abundance of literature illustrating different classes of probe development, a concise summary of newly developed fluorophores remains inadequate. In this review, we systematically summarize the chronological discovery of traditional fluorophores along with new fluorophores. We briefly discuss traditional fluorophores ranging from visible to near-infrared (NIR) in the context of cellular imaging and in vivo imaging. Furthermore, we explore ten new core fluorophores developed between 2007 and 2022, which exhibit advanced optical properties, providing new insights into bioimaging. We illustrate the utilization of new fluorophores in cellular imaging of biomolecules, such as reactive oxygen species (ROS), reactive nitrogen species (RNS), and proteins and microenvironments, especially pH and viscosity. Few of the fluorescent probes provided new insights into disease progression. Furthermore, we speculate on the potential prospects and significant challenges of existing fluorophores and their potential biomedical research applications. By addressing these aspects, we intend to illuminate the compelling advancements in fluorescent probe development and their potential influence across various fields.
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Affiliation(s)
- Subrata Munan
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi NCR, NH 91, Tehsil Dadri 201314, Uttar Pradesh, India.
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
| | - Animesh Samanta
- Molecular Sensors and Therapeutics (MST) Research Laboratory, Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi NCR, NH 91, Tehsil Dadri 201314, Uttar Pradesh, India.
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3
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Kwon HY, Chang YT, Kang NY. Discovery of Live Cell Selective Fluorescent Probes and Elucidation of Their Mechanisms: Case Study of B Cell Selective Probe CDgB. Methods Mol Biol 2024; 2779:305-321. [PMID: 38526792 DOI: 10.1007/978-1-0716-3738-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The development of small-molecule fluorescent probes for specific immune cell identification offers an economical alternative to expensive antibodies. Moreover, it enables the identification of live target cells and provides insights into the distinct properties of cells, leveraging their specific staining mechanisms. This chapter presents a comprehensive elucidation of the methodology employed for screening fluorescent compounds using flow cytometry measurements. A novel analytical approach is proposed to distinguish a fluorescent compound with a specific carbon length for B lymphocytes, involving an assessment of the staining index and the predominant ratio of immune cells. Moreover, a protocol is presented for investigating the staining mechanisms of these probes by employing cell mimicking models such as small unilamellar vesicles (SUVs).
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Affiliation(s)
- Haw-Young Kwon
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Republic of Korea
- SenPro, C5 building, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Republic of Korea
- SenPro, C5 building, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Nam-Young Kang
- SenPro, C5 building, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea.
- Department of Creative IT Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea.
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4
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Wang M, Zhang Z, Jing B, Dong X, Guo K, Deng J, Wang Z, Wan W, Jin W, Gao Z, Liu Y. Tailoring the Amphiphilicity of Fluorescent Protein Chromophores to Detect Intracellular Proteome Aggregation in Diverse Biological Samples. Anal Chem 2023; 95:11751-11760. [PMID: 37506028 DOI: 10.1021/acs.analchem.3c01903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The formation of amorphous misfolded and aggregated proteins is a hallmark of proteome stress in diseased cells. Given its lack of defined targeting sites, the rational design of intracellular proteome aggregation sensors has been challenging. Herein, we modulate the amphiphilicity of fluorescent protein chromophores to enable selective detection of aggregated proteins in different biological samples, including recombinant proteins, stressed live cells, intoxicated mouse liver tissue, and human hepatocellular carcinoma tissue. By tuning the number of hydroxyl groups, we optimize the selectivity of fluorescent protein chromophores toward aggregated proteins in these biological samples. In recombinant protein applications, the most hydrophobic P0 (cLogP = 5.28) offers the highest fold change (FC = 31.6), sensitivity (LLOD = 0.1 μM), and brightness (Φ = 0.20) upon binding to aggregated proteins. In contrast, P4 of balanced amphiphilicity (cLogP = 2.32) is required for selective detection of proteome stresses in live cells. In mouse and human liver histology tissues, hydrophobic P1 exhibits the best performance in staining the aggregated proteome. Overall, the amphiphilicity of fluorescent chromophores governs the sensor's performance by matching the diverse nature of different biological samples. Together with common extracellular amyloid sensors (e.g., Thioflavin T), these sensors developed herein for intracellular amorphous aggregation complement the toolbox to study protein aggregation.
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Affiliation(s)
- Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenduo Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Biao Jing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Kun Guo
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Jintai Deng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Zhiming Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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5
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Lv S, Wang C, Xue K, Wang J, Xiao M, Sun Z, Han L, Shi L, Zhu C. Activated alkyne-enabled turn-on click bioconjugation with cascade signal amplification for ultrafast and high-throughput antibiotic screening. Proc Natl Acad Sci U S A 2023; 120:e2302367120. [PMID: 37364107 PMCID: PMC10318996 DOI: 10.1073/pnas.2302367120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023] Open
Abstract
Antimicrobial susceptibility testing plays a pivotal role in the discovery of new antibiotics. However, the development of simple, sensitive, and rapid assessment approaches remains challenging. Herein, we report an activated alkyne-based cascade signal amplification strategy for ultrafast and high-throughput antibiotic screening. First of all, a novel water-soluble aggregation-induced emission (AIE) luminogen is synthesized, which contains an activated alkyne group to enable fluorescence turn-on and metal-free click bioconjugation under physiological conditions. Taking advantage of the in-house established method for bacterial lysis, a number of clickable biological substances (i.e., bacterial solutes and debris) are released from the bacterial bodies, which remarkably increases the quantity of analytes. By means of the activated alkyne-mediated turn-on click bioconjugation, the system fluorescence signal is significantly amplified due to the increased labeling sites as well as the AIE effect. Such a cascade signal amplification strategy efficiently improves the detection sensitivity and thus enables ultrafast antimicrobial susceptibility assessment. By integration with a microplate reader, this approach is further applied to high-throughput antibiotic screening.
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Affiliation(s)
- Shuyi Lv
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Chao Wang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Ke Xue
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Jiaxin Wang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Minghui Xiao
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Zhencheng Sun
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Lei Han
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, Shandong266109, China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
| | - Chunlei Zhu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin300071, China
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6
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Evstigneeva SS, Chumakov DS, Tumskiy RS, Khlebtsov BN, Khlebtsov NG. Detection and imaging of bacterial biofilms with glutathione-stabilized gold nanoclusters. Talanta 2023; 264:124773. [PMID: 37320983 DOI: 10.1016/j.talanta.2023.124773] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/25/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
Bacterial biofilms colonize chronic wounds and surfaces of medical devices, thus making the development of reliable methods for imaging and detection of biofilms crucial. Although fluorescent identification of bacteria is sensitive and non-destructive, the lack of biofilm-specific fluorescent dyes limits the application of this technique to biofilm detection. Here, we demonstrate, for the first time, that fluorescent glutathione-stabilized gold nanoclusters (GSH-AuNCs) without targeting ligands can specifically interact with extracellular matrix components of Gram-negative and Gram-positive bacterial biofilms resulting in fluorescent staining of bacterial biofilms. By contrast, fluorescent bovine serum albumin-stabilized gold nanoclusters and 11-mercaptoundecanoic acid - stabilized gold nanoclusters do not stain the extracellular matrix of biofilms. According to molecular docking studies, GSH-AuNCs show affinity to several targets in extracellular matrix, including amyloid-anchoring proteins, matrix proteins and polysaccharides. Some experimental evidence was obtained for the interaction of GSH-AuNCs with the lipopolysaccharide (LPS) that was isolated from the matrix of Azospirillum baldaniorum biofilms. Based on GSH-AuNCs properties, we propose a new fluorescent method for the measurement of biofilm biomass with a limit of detection 1.7 × 105 CFU/mL. The sensitivity of the method is 10-fold higher than the standard biofilm quantification with the crystal violet assay. There is a good linear relationship between the fluorescence intensity from the biofilms and the number of CFU from the biofilms in the range from 2.6 × 105 to 6.7 × 107 CFU/mL. The developed nanocluster-mediated method of biofilm staining was successfully applied for quantitative detection of biofilm formation on urinary catheter surface. The presented data suggest that fluorescent GSH-AuNCs can be used to diagnose medical device-associated infections.
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Affiliation(s)
- S S Evstigneeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 13 Prospekt Entuziastov, Saratov, 410049, Russia.
| | - D S Chumakov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - R S Tumskiy
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - B N Khlebtsov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 13 Prospekt Entuziastov, Saratov, 410049, Russia; Institute of Physics, Saratov State University, 410012, Saratov, Russia
| | - N G Khlebtsov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 13 Prospekt Entuziastov, Saratov, 410049, Russia; Institute of Physics, Saratov State University, 410012, Saratov, Russia
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7
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Beg AZ, Rashid F, Talat A, Haseen MA, Raza N, Akhtar K, Dueholm MKD, Khan AU. Functional Amyloids in Pseudomonas aeruginosa Are Essential for the Proteome Modulation That Leads to Pathoadaptation in Pulmonary Niches. Microbiol Spectr 2023; 11:e0307122. [PMID: 36475836 PMCID: PMC9927170 DOI: 10.1128/spectrum.03071-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
Persistence and survival of Pseudomonas aeruginosa in chronic lung infections is closely linked to the biofilm lifestyle. One biofilm component, functional amyloid of P. aeruginosa (Fap), imparts structural adaptations for biofilms; however, the role of Fap in pathogenesis is still unclear. Conservation of the fap operon encoding Fap and P. aeruginosa being an opportunistic pathogen of lung infections prompted us to explore its role in lung infection. We found that Fap is essential for establishment of lung infection in rats, as its genetic exclusion led to mild focal infection with quick resolution. Moreover, without an underlying cystic fibrosis (CF) genetic disorder, overexpression of Fap reproduced the CF pathotype. The molecular basis of Fap-mediated pulmonary adaptation was explored through surface-associated proteomics in vitro. Differential proteomics positively associated Fap expression with activation of known proteins related to pulmonary pathoadaptation, attachment, and biofilm fitness. The aggregative bacterial phenotype in the pulmonary niche correlated with Fap-influenced activation of biofilm sustainability regulators and stress response regulators that favored persistence-mediated establishment of pulmonary infection. Fap overexpression upregulated proteins that are abundant in the proteome of P. aeruginosa in colonizing CF lungs. Planktonic lifestyle, defects in anaerobic pathway, and neutrophilic evasion were key factors in the absence of Fap that impaired establishment of infection. We concluded that Fap is essential for cellular equilibration to establish pulmonary infection. Amyloid-induced bacterial aggregation subverted the immune response, leading to chronic infection by collaterally damaging tissue and reinforcing bacterial persistence. IMPORTANCE Pseudomonas aeruginosa is inextricably linked with chronic lung infections. In this study, the well-conserved Fap operon was found to be essential for pathoadaptation in pulmonary infection in a rat lung model. Moreover, the presence of Fap increased pathogenesis and biofilm sustainability by modulating bacterial physiology. Hence, a pathoadaptive role of Fap in pulmonary infections can be exploited for clinical application by targeting amyloids. Furthermore, genetic conservation and extracellular exposure of Fap make it a commendable target for such interventions.
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Affiliation(s)
- Ayesha Z. Beg
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | | | - Absar Talat
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohd Azam Haseen
- Department of Cardiothoracic Surgery, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Nadeem Raza
- Department of Anaesthesiology, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Kafil Akhtar
- Pathology Department, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Asad U. Khan
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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8
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Shen D, Jin W, Zhao Q, Wang M, Zhang B, Feng H, Wan W, Bai Y, Lyu H, Sun J, Zhang L, Liu Y. Covalent Solvatochromic Proteome Stress Sensor Based on the Schiff Base Reaction. Anal Chem 2022; 94:14143-14150. [PMID: 36194526 DOI: 10.1021/acs.analchem.2c01281] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Covalent-type probes or sensors have been seldom reported for aggregated proteins. Herein, we reported a series of covalent solvatochromic probes to selectively modify and detect aggregated proteomes through the Schiff base reaction. Such covalent modification was discovered by serendipity using the P1 probe with an aldehyde functional group, exhibiting enhanced fluorescence intensity and unusually large blue shift upon protein aggregation. Supported by the biochemical and mass spectrometry results, we identified that this probe can modify the lysine residue of aggregated proteins selectively over folded ones via the Schiff base reaction. The generality of designing such a covalent-type probe was demonstrated in multiple probe scaffolds using different model proteins. Finally, we exploited the distinct solvatochromism of P1 after Schiff base linkage with aggregated proteins to visualize the distinct morphology of aggregated proteomes, as well as to quantify the polarity heterogeneity inside it. This work may intrigue the exploration of other chemical reaction types to covalently functionalize aggregated proteins that were difficult to analyze.
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Affiliation(s)
- Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Beirong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Feng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Jialu Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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9
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Alemneh ST, Emire SA, Jekle M, Hitzmann B. Effect of Refrigerated Storage on Some Physicochemical Characteristics of a
Teff‐Based
Fermented Beverage and on Viability of the Fermenting
Lactiplantibacillus plantarum
and
Lacticaseibacillus rhamnosus
Used. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.17034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sendeku Takele Alemneh
- Department of Process Analytics and Cereal Science Institute of Food Science and Biotechnology University of Hohenheim Stuttgart Germany
| | - Shimelis Admassu Emire
- Food Engineering Addis Ababa Institute of Technology Addis Ababa University Addis Ababa Ethiopia
| | - Mario Jekle
- Department of Plant‐Based Foods Institute of Food Science and Biotechnology University of Hohenheim Stuttgart Germany
| | - Bernd Hitzmann
- Department of Process Analytics and Cereal Science Institute of Food Science and Biotechnology University of Hohenheim Stuttgart Germany
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10
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Recent Advances in Intrinsically Fluorescent Polydopamine Materials. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Fluorescence nanoparticles have gained much attention due to their unique properties in the sensing and imaging fields. Among the very successful candidates are fluorescent polydopamine (FPDA) nanoparticles, attributed to their simplicity in tracing and excellent biocompatibility. This article aims to highlight the recent achievements in FPDA materials, especially on the part of luminescence mechanisms. We focus on the intrinsic fluorescence of PDA and will not discuss fluorescent reaction with a fluorometric reagent or coupling reaction with a fluorophore, which may cause more in vivo interferences. We believe that intrinsic FPDA presents great potential in bioapplications.
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11
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Zein HF, Alam I, Asanithi P, Sutthibutpong T. Molecular dynamics study on the effects of charged amino acid distribution under low pH condition to the unfolding of hen egg white lysozyme and formation of beta strands. PLoS One 2022; 17:e0249742. [PMID: 35324907 PMCID: PMC8946743 DOI: 10.1371/journal.pone.0249742] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 02/23/2022] [Indexed: 11/19/2022] Open
Abstract
Aggregation of unfolded or misfolded proteins into amyloid fibrils can cause various diseases in humans. However, the fibrils synthesized in vitro can be developed toward useful biomaterials under some physicochemical conditions. In this study, atomistic molecular dynamics simulations were performed to address the mechanism of beta-sheet formation of the unfolded hen egg-white lysozyme (HEWL) under a high temperature and low pH. Simulations of the protonated HEWL at pH 2 and the non-protonated HEWL at pH 7 were performed at the highly elevated temperature of 450 K to accelerate the unfolding, followed by the 333 K temperature to emulate some previous in vitro studies. The simulations showed that HEWL unfolded faster, and higher beta-strand contents were observed at pH 2. In addition, one of the simulation replicas at pH 2 showed that the beta-strand forming sequence was consistent with the 'K-peptide', proposed as the core region for amyloidosis in previous experimental studies. Beta-strand formation mechanisms at the earlier stage of amyloidosis were explained in terms of the radial distribution of the amino acids. The separation between groups of positively charged sidechains from the hydrophobic core corresponded to the clustering of the hydrophobic residues and beta-strand formation.
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Affiliation(s)
- Husnul Fuad Zein
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
- Department of Physics, Theoretical and Computational Physics Group, KMUTT, Thung Khru, Bangkok, Thailand
- Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
| | - Ibrar Alam
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
| | - Piyapong Asanithi
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
| | - Thana Sutthibutpong
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
- Department of Physics, Theoretical and Computational Physics Group, KMUTT, Thung Khru, Bangkok, Thailand
- Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
- Center of Excellence in Theoretical and Computational Science (TaCS-CoE), Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Thung Khru, Bangkok, Thailand
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12
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Wang J, Jiang Z, Wei Y, Wang W, Wang F, Yang Y, Song H, Yuan Q. Multiplexed Identification of Bacterial Biofilm Infections Based on Machine-Learning-Aided Lanthanide Encoding. ACS NANO 2022; 16:3300-3310. [PMID: 35099174 DOI: 10.1021/acsnano.1c11333] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pathogenic biofilms are up to 1000-fold more drug-resistant than planktonic pathogens and cause about 80% of all chronic infections worldwide. The lack of prompt and reliable biofilm identification methods seriously prohibits the diagnosis and treatment of biofilm infections. Here, we developed a machine-learning-aided cocktail assay for prompt and reliable biofilm detection. Lanthanide nanoparticles with different emissions, surface charges, and hydrophilicity are formulated into the cocktail kits. The lanthanide nanoparticles in the cocktail kits can offer competitive interactions with the biofilm and further maximize the charge and hydrophilicity differences between biofilms. The physicochemical heterogeneities of biofilms were transformed into luminescence intensity at different wavelengths by the cocktail kits. The luminescence signals were used as learning data to train the random forest algorithm, and the algorithm could identify the unknown biofilms within minutes after training. Electrostatic attractions and hydrophobic-hydrophobic interactions were demonstrated to dominate the binding of the cocktail kits to the biofilms. By rationally designing the charge and hydrophilicity of the cocktail kit, unknown biofilms of pathogenic clinical isolates were identified with an overall accuracy of over 80% based on the random forest algorithm. Moreover, the antibiotic-loaded cocktail nanoprobes efficiently eradicated biofilms since the nanoprobes could penetrate deep into the biofilms. This work can serve as a reliable technique for the diagnosis of biofilm infections and it can also provide instructions for the design of multiplex assays for detecting biochemical compounds beyond biofilms.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan 430072, China
| | - Zhuoran Jiang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan 430072, China
| | - Yurong Wei
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan 430072, China
| | - Wenjie Wang
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Fubing Wang
- Department of Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430062, China
| | - Yanbing Yang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan 430072, China
| | - Heng Song
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan 430072, China
| | - Quan Yuan
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, School of Microelectronics, Wuhan University, Wuhan 430072, China
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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13
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Abstract
Live cell discrimination is the first and essential step to understand complex biosystems. Conventional cell discrimination involving various antibodies relies on selective surface biomarkers. Compared to antibodies, the fluorescent probe strategy allows the utilisation of intracellular biomarkers, providing broader options with unique chemical principles to achieve the live cell distinction. In general, fluorescent probes can be retained in cells by interacting with biomolecules, accumulating via transporters, and participating in metabolism. Based on the target difference, fluorescent probe strategy can be divided into several categories: protein-oriented live cell distinction (POLD), carbohydrate-oriented live cell distinction (COLD), DNA-oriented live cell distinction (DOLD), gating-oriented live cell distinction (GOLD), metabolism-oriented live cell distinction (MOLD) and lipid-oriented live cell distinction (LOLD). In this review, we will outline the concepts and mechanisms of different strategies, introduce their applications in cell-type discrimination, and discuss their advantages and challenges in this area. We expect this tutorial will provide a new perspective on the mechanisms of fluorescent probe strategy and facilitate the development of cell-type-specific probes.
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Affiliation(s)
- Xiao Liu
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea. .,Department of Chemistry, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Young-Tae Chang
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Republic of Korea. .,Department of Chemistry, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
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14
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Dong X, Wan W, Zeng L, Jin W, Huang Y, Shen D, Bai Y, Zhao Q, Zhang L, Liu Y, Gao Z. Regulation of Fluorescence Solvatochromism To Resolve Cellular Polarity upon Protein Aggregation. Anal Chem 2021; 93:16447-16455. [PMID: 34859995 DOI: 10.1021/acs.analchem.1c03401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Common solvatochromic fluorophores exhibit a bathochromic fluorescence emission wavelength shift accompanied by intensity attenuation due to the presence of nonradiative decay pathways at the excited state. Such intrinsic but inevitable fluorescence quenching of solvatochromism impedes its applications to faithfully quantify local polarity, especially in a polar environment. Herein, we report a new donor-π-acceptor (D-π-A) type solvatochromic fluorophore scaffold containing a perfluorophenyl group that exhibits both a solvatochromic emission wavelength shift and a controllable emission intensity upon polarity fluctuation. The regulation of fluorescence solvatochromism and colors was achieved by tuning the aryl donors. We exploited such desired solvatochromism of these probes to monitor protein misfolding and aggregation via wavelength shift. Finally, the polarity of pathogenic aggregated proteins was quantified by HaloTag bioorthogonal labeling technology in live cells. While much effort has been devoted to resolving the morphology of pathogenic aggregated proteins, this work provides quantitative hints regarding the chemical information at this disease-related protein interphase.
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Affiliation(s)
- Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, P. R. China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Lianggang Zeng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of the Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, P. R. China
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15
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Cruz A, Condinho M, Carvalho B, Arraiano CM, Pobre V, Pinto SN. The Two Weapons against Bacterial Biofilms: Detection and Treatment. Antibiotics (Basel) 2021; 10:1482. [PMID: 34943694 PMCID: PMC8698905 DOI: 10.3390/antibiotics10121482] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
Bacterial biofilms are defined as complex aggregates of bacteria that grow attached to surfaces or are associated with interfaces. Bacteria within biofilms are embedded in a self-produced extracellular matrix made of polysaccharides, nucleic acids, and proteins. It is recognized that bacterial biofilms are responsible for the majority of microbial infections that occur in the human body, and that biofilm-related infections are extremely difficult to treat. This is related with the fact that microbial cells in biofilms exhibit increased resistance levels to antibiotics in comparison with planktonic (free-floating) cells. In the last years, the introduction into the market of novel compounds that can overcome the resistance to antimicrobial agents associated with biofilm infection has slowed down. If this situation is not altered, millions of lives are at risk, and this will also strongly affect the world economy. As such, research into the identification and eradication of biofilms is important for the future of human health. In this sense, this article provides an overview of techniques developed to detect and imaging biofilms as well as recent strategies that can be applied to treat biofilms during the several biofilm formation steps.
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Affiliation(s)
- Adriana Cruz
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Manuel Condinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Beatriz Carvalho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Cecília M. Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; (M.C.); (B.C.); (C.M.A.)
| | - Sandra N. Pinto
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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16
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Wagh SB, Maslivetc VA, La Clair JJ, Kornienko A. Lessons in Organic Fluorescent Probe Discovery. Chembiochem 2021; 22:3109-3139. [PMID: 34062039 PMCID: PMC8595615 DOI: 10.1002/cbic.202100171] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/22/2021] [Indexed: 02/03/2023]
Abstract
Fluorescent probes have gained profound use in biotechnology, drug discovery, medical diagnostics, molecular and cell biology. The development of methods for the translation of fluorophores into fluorescent probes continues to be a robust field for medicinal chemists and chemical biologists, alike. Access to new experimental designs has enabled molecular diversification and led to the identification of new approaches to probe discovery. This review provides a synopsis of the recent lessons in modern fluorescent probe discovery.
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Affiliation(s)
- Sachin B Wagh
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
| | - Vladimir A Maslivetc
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
| | - James J La Clair
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA, 92163-1062, USA
| | - Alexander Kornienko
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos, USA
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17
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Tan S, Luo W, Zhang Y, Ren XK, Liu Y, Chen Z, Zeng Q. Structural and Nanotribological Properties of a BODIPY Self-Assembly. Front Chem 2021; 9:704915. [PMID: 34422764 PMCID: PMC8377353 DOI: 10.3389/fchem.2021.704915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022] Open
Abstract
Boron-dipyrromethenes (BODIPY) are promising functional dyes, whose exceptional optical properties are closely related to their supramolecular assembly. Herein, the self-assembly of a BODIPY derivative functionalized with uracil groups is explicitly and thoroughly investigated by using scanning tunneling microscopy (STM). Based on the simulation and calculation by density functional theory (DFT) method, it can be concluded that the construction of ordered self-assembly structure is attributed to the formation of hydrogen bonds between uracil groups. Moreover, the nanotribological property of the self-assembly on HOPG surface is measured by using atomic force microscopy (AFM). The effort on self-assembly of the BODIPY derivative could enhance the understanding of surface assembly mechanism.
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Affiliation(s)
- Shanchao Tan
- State Key Laboratory of Tribology, Tsinghua University, Beijing, China.,CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, China
| | - Wendi Luo
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanophotonic Materials and Devices, CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, China
| | - Yongjie Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xiang-Kui Ren
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yuhong Liu
- State Key Laboratory of Tribology, Tsinghua University, Beijing, China
| | - Zhijian Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Qingdao Zeng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, China.,Center of Materials Science and Optoelectonics Engineering, University of Chinese Academy of Sciences, Beijing, China
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18
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Bai Y, Wan W, Huang Y, Jin W, Lyu H, Xia Q, Dong X, Gao Z, Liu Y. Quantitative interrogation of protein co-aggregation using multi-color fluorogenic protein aggregation sensors. Chem Sci 2021; 12:8468-8476. [PMID: 34221329 PMCID: PMC8221170 DOI: 10.1039/d1sc01122g] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022] Open
Abstract
Co-aggregation of multiple pathogenic proteins is common in neurodegenerative diseases but deconvolution of such biochemical process is challenging. Herein, we developed a dual-color fluorogenic thermal shift assay to simultaneously report on the aggregation of two different proteins and quantitatively study their thermodynamic stability during co-aggregation. Expansion of spectral coverage was first achieved by developing multi-color fluorogenic protein aggregation sensors. Orthogonal detection was enabled by conjugating sensors of minimal fluorescence crosstalk to two different proteins via sortase-tag technology. Using this assay, we quantified shifts in melting temperatures in a heterozygous model protein system, revealing that the thermodynamic stability of wild-type proteins was significantly compromised by the mutant ones but not vice versa. We also examined how small molecule ligands selectively and differentially interfere with such interplay. Finally, we demonstrated these sensors are suited to visualize how different proteins exert influence on each other upon their co-aggregation in live cells.
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Affiliation(s)
- Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University 467 Zhongshan Road Dalian 116044 China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
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19
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Zaman M, Andreasen M. Modulating Kinetics of the Amyloid-Like Aggregation of S. aureus Phenol-Soluble Modulins by Changes in pH. Microorganisms 2021; 9:microorganisms9010117. [PMID: 33430169 PMCID: PMC7825627 DOI: 10.3390/microorganisms9010117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022] Open
Abstract
The pathogen Staphylococcus aureus is recognized as one of the most frequent causes of biofilm-associated infections. The recently identified phenol-soluble modulin (PSM) peptides act as the key molecular effectors of staphylococcal biofilm maturation and promote the formation of an aggregated fibril structure. The aim of this study was to evaluate the effect of various pH values on the formation of functional amyloids of individual PSM peptides. Here, we combined a range of biophysical, chemical kinetics and microscopic techniques to address the structure and aggregation mechanism of individual PSMs under different conditions. We established that there is a pH-induced switch in PSM aggregation kinetics. Different lag times and growth of fibrils were observed, which indicates that there was no clear correlation between the rates of fibril elongation among different PSMs. This finding confirms that pH can modulate the aggregation properties of these peptides and suggest a deeper understanding of the formation of aggregates, which represents an important basis for strategies to interfere and might help in reducing the risk of biofilm-related infections.
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20
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Liu YN, Lv ZT, Lv WL, Liu XW. Plasmonic probing of the adhesion strength of single microbial cells. Proc Natl Acad Sci U S A 2020; 117:27148-27153. [PMID: 33060295 PMCID: PMC7959563 DOI: 10.1073/pnas.2010136117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Probing the binding between a microbe and surface is critical for understanding biofilm formation processes, developing biosensors, and designing biomaterials, but it remains a challenge. Here, we demonstrate a method to measure the interfacial forces of bacteria attached to the surface. We tracked the intrinsic fluctuations of individual bacterial cells using an interferometric plasmonic imaging technique. Unlike the existing methods, this approach determined the potential energy profile and quantified the adhesion strength of single cells by analyzing the fluctuations. This method provides insights into biofilm formation and can also serve as a promising platform for investigating biological entity/surface interactions, such as pathogenicity, microbial cell capture and detection, and antimicrobial interface screening.
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Affiliation(s)
- Yi-Nan Liu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026 Hefei, China
| | - Zhen-Ting Lv
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026 Hefei, China
| | - Wen-Li Lv
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026 Hefei, China
| | - Xian-Wei Liu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026 Hefei, China;
- Department of Applied Chemistry, University of Science and Technology of China, 230026 Hefei, China
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21
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Gray ALH, Antevska A, Oluwatoba DS, Schonfeld GE, Lazar Cantrell KL, Do TD. Cytotoxicity of α-Helical, Staphylococcus aureus PSMα3 Investigated by Post-Ion-Mobility Dissociation Mass Spectrometry. Anal Chem 2020; 92:11802-11808. [PMID: 32786488 DOI: 10.1021/acs.analchem.0c01974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Our knowledge of amyloid formation and cytotoxicity originating from self-assembly of α-helical peptides is incomplete. PSMα3 is the only system where high-resolution X-ray crystallography and toxicity data are available. Oligomers of multiple α-helical monomers are less stable than those of β-strands, partially due to the lack of a consistent hydrogen-bonding network. It is challenging to preserve such oligomers in the gas phase where mass-selected structural studies using ion-mobility spectrometry mass spectrometry (IMS-MS) could be performed. As the oligomers fall apart after exiting the drift cell of the mass spectrometer, novel features that have shorter (a loss of charged species) or longer (a loss of neutral species) arrival times than expected are present together with those from the intact species. By obtaining a complete data set of PSMα3 peptides in solution and with n-dodecyl-β-d-maltoside, a micelle-forming detergent, we are able to discern the dissociated from the intact oligomers and detergent-bound complexes and correlate the reported cytotoxicity to the peptide oligomeric structures and their interactions with membrane mimetics. The study sheds new insights into the interpretation of IMS-MS data from biomolecular self-assembly studies-an important and timely topic.
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Affiliation(s)
- Amber L H Gray
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Aleksandra Antevska
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Damilola S Oluwatoba
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Grace E Schonfeld
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | | | - Thanh D Do
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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22
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Moshynets O, Chernii S, Chernii V, Losytskyy M, Karakhim S, Czerwieniec R, Pekhnyo V, Yarmoluk S, Kovalska V. Fluorescent β-ketoenole AmyGreen dye for visualization of amyloid components of bacterial biofilms. Methods Appl Fluoresc 2020; 8:035006. [PMID: 32375137 DOI: 10.1088/2050-6120/ab90e0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Green-emitting water-soluble amino-ketoenole dye AmyGreen is proposed as an efficient fluorescent stain for visualization of bacterial amyloids in biofilms and the detection of pathological amyloids in vitro. This dye is almost non-fluorescent in solution, displays strong green emission in the presence of amyloid fibril of proteins. AmyGreen is also weakly fluorescent in presence to biomolecules that are components of cells, extracellular matrix or medium: nucleic acids, polysaccharides, lipids, and proteins. Thus, the luminescence turn-on behavior of AmyGreen can be utilized for visualization of amyloid components of bacterial biofilm extracellular matrix. Herein we report the application of AmyGreen for fluorescent staining of a number of amyloid-contained bacteria biofilms produced by Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Bordetella avium, and Staphylococcus aureus. The effectiveness of AmyGreen was compared to traditional amyloid sensitive dye Thioflavine T. The main advantage of AmyGreen (concentration 10-5 M) is a higher sensitivity in the visualization of amyloid biofilm components over Thioflavine T (10-4 M) as it was revealed when staining E. coli and K. pneumoniae bacterial biofilms. Besides, AmyGreen displays lower cross-selectivity to nucleic acids as demonstrated both in in-solution experiments and upon staining of eukaryotic human mesenchymal stem cells used as amyloid-free negative control over amyloid-rich bacterial biofilms. The results point to a lower risk of false-positive response upon determination of amyloid components of bacterial biofilm using AmyGreen. Co-staining of biofilm by AmyGreen and cellulose sensitive dye Calcofluor White show difference in their staining patterns and localization, indicating separation of polysaccharide-rich and amyloid-rich regions of investigated biofilms. Thus, we suggest the new AmyGreen stain for visualization and differentiation of amyloid fibrils in bacterial biofilms to be used solely and in combination with other stains for confocal and fluorescence microscopy analysis.
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Affiliation(s)
- Olena Moshynets
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
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23
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Jia Z, Gwynne L, Sedgwick AC, Müller M, Williams GT, Jenkins ATA, James TD, Schönherr H. Enhanced Colorimetric Differentiation between Staphylococcus aureus and Pseudomonas aeruginosa Using a Shape-Encoded Sensor Hydrogel. ACS APPLIED BIO MATERIALS 2020; 3:4398-4407. [DOI: 10.1021/acsabm.0c00403] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Zhiyuan Jia
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany
| | - Lauren Gwynne
- Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
| | - Adam C. Sedgwick
- Department of Chemistry, The University of Texas at Austin, 105 E 24th street A5300, Austin, Texas 78712-1224, United States
| | - Mareike Müller
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany
| | | | | | - Tony D. James
- Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
| | - Holger Schönherr
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany
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Barran-Berdon AL, Ocampo S, Haider M, Morales-Aparicio J, Ottenberg G, Kendall A, Yarmola E, Mishra S, Long JR, Hagen SJ, Stubbs G, Brady LJ. Enhanced purification coupled with biophysical analyses shows cross-β structure as a core building block for Streptococcus mutans functional amyloids. Sci Rep 2020; 10:5138. [PMID: 32198417 PMCID: PMC7083922 DOI: 10.1038/s41598-020-62115-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/14/2020] [Indexed: 11/10/2022] Open
Abstract
Streptococcus mutans is an etiologic agent of human dental caries that forms dental plaque biofilms containing functional amyloids. Three amyloidogenic proteins, P1, WapA, and Smu_63c were previously identified. C123 and AgA are naturally occurring amyloid-forming fragments of P1 and WapA, respectively. We determined that four amyloidophilic dyes, ThT, CDy11, BD-oligo, and MK-H4, differentiate C123, AgA, and Smu_63c amyloid from monomers, but non-specific binding to bacterial cells in the absence of amyloid precludes their utility for identifying amyloid in biofilms. Congo red-induced birefringence is a more specific indicator of amyloid formation and differentiates biofilms formed by wild-type S. mutans from a triple ΔP1/WapA/Smu_63c mutant with reduced biofilm forming capabilities. Amyloid accumulation is a late event, appearing in older S. mutans biofilms after 60 hours of growth. Amyloid derived from pure preparations of all three proteins is visualized by electron microscopy as mat-like structures. Typical amyloid fibers become evident following protease digestion to eliminate non-specific aggregates and monomers. Amyloid mats, similar in appearance to those reported in S. mutans biofilm extracellular matrices, are reconstituted by co-incubation of monomers and amyloid fibers. X-ray fiber diffraction of amyloid mats and fibers from all three proteins demonstrate patterns reflective of a cross-β amyloid structure.
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Affiliation(s)
- Ana L Barran-Berdon
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Sebastian Ocampo
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Momin Haider
- Department of Physics, University of Florida, Gainesville, Florida, USA
| | | | - Gregory Ottenberg
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Amy Kendall
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Elena Yarmola
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Surabhi Mishra
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Joanna R Long
- Department of Biochemistry, University of Florida, Gainesville, Florida, USA
| | - Stephen J Hagen
- Department of Physics, University of Florida, Gainesville, Florida, USA
| | - Gerald Stubbs
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - L Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA.
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25
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Abdul Hamid AI, Nakusi L, Givskov M, Chang YT, Marquès C, Gueirard P. A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms. BMC Microbiol 2020; 20:22. [PMID: 31996131 PMCID: PMC6990489 DOI: 10.1186/s12866-019-1635-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/07/2019] [Indexed: 11/10/2022] Open
Abstract
Background Staphylococcus aureus is a human pathogen that is a common cause of nosocomial infections and infections on indwelling medical devices, mainly due to its ability to shift between the planktonic and the biofilm/sessile lifestyle. Biofilm infections present a serious problem in human medicine as they often lead to bacterial persistence and thus to chronic infections. The immune responses elicited by biofilms have been described as specific and ineffective. In the few experiments performed in vivo, the importance of neutrophils and macrophages as a first line of defence against biofilm infections was clearly established. However, the bilateral interactions between biofilms and myeloid cells remain poorly studied and analysis of the dynamic processes at the cellular level in tissues inoculated with biofilm bacteria is still an unexplored field. It is urgent, therefore, to develop biologically sound experimental approaches in vivo designed to extract specific immune signatures from the planktonic and biofilm forms of bacteria. Results We propose an in vivo transgenic mouse model, used in conjunction with intravital confocal microscopy to study the dynamics of host inflammatory responses to bacteria. Culture conditions were created to prepare calibrated inocula of fluorescent planktonic and biofilm forms of bacteria. A confocal imaging acquisition and analysis protocol was then drawn up to study the recruitment of innate immune cells in the skin of LysM-EGFP transgenic mice. Using the mouse ear pinna model, we showed that inflammatory responses to S. aureus can be quantified over time and that the dynamics of innate immune cells after injection of either the planktonic or biofilm form can be characterized. First results showed that the ability of phagocytic cells to infiltrate the injection site and their motility is not the same in planktonic and biofilm forms of bacteria despite the cells being considerably recruited in both cases. Conclusion We developed a mouse model of infection to compare the dynamics of the inflammatory responses to planktonic and biofilm bacteria at the tissue and cellular levels. The mouse ear pinna model is a powerful imaging system to analyse the mechanisms of biofilm tolerance to immune attacks.
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Affiliation(s)
- Aizat Iman Abdul Hamid
- Laboratoire Microorganismes : Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, Clermont Ferrand, France
| | - Laurence Nakusi
- Laboratoire Microorganismes : Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, Clermont Ferrand, France
| | - Mickael Givskov
- Costerton Biofilm Center, department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Young-Tae Chang
- Center for Self-assembly and Complexity, IBS and Department of Chemistry, POSTECH, Pohang, Republic of Korea
| | - Claire Marquès
- Laboratoire Microorganismes : Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, Clermont Ferrand, France
| | - Pascale Gueirard
- Laboratoire Microorganismes : Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, Clermont Ferrand, France.
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26
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Sensitive detection of a bacterial pathogen using allosteric probe-initiated catalysis and CRISPR-Cas13a amplification reaction. Nat Commun 2020; 11:267. [PMID: 31937772 PMCID: PMC6959245 DOI: 10.1038/s41467-019-14135-9] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 12/13/2019] [Indexed: 12/26/2022] Open
Abstract
The ability to detect low numbers of microbial cells in food and clinical samples is highly valuable but remains a challenge. Here we present a detection system (called ‘APC-Cas’) that can detect very low numbers of a bacterial pathogen without isolation, using a three-stage amplification to generate powerful fluorescence signals. APC-Cas involves a combination of nucleic acid-based allosteric probes and CRISPR-Cas13a components. It can selectively and sensitively quantify Salmonella Enteritidis cells (from 1 to 105 CFU) in various types of samples such as milk, showing similar or higher sensitivity and accuracy compared with conventional real-time PCR. Furthermore, APC-Cas can identify low numbers of S. Enteritidis cells in mouse serum, distinguishing mice with early- and late-stage infection from uninfected mice. Our method may have potential clinical applications for early diagnosis of pathogens. The detection of pathogens in food and clinical samples remains a challenge. Here, Shen et al. present a detection system, involving a combination of nucleic acid-based allosteric probes and CRISPR-Cas13a components, that can detect very low numbers of a bacterial pathogen in milk and serum samples without isolation.
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27
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Subiros-Funosas R, Ho VCL, Barth ND, Mendive-Tapia L, Pappalardo M, Barril X, Ma R, Zhang CB, Qian BZ, Sintes M, Ghashghaei O, Lavilla R, Vendrell M. Fluorogenic Trp(redBODIPY) cyclopeptide targeting keratin 1 for imaging of aggressive carcinomas. Chem Sci 2019; 11:1368-1374. [PMID: 34123261 PMCID: PMC8148049 DOI: 10.1039/c9sc05558d] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
Keratin 1 (KRT1) is overexpressed in squamous carcinomas and associated with aggressive pathologies in breast cancer. Herein we report the design and preparation of the first Trp-based red fluorogenic amino acid, which is synthetically accessible in a few steps and displays excellent photophysical properties, and its application in a minimally-disruptive labelling strategy to prepare a new fluorogenic cyclopeptide for imaging of KRT1+ cells in whole intact tumour tissues.
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Affiliation(s)
- Ramon Subiros-Funosas
- Centre for Inflammation Research, University of Edinburgh 47 Little France Crescent EH16 4TJ Edinburgh UK
| | - Vivian Cheuk Lam Ho
- Centre for Inflammation Research, University of Edinburgh 47 Little France Crescent EH16 4TJ Edinburgh UK
| | - Nicole D Barth
- Centre for Inflammation Research, University of Edinburgh 47 Little France Crescent EH16 4TJ Edinburgh UK
| | - Lorena Mendive-Tapia
- Centre for Inflammation Research, University of Edinburgh 47 Little France Crescent EH16 4TJ Edinburgh UK
| | - Morena Pappalardo
- Laboratory of Physical Chemistry, Facultat de Farmàcia, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB) Av. Joan XXIII s/n 08028 Barcelona Spain
| | - Xavier Barril
- Laboratory of Physical Chemistry, Facultat de Farmàcia, Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB) Av. Joan XXIII s/n 08028 Barcelona Spain
| | - Ruoyu Ma
- MRC Centre for Reproductive Health, University of Edinburgh 47 Little France Crescent EH16 4TJ Edinburgh UK
| | - Cheng-Bin Zhang
- MRC Centre for Reproductive Health, University of Edinburgh 47 Little France Crescent EH16 4TJ Edinburgh UK
| | - Bin-Zhi Qian
- MRC Centre for Reproductive Health, University of Edinburgh 47 Little France Crescent EH16 4TJ Edinburgh UK
| | - Miquel Sintes
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy, University of Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB) Avda Joan XXIII 27-30 Barcelona 08028 Spain
| | - Ouldouz Ghashghaei
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy, University of Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB) Avda Joan XXIII 27-30 Barcelona 08028 Spain
| | - Rodolfo Lavilla
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy, University of Barcelona and Institut de Biomedicina de la Universitat de Barcelona (IBUB) Avda Joan XXIII 27-30 Barcelona 08028 Spain
| | - Marc Vendrell
- Centre for Inflammation Research, University of Edinburgh 47 Little France Crescent EH16 4TJ Edinburgh UK
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28
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Choi YK, Kim JJ, Chang YT. Holding-Oriented versus Gating-Oriented Live-Cell Distinction: Highlighting the Role of Transporters in Cell Imaging Probe Development. Acc Chem Res 2019; 52:3097-3107. [PMID: 31265234 DOI: 10.1021/acs.accounts.9b00253] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Small molecule imaging probes are powerful tools to understand complex biological systems. The mainstreams of imaging probe developments have been focused on the target holding of the probes; the holding targets are often cell-type-specific biomarkers. This type of the probe mechanism can be designated as holding-oriented live-cell distinction (HOLD). Our group has worked on the development of cell-type-selective probes using a diversity-oriented fluorescence library approach (DOFLA), where unbiased phenotypic screening is employed using fluorescent library compounds. Through the conventional target identification methods such as an affinity-based analysis, we elucidated that some of the probe mechanisms are HOLD. However, we also realized that sometimes there is no specific holding target for probes or the holding targets are ubiquitous. The observation led us to test an alternative mechanism of cell-type-specific probes as gating-oriented live-cell distinction (GOLD). We started to examine the gating mechanism of probes, which is mainly based on transporters but which does not necessarily require probe holding to cellular targets. Transporters can control the in and out movement of various nutrients and chemicals. Different expression levels of transporters in various cell types could provide the molecular mechanism of differential staining of cells by regulating the intracellular accumulation of a certain specific probe. A number of GOLD probes have been developed by modifying or mimicking endogenous substrates of transporters such as inorganic ions, glucose, amino acids, or neurotransmitters, utilizing broad substrate specificity of transporters. The radiolabeled or fluorophore-conjugated substrate mimetics have been widely used for live cell distinction and various applications such as disease-related cell or tissue imaging. In humans, there are about 400 solute carrier (SLC) transporters and 50 ATP-binding cassette (ABC) transporters. Since some transporters have broad substrate specificity, they can transport not only derivatives of endogenous natural substrates but also totally synthetic diverse imaging probes, such as DOFLA probes. Without preconsidering the structure of endogenous substrates, we recently demonstrated a series of live-cell imaging probes and elucidated their molecular mechanism as a gating one, either by SLC or ABC transporters. Transporter inhibitor panel and CRISPR-based transporter libraries could provide a systematic gating target elucidation platform. Considering the generality of DOFLA and the CRISPR-based genomic tool for transporter systems (>450 in humans), the GOLD approach will offer new insight and promise for unprecedented levels of novel cell imaging probe development.
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Affiliation(s)
- Yun-Kyu Choi
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Jong-Jin Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea
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29
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Zhou EY, Knox HJ, Liu C, Zhao W, Chan J. A Conformationally Restricted Aza-BODIPY Platform for Stimulus-Responsive Probes with Enhanced Photoacoustic Properties. J Am Chem Soc 2019; 141:17601-17609. [PMID: 31660741 PMCID: PMC6942515 DOI: 10.1021/jacs.9b06694] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Photoacoustic (PA) dyes, which absorb near-infrared (NIR) light to generate an ultrasonic signal, can be detected at centimeter depths in tissues with significantly higher resolution than dyes imaged with fluorescence-based methods. As such, PA agents show great promise as research tools for the study of live-animal disease models. However, the development of activatable PA probes has been hampered by the relative scarcity of appropriate PA-active molecular platforms with properties that can be manipulated in a rational manner. Herein we synthesized and evaluated six modifications to the aza-BODIPY dye platform with respect to their absorbance, fluorescence, and PA properties. We identified a promising conformationally restricted aza-BODIPY (CRaB) scaffold that prioritizes three criteria necessary for the design of stimulus-responsive dyes with optimal ratiometric PA response: absorbance at NIR wavelengths, strong PA intensity, and large Δλ upon interaction with the desired stimulus. Using this scaffold, we synthesized three chemically diverse stimulus-responsive PA probes and demonstrated between 2- and 8-fold improvements in theoretical ratiometric response in vitro. This suggests that improvements in PA parameters are generalizable. Finally, we validated the in vitro turnover of each CRaB PA probe and demonstrated the in vivo potential of the CRaB scaffold by direct comparison to an established hypoxia-responsive probe for the detection of tumor hypoxia.
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Affiliation(s)
- Effie Y. Zhou
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Hailey J. Knox
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Chang Liu
- School of Pharmacy, Institutes of Integrative Medicine, Fudan University, Shanghai, 201203, P. R. China
| | - Weili Zhao
- School of Pharmacy, Institutes of Integrative Medicine, Fudan University, Shanghai, 201203, P. R. China
- Key Laboratory for Special Functional Materials of the Ministry of Education, Henan University, Kaifeng, 475004, P. R. China
| | - Jefferson Chan
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
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30
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Aliyan A, Cook NP, Martí AA. Interrogating Amyloid Aggregates using Fluorescent Probes. Chem Rev 2019; 119:11819-11856. [DOI: 10.1021/acs.chemrev.9b00404] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amir Aliyan
- Pasargad Institute for Advanced Innovative Solutions (PIAIS), Tehran, Iran 1991633361
- Khatam University, Tehran, Iran 1991633356
| | - Nathan P. Cook
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, United States
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31
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Welling MM, Hensbergen AW, Bunschoten A, Velders AH, Scheper H, Smits WK, Roestenberg M, van Leeuwen FWB. Fluorescent imaging of bacterial infections and recent advances made with multimodal radiopharmaceuticals. Clin Transl Imaging 2019. [DOI: 10.1007/s40336-019-00322-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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32
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Sedki M, Hassan RYA, Andreescu S, El-Sherbiny IM. Online-monitoring of biofilm formation using nanostructured electrode surfaces. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2019; 100:178-185. [PMID: 30948051 DOI: 10.1016/j.msec.2019.02.112] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/04/2019] [Accepted: 02/28/2019] [Indexed: 01/10/2023]
Abstract
The direct monitoring of biofilm formation enables valuable insights into the industrial processes, microbiology, and biomedical applications. Therefore, in the present study, nano-structured bioelectrochemical platforms were designed for sensing the formation of biofilm of P. aeruginosa along with monitoring its electrochemical/morphological changes under different stresses. Through the assay optimizations, the performances of different electrode modifiers such as reduced graphene oxide (rGO) nanosheets, hyperbranched chitosan nanoparticles (HBCs NPs), and rGO-HBCs nano-composite were tested to assess the influence of the electrode materials on biofilm progression. As a need for the anodic respiration, the bioelectrochemical responses of the adhered bacterial cells changed from a non-electrochemically active (planktonic state) to an electrochemically active (biofilm matrix) state. Our results demonstrated that electrode modifications with conductive nanostructured elements is highly sensitive and enable direct assay for the biofilm formation without any preachments. Consequently, the morphological changes in bacterial cell wall, upon switching from the planktonic state to the biofilm matrix were imaged using scanning electron microscopy (SEM), and the changes in cell wall chemical composition were monitored by the Energy Dispersive X-ray analysis (EDX). Thus, the designed microbial electrochemical system (MES) was successfully used to monitor changes in the biofilm matrix under different stresses through direct measurements of electron exchanges.
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Affiliation(s)
- Mohammed Sedki
- Nanomaterials Laboratory, Center for Materials Science, Zewail City of Science and Technology, 6th October City, 12588 Giza, Egypt
| | - Rabeay Y A Hassan
- Nanomaterials Laboratory, Center for Materials Science, Zewail City of Science and Technology, 6th October City, 12588 Giza, Egypt; Applied Organic Chemistry Department, National Research Centre (NRC), Dokki, 12622 Giza, Egypt.
| | - Silvana Andreescu
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Ibrahim M El-Sherbiny
- Nanomaterials Laboratory, Center for Materials Science, Zewail City of Science and Technology, 6th October City, 12588 Giza, Egypt.
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33
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Christensen LF, Jensen KF, Nielsen J, Vad BS, Christiansen G, Otzen DE. Reducing the Amyloidogenicity of Functional Amyloid Protein FapC Increases Its Ability To Inhibit α-Synuclein Fibrillation. ACS OMEGA 2019; 4:4029-4039. [PMID: 31459612 PMCID: PMC6647998 DOI: 10.1021/acsomega.8b03590] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/11/2019] [Indexed: 05/15/2023]
Abstract
Functional amyloid (FA) proteins have evolved to assemble into fibrils with a characteristic cross-β structure, which stabilizes biofilms and contributes to bacterial virulence. Some of the most studied bacterial FAs are the curli protein CsgA, expressed in a wide range of bacteria, and FapC, produced mainly by members of the Pseudomonas genus. Though unrelated, both CsgA and FapC contain imperfect repeats believed to drive the formation of amyloid fibrils. While much is known about CsgA biogenesis and fibrillation, the mechanism of FapC fibrillation remains less explored. Here, we show that removing the three imperfect repeats of FapC (FapC ΔR1R2R3) slows down the fibrillation but does not prevent it. The increased lag phase seen for FapC ΔR1R2R3 allows for disulfide bond formation, which further delays fibrillation. Remarkably, these disulfide-bonded species of FapC ΔR1R2R3 also significantly delay the fibrillation of human α-synuclein, a key protein in Parkinson's disease pathology. This attenuation of α-synuclein fibrillation was not seen for the reduced form of FapC ΔR1R2R3. The results presented here shed light on the FapC fibrillation mechanism and emphasize how unrelated fibrillation systems may share such common fibril formation mechanisms, allowing inhibitors of one fibrillating protein to affect a completely different protein.
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Affiliation(s)
- Line Friis
Bakmann Christensen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Kirstine Friis Jensen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Brian Stougaard Vad
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Gunna Christiansen
- Section
for Medical Microbiology and Immunology, Department of Biomedicine, Aarhus University, Vennelyst Boulevard 4, 8000 Aarhus C, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
- E-mail:
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34
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Kwon HY, Kim JY, Liu X, Lee JY, Yam JKH, Dahl Hultqvist L, Xu W, Rybtke M, Tolker-Nielsen T, Heo W, Kim JJ, Kang NY, Joo T, Yang L, Park SJ, Givskov M, Chang YT. Visualizing biofilm by targeting eDNA with long wavelength probe CDr15. Biomater Sci 2019; 7:3594-3598. [DOI: 10.1039/c9bm00152b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a small molecule CDr15, which has eDNA selectivity of bacterial biofilm.
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35
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Xu Y, Luo Z, Chen J, Huang Z, Wang X, An H, Duan Y. Ω-Shaped Fiber-Optic Probe-Based Localized Surface Plasmon Resonance Biosensor for Real-Time Detection of Salmonella Typhimurium. Anal Chem 2018; 90:13640-13646. [PMID: 30359519 DOI: 10.1021/acs.analchem.8b03905] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A novel, Ω-shaped fiber-optic localized surface plasmon resonance (FOLSPR) biosensor was designed for sensitive real-time and label-free bacterial detection. The designed Ω-shaped fiber-optic probe exhibits an outstanding sensitivity, due to the effect of unique geometry on performance. The results show that refractive index (RI) sensitivity of the Ω-shaped fiber-optic probe is 14 times and 2.5 times higher than those of the straight-shaped and the U-shaped FOLSPR, respectively. In addition, the reason for the geometry and the bending radius effects on RI sensitivity was discussed by investigating the relationship between RI sensitivity and the bending area. The results show that RI sensitivity was enhanced with the increase of bending area, and the best RI sensitivity obtained by Ω-shaped FOLSPR was 64.582 (a.u.)/RIU. Combined with this newly designed Ω-shaped FOLSPR biosensor, a real-time, label-free, sensitive, and highly selective bacterial detection method was established. In this work, the aptamers immobilized on the surface of FOLSPR could specifically capture Salmonella Typhimurium, resulting in an intense change of the absorption peak. In line with this principle, the FOLSPR biosensor achieved high detection sensitivity for Salmonella Typhimurium down to 128 CFU/mL within a linear range from 5 × 102 to 1 × 108 CFU/mL and showed good selectivity for Salmonella Typhimurium detection compared to other bacteria. Furthermore, the FOLSPR biosensor was successfully applied to the detection of Salmonella Typhimurium in a chicken sample with the recoveries of 85-123%. With these characteristics, the novel biosensor is a potential alternative tool in food analysis and environmental monitoring.
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Affiliation(s)
- Ya Xu
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences , Sichuan University , Chengdu , Sichuan 610065 , P. R. China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences , Sichuan University , Chengdu , Sichuan 610065 , P. R. China
| | - Junman Chen
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences , Sichuan University , Chengdu , Sichuan 610065 , P. R. China
| | - Zhijun Huang
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences , Sichuan University , Chengdu , Sichuan 610065 , P. R. China
| | - Xu Wang
- School of Manufacturing Science and Engineering , Sichuan University , Chengdu , Sichuan 610065 , P. R. China
| | - Huifang An
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences , Sichuan University , Chengdu , Sichuan 610065 , P. R. China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences , Sichuan University , Chengdu , Sichuan 610065 , P. R. China
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36
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Rouse SL, Matthews SJ, Dueholm MS. Ecology and Biogenesis of Functional Amyloids in Pseudomonas. J Mol Biol 2018; 430:3685-3695. [PMID: 29753779 PMCID: PMC6173800 DOI: 10.1016/j.jmb.2018.05.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 12/02/2022]
Abstract
Functional amyloids can be found in the extracellular matrix produced by many bacteria during biofilm growth. They mediate the initial attachment of bacteria to surfaces and provide stability and functionality to mature biofilms. Efficient amyloid biogenesis requires a highly coordinated system of amyloid subunits, molecular chaperones and transport systems. The functional amyloid of Pseudomonas (Fap) represents such a system. Here, we review the phylogenetic diversification of the Fap system, its potential ecological role and the dedicated machinery required for Fap biogenesis, with a particular focus on the amyloid exporter FapF, the structure of which has been recently resolved. We also present a sequence covariance-based in silico model of the FapC fiber-forming subunit. Finally, we highlight key questions that remain unanswered and we believe deserve further attention by the scientific community.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Stephen J Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Morten S Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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Wei X, Zhou W, Sanjay ST, Zhang J, Jin Q, Xu F, Dominguez DC, Li X. Multiplexed Instrument-Free Bar-Chart SpinChip Integrated with Nanoparticle-Mediated Magnetic Aptasensors for Visual Quantitative Detection of Multiple Pathogens. Anal Chem 2018; 90:9888-9896. [PMID: 30028601 PMCID: PMC6157022 DOI: 10.1021/acs.analchem.8b02055] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A portable multiplexed bar-chart SpinChip (MB-SpinChip) integrated with nanoparticle-mediated magnetic aptasensors was developed for visual quantitative instrument-free detection of multiple pathogens. This versatile multiplexed SpinChip combines aptamer-specific recognition and nanoparticle-catalyzed pressure amplification to achieve a sample-to-answer output for sensitive point-of-care testing (POCT). This is the first report of pathogen detection using a volumetric bar-chart chip, and it is also the first bar-chart chip using a "spinning" mechanism to achieve multiplexed bar-chart detection. Additionally, the introduction of the spin unit not only enabled convenient sample introduction from one inlet to multiple separate channels in the multiplexed detection, but also elegantly solved the pressure cross-interference problem in the multiplexed volumetric bar-chart chip. This user-friendly MB-SpinChip allows visual quantitative detection of multiple pathogens simultaneously with high sensitivity but without utilizing any specialized instruments. Using this MB-SpinChip, three major foodborne pathogens including Salmonella enterica, Escherichia coli, and Listeria monocytogenes were specifically quantified in apple juice with limits of detection of about 10 CFU/mL. This MB-SpinChip with a bar-chart-based visual quantitative readout has great potential for the rapid simultaneous detection of various pathogens at the point of care and wide applications in food safety, environmental surveillance, and infectious disease diagnosis.
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Affiliation(s)
- Xiaofeng Wei
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Wan Zhou
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Sharma T. Sanjay
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Jie Zhang
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Qijie Jin
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
- College of Materials Science and Engineering, Nanjing Tech University, Nanjing, 210009, People’s Republic of China
| | - Feng Xu
- Bioinspired Engineering and Biomechanics Center, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Delfina C. Dominguez
- College of Health Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - XiuJun Li
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
- Biomedical Engineering, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
- Border Biomedical Research Center, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
- Environmental Science and Engineering, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
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38
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Zhang P, Chen YP, Qiu JH, Dai YZ, Feng B. Imaging the Microprocesses in Biofilm Matrices. Trends Biotechnol 2018; 37:214-226. [PMID: 30075862 DOI: 10.1016/j.tibtech.2018.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/07/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022]
Abstract
Biofilms, which are aggregates of microorganisms and extracellular matrices, widely colonize natural water bodies, wastewater treatment systems, and body tissues, and have vital roles in water purification, biofouling, and infectious diseases. Recently, multiple imaging modalities have been developed to visualize the morphological structure and material distribution within biofilms and to probe the microprocesses in biofilm matrices, including biofilm formation, transfer and metabolism of substrates, and cell-cell communication. These technologies have improved our understanding of biofilm control and the fates of substrates in biofilms. In this review, we describe the principles of various imaging techniques and discuss the advantages and limitations of each approach to characterizing microprocesses in biofilm matrices.
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Affiliation(s)
- Peng Zhang
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
| | - Ju-Hui Qiu
- College of Bioengineering, Chongqing University, Chongqing 400045, China
| | - You-Zhi Dai
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Bo Feng
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
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39
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Van Gerven N, Van der Verren SE, Reiter DM, Remaut H. The Role of Functional Amyloids in Bacterial Virulence. J Mol Biol 2018; 430:3657-3684. [PMID: 30009771 PMCID: PMC6173799 DOI: 10.1016/j.jmb.2018.07.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 12/14/2022]
Abstract
Amyloid fibrils are best known as a product of human and animal protein misfolding disorders, where amyloid formation is associated with cytotoxicity and disease. It is now evident that for some proteins, the amyloid state constitutes the native structure and serves a functional role. These functional amyloids are proving widespread in bacteria and fungi, fulfilling diverse functions as structural components in biofilms or spore coats, as toxins and surface-active fibers, as epigenetic material, peptide reservoirs or adhesins mediating binding to and internalization into host cells. In this review, we will focus on the role of functional amyloids in bacterial pathogenesis. The role of functional amyloids as virulence factor is diverse but mostly indirect. Nevertheless, functional amyloid pathways deserve consideration for the acute and long-term effects of the infectious disease process and may form valid antimicrobial targets. Functional amyloids are widespread in bacteria, pathogenic and non-pathogenic. Bacterial biofilms most commonly function as structural support in the extracellular matrix of biofilms or spore coats, and in cell–cell and cell-surface adherence. The amyloid state can be the sole structured and functional state, or can be facultative, as a secondary state to folded monomeric subunits. Bacterial amyloids can enhance virulence by increasing persistence, cell adherence and invasion, intracellular survival, and pathogen spread by increased environmental survival. Bacterial amyloids may indirectly inflict disease by triggering inflammation, contact phase activation and possibly induce or aggravate human pathological aggregation disorders.
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Affiliation(s)
- Nani Van Gerven
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Sander E Van der Verren
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Dirk M Reiter
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium.
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40
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Qi GB, Gao YJ, Wang L, Wang H. Self-Assembled Peptide-Based Nanomaterials for Biomedical Imaging and Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703444. [PMID: 29460400 DOI: 10.1002/adma.201703444] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/22/2017] [Indexed: 05/22/2023]
Abstract
Peptide-based materials are one of the most important biomaterials, with diverse structures and functionalities. Over the past few decades, a self-assembly strategy is introduced to construct peptide-based nanomaterials, which can form well-controlled superstructures with high stability and multivalent effect. More recently, peptide-based functional biomaterials are widely utilized in clinical applications. However, there is no comprehensive review article that summarizes this growing area, from fundamental research to clinic translation. In this review, the recent progress of peptide-based materials, from molecular building block peptides and self-assembly driving forces, to biomedical and clinical applications is systematically summarized. Ex situ and in situ constructed nanomaterials based on functional peptides are presented. The advantages of intelligent in situ construction of peptide-based nanomaterials in vivo are emphasized, including construction strategy, nanostructure modulation, and biomedical effects. This review highlights the importance of self-assembled peptide nanostructures for nanomedicine and can facilitate further knowledge and understanding of these nanosystems toward clinical translation.
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Affiliation(s)
- Guo-Bin Qi
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Yu-Juan Gao
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Lei Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
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41
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Antonets KS, Kliver SF, Nizhnikov AA. Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order Rhizobiales. Evol Bioinform Online 2018; 14:1176934318768781. [PMID: 29720870 PMCID: PMC5922492 DOI: 10.1177/1176934318768781] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/27/2018] [Indexed: 11/16/2022] Open
Abstract
Amyloids are protein fibrils with a highly ordered spatial structure called cross-β. To date, amyloids were shown to be implicated in a wide range of biological processes, both pathogenic and functional. In bacteria, functional amyloids are involved in forming biofilms, storing toxins, overcoming the surface tension, and other functions. Rhizobiales represent an economically important group of Alphaproteobacteria, various species of which are not only capable of fixing nitrogen in the symbiosis with leguminous plants but also act as the causative agents of infectious diseases in animals and plants. Here, we implemented bioinformatic screening for potentially amyloidogenic proteins in the proteomes of more than 80 species belonging to the order Rhizobiales. Using SARP (Sequence Analysis based on the Ranking of Probabilities) and Waltz bioinformatic algorithms, we identified the biological processes, where potentially amyloidogenic proteins are overrepresented. We detected protein domains and regions associated with amyloidogenic sequences in the proteomes of various Rhizobiales species. We demonstrated that amyloidogenic regions tend to occur in the membrane or extracellular proteins, many of which are involved in pathogenesis-related processes, including adhesion, assembly of flagellum, and transport of siderophores and lipopolysaccharides, and contain domains typical of the virulence factors (hemolysin, RTX, YadA, LptD); some of them (rhizobiocins, LptD) are also related to symbiosis.
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Affiliation(s)
- Kirill S Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russian Federation.,Department of Genetics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Sergey F Kliver
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russian Federation.,Department of Genetics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Anton A Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russian Federation.,Department of Genetics, St. Petersburg State University, St. Petersburg, Russian Federation
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Kim HJ, Seo YH, An S, Jo A, Kwon IC, Kim S. Chemiluminescence imaging of Duox2-derived hydrogen peroxide for longitudinal visualization of biological response to viral infection in nasal mucosa. Am J Cancer Res 2018; 8:1798-1807. [PMID: 29556357 PMCID: PMC5858501 DOI: 10.7150/thno.22481] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 02/02/2018] [Indexed: 12/15/2022] Open
Abstract
Rationale: Hydrogen peroxide (H2O2) provides an important mechanism for resisting infectious pathogens within the respiratory tract, and accordingly, the in situ analysis of H2O2 generation in real time provides a valuable tool for assessing immune response. Methods: In this study, we applied a chemiluminescent nanoparticle-based real-time imaging approach to noninvasive evaluation of the Duox2-mediated H2O2 generation after viral infection, and assessed its usefulness for analytical purposes in mouse nasal mucosa. The chemiluminescent nanoprobe employed herein (BioNT) possesses appropriate physicochemical properties, such as high sensitivity and selectivity toward H2O2, no background noise, deliverability to the respiratory tract, and capability of multiple injections to a single animal subject for long-term repetitive imaging. Results: The favorable characteristics of BioNT allowed for a longitudinal study with the same mice to noninvasively evaluate the long-term evolution of endogenous H2O2 in the nasal epithelium after infection with influenza A virus (WS/33/H1N1). We found that nasal epithelial cells by themselves respond to viral infection by generating H2O2, and that the in vivo cumulative H2O2 level in the nasal mucosa peaks at day 3 post-infection. Such in vitro and in vivo temporal behaviors of the endogenous H2O2 generation showed a good correlation with those of Duox2 expression after infection. This correlation could be further confirmed with Duox2-deficient subjects (Duox2-knockdown NHNE cells and Duox2-knockout mutant mice) where no H2O2-induced chemiluminescence was detectable even after viral infection. Importantly, upon knock-down of Duox2 expression, the condition of mice caused by viral infection in the upper airway was significantly aggravated, evidencing the involvement of Duox2 in the immune defense. Conclusion: All these results reveal a critical role of Duox2 in the infection-induced H2O2 production and the H2O2-mediated immune response to infection in the respiratory tract, well elucidating the potential of BioNT as a noninvasive tool for fundamental in vivo studies of infectious diseases.
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43
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Kwon HY, Kim JY, Lee JY, Yam JKH, Hultqvist LD, Xu W, Rybtke M, Tolker-Nielsen T, Kim JJ, Kang NY, Yang L, Park SJ, Givskov M, Chang YT. CDy14: a novel biofilm probe targeting exopolysaccharide Psl. Chem Commun (Camb) 2018; 54:11865-11868. [DOI: 10.1039/c8cc05544k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed CDy14, which is the first small molecule probe for Psl target in bacterial biofilm.
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Affiliation(s)
- Haw-Young Kwon
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS)
- Pohang 37673
- Republic of Korea
| | - Jun-Young Kim
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research
- Singapore
| | - Jung Yeol Lee
- New drug discovery Center, Daegu-Gyeongbuk Medivalley Innovation Foundation (DGMIF)
- Daegu
- Republic of Korea
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University
- Singapore
| | - Louise Dahl Hultqvist
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen
- DK-2200 Copenhagen
- Denmark
| | - Wang Xu
- Department of Chemistry & Med Chem Program, Life Sciences Institute, National University of Singapore
- Singapore
| | - Morten Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen
- DK-2200 Copenhagen
- Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen
- DK-2200 Copenhagen
- Denmark
| | - Jong-Jin Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS)
- Pohang 37673
- Republic of Korea
| | - Nam-Young Kang
- New drug discovery Center, Daegu-Gyeongbuk Medivalley Innovation Foundation (DGMIF)
- Daegu
- Republic of Korea
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University
- Singapore
| | - Sung-Jin Park
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research
- Singapore
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University
- Singapore
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen
- DK-2200 Copenhagen
- Denmark
| | - Young-Tae Chang
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS)
- Pohang 37673
- Republic of Korea
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research
- Singapore
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44
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Kovalska V, Chernii S, Losytskyy M, Tretyakova I, Dovbii Y, Gorski A, Chernii V, Czerwieniec R, Yarmoluk S. Design of functionalized β-ketoenole derivatives as efficient fluorescent dyes for detection of amyloid fibrils. NEW J CHEM 2018. [DOI: 10.1039/c8nj01020j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functionalized β-ketoenoles for efficient fluorescence sensing of protein amyloid fibrils giving strong emission increase up to 0.5 QY are designed.
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Affiliation(s)
| | - Svitlana Chernii
- Institute of Molecular Biology and Genetics NASU
- 03143 Kyiv
- Ukraine
- V.I. Vernadskii Institute of General and Inorganic Chemistry NASU
- 03080 Kyiv
| | - Mykhaylo Losytskyy
- V.I. Vernadskii Institute of General and Inorganic Chemistry NASU
- 03080 Kyiv
- Ukraine
- Taras Shevchenko National University of Kyiv
- Kyiv-01601
| | - Iryna Tretyakova
- V.I. Vernadskii Institute of General and Inorganic Chemistry NASU
- 03080 Kyiv
- Ukraine
| | - Yan Dovbii
- V.I. Vernadskii Institute of General and Inorganic Chemistry NASU
- 03080 Kyiv
- Ukraine
| | - Alexandr Gorski
- Institute of Physical Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
| | - Victor Chernii
- V.I. Vernadskii Institute of General and Inorganic Chemistry NASU
- 03080 Kyiv
- Ukraine
| | | | - Sergiy Yarmoluk
- Institute of Molecular Biology and Genetics NASU
- 03143 Kyiv
- Ukraine
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45
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Wagner S, Hauck D, Hoffmann M, Sommer R, Joachim I, Müller R, Imberty A, Varrot A, Titz A. Covalent Lectin Inhibition and Application in Bacterial Biofilm Imaging. Angew Chem Int Ed Engl 2017; 56:16559-16564. [PMID: 28960731 PMCID: PMC5767747 DOI: 10.1002/anie.201709368] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Indexed: 12/12/2022]
Abstract
Biofilm formation by pathogenic bacteria is a hallmark of chronic infections. In many cases, lectins play key roles in establishing biofilms. The pathogen Pseudomonas aeruginosa often exhibiting various drug resistances employs its lectins LecA and LecB as virulence factors and biofilm building blocks. Therefore, inhibition of the function of these proteins is thought to have potential in developing "pathoblockers" preventing biofilm formation and virulence. A covalent lectin inhibitor specific to a carbohydrate binding site is described for the first time. Its application in the LecA-specific in vitro imaging of biofilms formed by P. aeruginosa is also reported.
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Affiliation(s)
- Stefanie Wagner
- Chemical Biology of CarbohydratesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)66123SaarbrückenGermany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-BraunschweigGermany
| | - Dirk Hauck
- Chemical Biology of CarbohydratesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)66123SaarbrückenGermany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-BraunschweigGermany
| | - Michael Hoffmann
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-BraunschweigGermany
- Microbial Natural SubstancesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)66123SaarbrückenGermany
| | - Roman Sommer
- Chemical Biology of CarbohydratesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)66123SaarbrückenGermany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-BraunschweigGermany
| | - Ines Joachim
- Chemical Biology of CarbohydratesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)66123SaarbrückenGermany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-BraunschweigGermany
| | - Rolf Müller
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-BraunschweigGermany
- Microbial Natural SubstancesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)66123SaarbrückenGermany
| | - Anne Imberty
- Université Grenoble AlpesCNRS, CERMAV38000GrenobleFrance
| | | | - Alexander Titz
- Chemical Biology of CarbohydratesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)66123SaarbrückenGermany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-BraunschweigGermany
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46
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Wagner S, Hauck D, Hoffmann M, Sommer R, Joachim I, Müller R, Imberty A, Varrot A, Titz A. Covalent Lectin Inhibition and Application in Bacterial Biofilm Imaging. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709368] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Stefanie Wagner
- Chemical Biology of Carbohydrates; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); 66123 Saarbrücken Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig; Germany
| | - Dirk Hauck
- Chemical Biology of Carbohydrates; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); 66123 Saarbrücken Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig; Germany
| | - Michael Hoffmann
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig; Germany
- Microbial Natural Substances; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); 66123 Saarbrücken Germany
| | - Roman Sommer
- Chemical Biology of Carbohydrates; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); 66123 Saarbrücken Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig; Germany
| | - Ines Joachim
- Chemical Biology of Carbohydrates; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); 66123 Saarbrücken Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig; Germany
| | - Rolf Müller
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig; Germany
- Microbial Natural Substances; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); 66123 Saarbrücken Germany
| | - Anne Imberty
- Université Grenoble Alpes; CNRS, CERMAV; 38000 Grenoble France
| | | | - Alexander Titz
- Chemical Biology of Carbohydrates; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); 66123 Saarbrücken Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig; Germany
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47
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Tokonami S, Iida T. Review: Novel sensing strategies for bacterial detection based on active and passive methods driven by external field. Anal Chim Acta 2017; 988:1-16. [DOI: 10.1016/j.aca.2017.07.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 07/15/2017] [Accepted: 07/17/2017] [Indexed: 01/09/2023]
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48
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Rouse SL, Hawthorne WJ, Berry JL, Chorev DS, Ionescu SA, Lambert S, Stylianou F, Ewert W, Mackie U, Morgan RML, Otzen D, Herbst FA, Nielsen PH, Dueholm M, Bayley H, Robinson CV, Hare S, Matthews S. A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis. Nat Commun 2017; 8:263. [PMID: 28811582 PMCID: PMC5557850 DOI: 10.1038/s41467-017-00361-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/23/2017] [Indexed: 11/25/2022] Open
Abstract
Gram-negative bacteria possess specialised biogenesis machineries that facilitate the export of amyloid subunits for construction of a biofilm matrix. The secretion of bacterial functional amyloid requires a bespoke outer-membrane protein channel through which unfolded amyloid substrates are translocated. Here, we combine X-ray crystallography, native mass spectrometry, single-channel electrical recording, molecular simulations and circular dichroism measurements to provide high-resolution structural insight into the functional amyloid transporter from Pseudomonas, FapF. FapF forms a trimer of gated β-barrel channels in which opening is regulated by a helical plug connected to an extended coil-coiled platform spanning the bacterial periplasm. Although FapF represents a unique type of secretion system, it shares mechanistic features with a diverse range of peptide translocation systems. Our findings highlight alternative strategies for handling and export of amyloid protein sequences. Gram-negative bacteria assemble biofilms from amyloid fibres, which translocate across the outer membrane as unfolded amyloid precursors through a secretion system. Here, the authors characterise the structural details of the amyloid transporter FapF in Pseudomonas.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - William J Hawthorne
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Jamie-Lee Berry
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Dror S Chorev
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sebastian Lambert
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Wiebke Ewert
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Uma Mackie
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK.,Walthamstow School for Girls, London, E17 9RZ, UK
| | - R Marc L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Centre for Insoluble Protein Structures (inSPIN), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Stephen Hare
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
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49
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Yu C, Miao W, Wang J, Hao E, Jiao L. PyrrolylBODIPYs: Syntheses, Properties, and Application as Environment-Sensitive Fluorescence Probes. ACS OMEGA 2017; 2:3551-3561. [PMID: 31457674 PMCID: PMC6641347 DOI: 10.1021/acsomega.7b00444] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/28/2017] [Indexed: 05/26/2023]
Abstract
Four pyrrole B-ring-functionalized pyrrolylBODIPYs and their B-ring unsubstituted analogues were synthesized from easily accessible starting 5-halo-2-formylpyrroles and were characterized by nuclear magnetic resonance, high-resolution mass spectrometry, X-ray analysis, and optical/electronic properties. In great contrast to the substitution(s) at the other two pyrrolic units, electron-donating substituent(s) at pyrrole B-ring bring significant blue shift of the absorption and emission bands. Cyclic voltammetry and density functional theory calculations indicate that this blue shift may be attributed to the increased highest occupied molecular orbital and the lowest unoccupied molecular orbital energy levels and the overall increase in the energy band gaps. These pyrrolylBODIPYs generally show intense absorption (centered at 570-624 nm) and fluorescence emission (582-654 nm) in nonpolar solvents. A gradual decrease in the fluorescence intensity was observed for these dyes with the increase in solvent dipolar moment, which combines with the red to far-red absorption/emission, rendering these pyrrolylBODIPYs potential applications as environment-sensitive fluorescence probes as demonstrated in this work for bovine serum albumin.
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50
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Ding P, Wang H, Song B, Ji X, Su Y, He Y. In Situ Live-Cell Nucleus Fluorescence Labeling with Bioinspired Fluorescent Probes. Anal Chem 2017. [DOI: 10.1021/acs.analchem.6b04427] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Pan Ding
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Institute of Functional Nano & Soft Materials (FUNSOM), and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO−CIC), Soochow University, Suzhou, Jiangsu 215123, China
| | - Houyu Wang
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Institute of Functional Nano & Soft Materials (FUNSOM), and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO−CIC), Soochow University, Suzhou, Jiangsu 215123, China
| | - Bin Song
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Institute of Functional Nano & Soft Materials (FUNSOM), and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO−CIC), Soochow University, Suzhou, Jiangsu 215123, China
| | - Xiaoyuan Ji
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Institute of Functional Nano & Soft Materials (FUNSOM), and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO−CIC), Soochow University, Suzhou, Jiangsu 215123, China
| | - Yuanyuan Su
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Institute of Functional Nano & Soft Materials (FUNSOM), and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO−CIC), Soochow University, Suzhou, Jiangsu 215123, China
| | - Yao He
- Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Institute of Functional Nano & Soft Materials (FUNSOM), and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO−CIC), Soochow University, Suzhou, Jiangsu 215123, China
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