1
|
Sánchez JM, López-Laguna H, Parladé E, Somma AD, Livieri AL, Álamo P, Mangues R, Unzueta U, Villaverde A, Vázquez E. Structural Stabilization of Clinically Oriented Oligomeric Proteins During their Transit through Synthetic Secretory Amyloids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309427. [PMID: 38501900 DOI: 10.1002/advs.202309427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/31/2024] [Indexed: 03/20/2024]
Abstract
Developing time-sustained drug delivery systems is a main goal in innovative medicines. Inspired by the architecture of secretory granules from the mammalian endocrine system it has generated non-toxic microscale amyloid materials through the coordination between divalent metals and poly-histidine stretches. Like their natural counterparts that keep the functionalities of the assembled protein, those synthetic structures release biologically active proteins during a slow self-disintegration process occurring in vitro and upon in vivo administration. Being these granules formed by a single pure protein species and therefore, chemically homogenous, they act as highly promising time-sustained drug delivery systems. Despite their enormous clinical potential, the nature of the clustering process and the quality of the released protein have been so far neglected issues. By using diverse polypeptide species and their protein-only oligomeric nanoscale versions as convenient models, a conformational rearrangement and a stabilization of the building blocks during their transit through the secretory granules, being the released material structurally distinguishable from the original source is proved here. This fact indicates a dynamic nature of secretory amyloids that act as conformational arrangers rather than as plain, inert protein-recruiting/protein-releasing granular depots.
Collapse
Affiliation(s)
- Julieta M Sánchez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
- Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT) (CONICET-Universidad Nacional de Córdoba), ICTA, FCEFyN, UNC, Av. Velez Sarsfield 1611, Córdoba, X5016GCA, Argentina
| | - Hèctor López-Laguna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
| | - Eloi Parladé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
| | - Angela Di Somma
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- Department of Chemical Sciences, University of Naples "Federico II", Vicinale Cupa Cintia 26, Naples, 20126, Italy
- CEINGE Advanced Biotechnologies, Via Gaetano Salvatore 486, Naples, 80131, Italy
| | - Andrea L Livieri
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
| | - Patricia Álamo
- Institut de Recerca Sant Pau (IR SANT PAU), Sant Quintí 77-79, Barcelona, 08041, Spain
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
- Institut de Recerca Sant Pau (IR SANT PAU), Sant Quintí 77-79, Barcelona, 08041, Spain
- Josep Carreras Leukaemia Research Institute, Barcelona, 08025, Spain
| | - Ugutz Unzueta
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
- Institut de Recerca Sant Pau (IR SANT PAU), Sant Quintí 77-79, Barcelona, 08041, Spain
- Josep Carreras Leukaemia Research Institute, Barcelona, 08025, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
| |
Collapse
|
2
|
Jordan J, Gibb CL, Tran T, Yao W, Rose A, Mague JT, Easson MW, Gibb BC. Anion Binding to Ammonium and Guanidinium Hosts: Implications for the Reverse Hofmeister Effects Induced by Lysine and Arginine Residues. J Org Chem 2024; 89:6877-6891. [PMID: 38662908 PMCID: PMC11110012 DOI: 10.1021/acs.joc.4c00242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024]
Abstract
Anions have a profound effect on the properties of soluble proteins. Such Hofmeister effects have implications in biologics stability, protein aggregation, amyloidogenesis, and crystallization. However, the interplay between the important noncovalent interactions (NCIs) responsible for Hofmeister effects is poorly understood. To contribute to improving this state of affairs, we report on the NCIs between anions and ammonium and guanidinium hosts 1 and 2, and the consequences of these. Specifically, we investigate the properties of cavitands designed to mimic two prime residues for anion-protein NCIs─lysines and arginines─and the solubility consequences of complex formation. Thus, we report NMR and ITC affinity studies, X-ray analysis, MD simulations, and anion-induced critical precipitation concentrations. Our findings emphasize the multitude of NCIs that guanidiniums can form and how this repertoire qualitatively surpasses that of ammoniums. Additionally, our studies demonstrate the ease by which anions can dispense with a fraction of their hydration-shell waters, rearrange those that remain, and form direct NCIs with the hosts. This raises many questions concerning how solvent shell plasticity varies as a function of anion, how the energetics of this impact the different NCIs between anions and ammoniums/guanidiniums, and how this affects the aggregation of solutes at high anion concentrations.
Collapse
Affiliation(s)
- Jacobs
H. Jordan
- The
Southern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 1100 Allen Toussaint Blvd., New Orleans, Louisiana 70124, United States
| | - Corinne L.D. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Thien Tran
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Wei Yao
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Austin Rose
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Joel T. Mague
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Michael W. Easson
- The
Southern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 1100 Allen Toussaint Blvd., New Orleans, Louisiana 70124, United States
| | - Bruce C. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| |
Collapse
|
3
|
Mirza Agha M, Tavili E, Dabirmanesh B. Functional amyloids. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:389-434. [PMID: 38811086 DOI: 10.1016/bs.pmbts.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
While amyloid has traditionally been viewed as a harmful formation, emerging evidence suggests that amyloids may also play a functional role in cell biology, contributing to normal physiological processes that have been conserved throughout evolution. Functional amyloids have been discovered in several creatures, spanning from bacteria to mammals. These amyloids serve a multitude of purposes, including but not limited to, forming biofilms, melanin synthesis, storage, information transfer, and memory. The functional role of amyloids has been consistently validated by the discovery of more functional amyloids, indicating a conceptual convergence. The biology of amyloids is well-represented by non-pathogenic amyloids, given the numerous ones already identified and the ongoing rate of new discoveries. In this chapter, functional amyloids in microorganisms, animals, and plants are described.
Collapse
Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elaheh Tavili
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| |
Collapse
|
4
|
Lu L, Zhao Y, Li M, Wang X, Zhu J, Liao L, Wang J. Contemporary strategies and approaches for characterizing composition and enhancing biofilm penetration targeting bacterial extracellular polymeric substances. J Pharm Anal 2024; 14:100906. [PMID: 38634060 PMCID: PMC11022105 DOI: 10.1016/j.jpha.2023.11.013] [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: 08/04/2023] [Revised: 11/08/2023] [Accepted: 11/26/2023] [Indexed: 04/19/2024] Open
Abstract
Extracellular polymeric substances (EPS) constitutes crucial elements within bacterial biofilms, facilitating accelerated antimicrobial resistance and conferring defense against the host's immune cells. Developing precise and effective antibiofilm approaches and strategies, tailored to the specific characteristics of EPS composition, can offer valuable insights for the creation of novel antimicrobial drugs. This, in turn, holds the potential to mitigate the alarming issue of bacterial drug resistance. Current analysis of EPS compositions relies heavily on colorimetric approaches with a significant bias, which is likely due to the selection of a standard compound and the cross-interference of various EPS compounds. Considering the pivotal role of EPS in biofilm functionality, it is imperative for EPS research to delve deeper into the analysis of intricate compositions, moving beyond the current focus on polymeric materials. This necessitates a shift from heavy reliance on colorimetric analytic methods to more comprehensive and nuanced analytical approaches. In this study, we have provided a comprehensive summary of existing analytical methods utilized in the characterization of EPS compositions. Additionally, novel strategies aimed at targeting EPS to enhance biofilm penetration were explored, with a specific focus on highlighting the limitations associated with colorimetric methods. Furthermore, we have outlined the challenges faced in identifying additional components of EPS and propose a prospective research plan to address these challenges. This review has the potential to guide future researchers in the search for novel compounds capable of suppressing EPS, thereby inhibiting biofilm formation. This insight opens up a new avenue for exploration within this research domain.
Collapse
Affiliation(s)
- Lan Lu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Yuting Zhao
- Meishan Pharmaceutical Vocational College, School of Pharmacy, Meishan, Sichuan, 620200, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Xiaobo Wang
- Hepatobiliary Surgery, Langzhong People's Hospital, Langzhong, Sichuan, 646000, China
| | - Jie Zhu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Li Liao
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| | - Jingya Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610000, China
| |
Collapse
|
5
|
Trubitsina NP, Matiiv AB, Rogoza TM, Zudilova AA, Bezgina MD, Zhouravleva GA, Bondarev SA. Role of the Gut Microbiome and Bacterial Amyloids in the Development of Synucleinopathies. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:523-542. [PMID: 38648770 DOI: 10.1134/s0006297924030118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 04/25/2024]
Abstract
Less than ten years ago, evidence began to accumulate about association between the changes in the composition of gut microbiota and development of human synucleinopathies, in particular sporadic form of Parkinson's disease. We collected data from more than one hundred and thirty experimental studies that reported similar results and summarized the frequencies of detection of different groups of bacteria in these studies. It is important to note that it is extremely rare that a unidirectional change in the population of one or another group of microorganisms (only an elevation or only a reduction) was detected in the patients with Parkinson's disease. However, we were able to identify several groups of bacteria that were overrepresented in the patients with Parkinson's disease in the analyzed studies. There are various hypotheses about the molecular mechanisms that explain such relationships. Usually, α-synuclein aggregation is associated with the development of inflammatory processes that occur in response to the changes in the microbiome. However, experimental evidence is accumulating on the influence of bacterial proteins, including amyloids (curli), as well as various metabolites, on the α-synuclein aggregation. In the review, we provided up-to-date information about such examples.
Collapse
Affiliation(s)
- Nina P Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Anton B Matiiv
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Tatyana M Rogoza
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- St. Petersburg Branch of the Vavilov Institute of General Genetics, Saint Petersburg, 198504, Russia
| | - Anna A Zudilova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Mariya D Bezgina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| |
Collapse
|
6
|
Tsai TY, Jhang WT, Hsu HK, Chan YT, Chang CF, Chen YR. Amyloid Modifier SERF1a Accelerates Alzheimer's Amyloid-β Fibrillization and Exacerbates the Cytotoxicity. ACS Chem Neurosci 2024; 15:479-490. [PMID: 38211979 DOI: 10.1021/acschemneuro.3c00403] [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: 01/13/2024] Open
Abstract
Alzheimer's disease (AD) is a devastating, progressive neurodegenerative disease affecting the elderly in the world. The pathological hallmark senile plaques are mainly composed of amyloid-β (Aβ), in which the main isoforms are Aβ40 and Aβ42. Aβ is prone to aggregate and ultimately forms amyloid fibrils in the brains of AD patients. Factors that alter the Aβ aggregation process have been considered to be potential targets for treatments of AD. Modifier of aggregation 4 (MOAG-4)/small EDRK-rich factor (SERF) was previously selected from a chemical mutagenesis screen and identified as an amyloid modifier that promotes amyloid aggregation for α-synuclein, huntingtin, and Aβ40. The interaction and effect of yeast ScSERF on Aβ40 were previously described. Here, we examined the human SERF1a effect on Aβ40 and Aβ42 fibrillization by the Thioflavin T assay and found that SERF1a accelerated Aβ fibrillization in a dose-dependent manner without changing the fibril amount and without incorporation. By Fourier transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM), we found that SERF1a altered the secondary structures and the morphology of Aβ fibrils. The electrospray ionization mass spectrometry (ESI-MS) and analytical ultracentrifugation (AUC) results showed that SERF1a binds to Aβ in a 1:1 stoichiometry. Moreover, the NMR study showed that SERF1a interacts with Aβ via its N-terminal region. Cytotoxicity assay demonstrated that SERF1a enhanced toxicity of Aβ intermediates, and the effect can be rescued by SERF1a antibody. Overall, our study provides the underlying molecular mechanism for the SERF1a effect on Aβ fibrillization and facilitates the therapeutic development of AD.
Collapse
Affiliation(s)
- Tien-Ying Tsai
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2, Nankang District, Taipei 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Ting Jhang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Hung-Kai Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Tsu Chan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 115, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei 115, Taiwan
| |
Collapse
|
7
|
Knights HE, Ramachandran VK, Jorrin B, Ledermann R, Parsons JD, Aroney STN, Poole PS. Rhizobium determinants of rhizosphere persistence and root colonization. THE ISME JOURNAL 2024; 18:wrae072. [PMID: 38690786 PMCID: PMC11103875 DOI: 10.1093/ismejo/wrae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Bacterial persistence in the rhizosphere and colonization of root niches are critical for the establishment of many beneficial plant-bacteria interactions including those between Rhizobium leguminosarum and its host legumes. Despite this, most studies on R. leguminosarum have focused on its symbiotic lifestyle as an endosymbiont in root nodules. Here, we use random barcode transposon sequencing to assay gene contributions of R. leguminosarum during competitive growth in the rhizosphere and colonization of various plant species. This facilitated the identification of 189 genes commonly required for growth in diverse plant rhizospheres, mutation of 111 of which also affected subsequent root colonization (rhizosphere progressive), and a further 119 genes necessary for colonization. Common determinants reveal a need to synthesize essential compounds (amino acids, ribonucleotides, and cofactors), adapt metabolic function, respond to external stimuli, and withstand various stresses (such as changes in osmolarity). Additionally, chemotaxis and flagella-mediated motility are prerequisites for root colonization. Many genes showed plant-specific dependencies highlighting significant adaptation to different plant species. This work provides a greater understanding of factors promoting rhizosphere fitness and root colonization in plant-beneficial bacteria, facilitating their exploitation for agricultural benefit.
Collapse
Affiliation(s)
- Hayley E Knights
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | | | - Beatriz Jorrin
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Raphael Ledermann
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Jack D Parsons
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Samuel T N Aroney
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Philip S Poole
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| |
Collapse
|
8
|
Rahman S, Das AK. Staphylococcal superantigen-like protein 10 enhances the amyloidogenic biofilm formation in Staphylococcus aureus. BMC Microbiol 2023; 23:390. [PMID: 38062361 PMCID: PMC10701973 DOI: 10.1186/s12866-023-03134-y] [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: 05/31/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Staphylococcus aureus is a highly infectious pathogen that represents a significant burden on the current healthcare system. Bacterial attachment to medical implants and host tissue, and the establishment of a mature biofilm, play an important role in chronic diseases such as endocarditis, osteomyelitis and wound infections. These biofilms decrease bacterial susceptibility to antibiotics and immune defences, making the infections challenging to treatment. S. aureus produces numerous exotoxins that contribute to the pathogenesis of the bacteria. In this study, we have identified a novel function of staphylococcal superantigen-like protein 10 (SSL10) in enhancing the formation of staphylococcal biofilms. Biofilm biomass is significantly increased when SSL10 is added exogenously to bacterial cultures, whereas SSL2 and SSL12 are found to be less active. Exogenously added SSL10 mask the surface charge of the bacterial cells and lowers their zeta potential, leading to the aggregation of the cells. Moreover, the biofilm formation by SSL10 is governed by amyloid aggregation, as evident from spectroscopic and microscopic studies. These findings thereby give the first overview of the SSL-mediated amyloid-based biofilm formation and further drive the future research in identifying potential molecules for developing new antibacterial therapies against Staphylococcus aureus.
Collapse
Affiliation(s)
- Shakilur Rahman
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
| |
Collapse
|
9
|
Galkin AP, Sysoev EI, Valina AA. Amyloids and prions in the light of evolution. Curr Genet 2023; 69:189-202. [PMID: 37165144 DOI: 10.1007/s00294-023-01270-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023]
Abstract
Functional amyloids have been identified in a wide variety of organisms including bacteria, fungi, plants, and vertebrates. Intracellular and extracellular amyloid fibrils of different proteins perform storage, protective, structural, and regulatory functions. The structural organization of amyloid fibrils determines their unique physical and biochemical properties. The formation of these fibrillar structures can provide adaptive advantages that are picked up by natural selection. Despite the great interest in functional and pathological amyloids, questions about the conservatism of the amyloid properties of proteins and the regularities in the appearance of these fibrillar structures in evolution remain almost unexplored. Using bioinformatics approaches and summarizing the data published previously, we have shown that amyloid fibrils performing similar functions in different organisms have been arising repeatedly and independently in the course of evolution. On the other hand, we show that the amyloid properties of a number of bacterial and eukaryotic proteins are evolutionarily conserved. We also discuss the role of protein-based inheritance in the evolution of microorganisms. Considering that missense mutations and the emergence of prions cause the same consequences, we propose the concept that the formation of prions, similarly to mutations, generally causes a negative effect, although it can also lead to adaptations in rare cases. In general, our analysis revealed certain patterns in the emergence and spread of amyloid fibrillar structures in the course of evolution.
Collapse
Affiliation(s)
- Alexey P Galkin
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, St. Petersburg, Russian Federation, 199034.
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation, 199034.
| | - Evgeniy I Sysoev
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, St. Petersburg, Russian Federation, 199034
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation, 199034
| | - Anna A Valina
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation, 199034
| |
Collapse
|
10
|
Yang J, Ding W, Zhu B, Zhen S, Kuang S, Yang J, Zhang C, Wang P, Yang F, Yang L, Yin W, Tanzi RE, Shen S, Ran C. Bioluminescence Imaging with Functional Amyloid Reservoirs in Alzheimer's Disease Models. Anal Chem 2023; 95:14261-14270. [PMID: 37712902 DOI: 10.1021/acs.analchem.3c02358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Bioluminescence imaging has changed the daily practice of preclinical research on cancer and other diseases over the last few decades; however, it has rarely been applied in preclinical research on Alzheimer's disease (AD). In this Article, we demonstrated that bioluminescence imaging could be used to report the levels of amyloid beta (Aβ) species in vivo. We hypothesized that AkaLumine, a newly discovered substrate for luciferase, could bind to Aβ aggregates and plaques. We further speculated that the Aβ aggregates/fibrils/plaques could be considered as "functional amyloids", which have a reservoir function to sequester and release AkaLumine to control the bioluminescence intensity, which could be used to report the levels of Aβs. Our hypotheses have been validated via in vitro solution tests, mimic studies with brain tissues and mice, two-photon imaging with AD mice, and in vivo bioluminescence imaging using transgenic AD mice that were virally transduced with AkaLuciferase (AkaLuc), a new luciferase that generates bioluminescence in the near-infrared window. As expected, compared to the control group, we observed that the Aβ group showed lower bioluminescence intensity due to AkaLumine sequestering at early time points, while higher intensity was due to AkaLumine releasing at later time points. Lastly, we demonstrated that this method could be used to monitor AD progression and the therapeutic effectiveness of avagacestat, a well-studied gamma-secretase inhibitor. Importantly, a good correlation (R2 = 0.81) was established between in vivo bioluminescence signals and Aβ burdens of the tested AD mice. We believe that our approach can be easily implemented into daily imaging experiments and has tremendous potential to change the daily practice of preclinical AD research.
Collapse
Affiliation(s)
- Jing Yang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Weihua Ding
- MGH Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Biyue Zhu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| | - Sherri Zhen
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Shi Kuang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| | - Jun Yang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| | - Can Zhang
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Peng Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Fan Yang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| | - Liuyue Yang
- MGH Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Wei Yin
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Shiqian Shen
- MGH Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| |
Collapse
|
11
|
Master NG, Markande AR. Importance of microbial amphiphiles: interaction potential of biosurfactants, amyloids, and other exo-polymeric-substances. World J Microbiol Biotechnol 2023; 39:320. [PMID: 37747579 DOI: 10.1007/s11274-023-03751-9] [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] [Received: 02/01/2023] [Accepted: 09/04/2023] [Indexed: 09/26/2023]
Abstract
Microorganisms produce a diverse group of biomolecules having amphipathic nature (amphiphiles). Microbial amphiphiles, including amyloids, bio-surfactants, and other exo-polymeric substances, play a crucial role in various biological processes and have gained significant attention recently. Although diverse in biochemical composition, these amphiphiles have been reported for common microbial traits like biofilm formation and pathogenicity due to their ability to act as surface active agents with active interfacial properties essential for microbes to grow in various niches. This enables microbes to reduce surface tension, emulsification, dispersion, and attachment at the interface. In this report, the ecological importance and biotechnological usage of important amphiphiles have been discussed. The low molecular weight amphiphiles like biosurfactants, siderophores, and peptides showing helical and antimicrobial activities have been extensively reported for their ability to work as quorum-sensing mediators. While high molecular weight amphiphiles make up amyloid fibers, exopolysaccharides, liposomes, or magnetosomes have been shown to have a significant influence in deciding microbial physiology and survival. In this report, we have discussed the functional similarities and biochemical variations of several amphipathic biomolecules produced by microbes, and the present report shows these amphiphiles showing polyphyletic and ecophysiological groups of microorganisms and hence can `be replaced in biotechnological applications depending on the compatibility of the processes.
Collapse
Affiliation(s)
- Nishita G Master
- Department of Biological Sciences, P.D. Patel Institute of Applied Sciences (PDPIAS), Charotar University of Science and Technology (CHARUSAT), Changa, Anand, Gujarat, 388421, India
| | - Anoop R Markande
- Department of Biological Sciences, P.D. Patel Institute of Applied Sciences (PDPIAS), Charotar University of Science and Technology (CHARUSAT), Changa, Anand, Gujarat, 388421, India.
| |
Collapse
|
12
|
Ma L, Jiang X, Huang Q, Chen W, Zhang H, Pei H, Cao Y, Wang H, Li H. Traditional Chinese medicine for the treatment of Alzheimer's disease: A focus on the microbiota-gut-brain axis. Biomed Pharmacother 2023; 165:115244. [PMID: 37516021 DOI: 10.1016/j.biopha.2023.115244] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/11/2023] [Accepted: 07/25/2023] [Indexed: 07/31/2023] Open
Abstract
Alzheimer's disease (AD), the most frequent cause of dementia, is a neurodegenerative disorder characterised by a progressive decline in cognitive function that is associated with the formation of amyloid beta plaques and neurofibrillary tangles. Gut microbiota comprises of a complex community of microorganisms residing in the gastrointestinal ecosystem. These microorganisms can participate in gut-brain axis activities, thereby affecting cognitive function and associated behaviours. Increasing evidence has indicated that gut dysbiosis can jeopardise host immune responses and promote inflammation, which may be an initiating factor for the onset and evolution of AD. Traditional Chinese medicine (TCM) is a promising resource which encompasses immense chemical diversity and multiple-target characteristics for the treatment of AD. Many TCMs regulate the gut microbiota during treatment of diseases, indicating that gut microbiota may be an important target for TCM efficacy. In this review, we summarised the role of the microbiota-gut-brain axis in the development of AD and the effects of TCM in treating AD by regulating the gut microbiota. We anticipate that this review will provide novel perspectives and strategies for future AD research and treatments.
Collapse
Affiliation(s)
- Lina Ma
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, PR China
| | - Xuefan Jiang
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, PR China
| | - Qiaoyi Huang
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, PR China
| | - Wenxuan Chen
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, PR China
| | - Huiqin Zhang
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, PR China
| | - Hui Pei
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, PR China
| | - Yu Cao
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, PR China
| | - Huichan Wang
- Institute of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, PR China
| | - Hao Li
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing 100102, PR China.
| |
Collapse
|
13
|
Shahpasand-Kroner H, Siddique I, Malik R, Linares GR, Ivanova MI, Ichida J, Weil T, Münch J, Sanchez-Garcia E, Klärner FG, Schrader T, Bitan G. Molecular Tweezers: Supramolecular Hosts with Broad-Spectrum Biological Applications. Pharmacol Rev 2023; 75:263-308. [PMID: 36549866 PMCID: PMC9976797 DOI: 10.1124/pharmrev.122.000654] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Lysine-selective molecular tweezers (MTs) are supramolecular host molecules displaying a remarkably broad spectrum of biologic activities. MTs act as inhibitors of the self-assembly and toxicity of amyloidogenic proteins using a unique mechanism. They destroy viral membranes and inhibit infection by enveloped viruses, such as HIV-1 and SARS-CoV-2, by mechanisms unrelated to their action on protein self-assembly. They also disrupt biofilm of Gram-positive bacteria. The efficacy and safety of MTs have been demonstrated in vitro, in cell culture, and in vivo, suggesting that these versatile compounds are attractive therapeutic candidates for various diseases, infections, and injuries. A lead compound called CLR01 has been shown to inhibit the aggregation of various amyloidogenic proteins, facilitate their clearance in vivo, prevent infection by multiple viruses, display potent anti-biofilm activity, and have a high safety margin in animal models. The inhibitory effect of CLR01 against amyloidogenic proteins is highly specific to abnormal self-assembly of amyloidogenic proteins with no disruption of normal mammalian biologic processes at the doses needed for inhibition. Therapeutic effects of CLR01 have been demonstrated in animal models of proteinopathies, lysosomal-storage diseases, and spinal-cord injury. Here we review the activity and mechanisms of action of these intriguing compounds and discuss future research directions. SIGNIFICANCE STATEMENT: Molecular tweezers are supramolecular host molecules with broad biological applications, including inhibition of abnormal protein aggregation, facilitation of lysosomal clearance of toxic aggregates, disruption of viral membranes, and interference of biofilm formation by Gram-positive bacteria. This review discusses the molecular and cellular mechanisms of action of the molecular tweezers, including the discovery of distinct mechanisms acting in vitro and in vivo, and the application of these compounds in multiple preclinical disease models.
Collapse
Affiliation(s)
- Hedieh Shahpasand-Kroner
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Ibrar Siddique
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Ravinder Malik
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Gabriel R Linares
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Magdalena I Ivanova
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Justin Ichida
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Tatjana Weil
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Jan Münch
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sanchez-Garcia
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Frank-Gerrit Klärner
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Thomas Schrader
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
14
|
Luo J, Chen J, Huang Y, You L, Dai Z. Engineering living materials by synthetic biology. BIOPHYSICS REVIEWS 2023; 4:011305. [PMID: 38505813 PMCID: PMC10903423 DOI: 10.1063/5.0115645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/18/2022] [Indexed: 03/21/2024]
Abstract
Natural biological materials are programmed by genetic information and able to self-organize, respond to environmental stimulus, and couple with inorganic matter. Inspired by the natural system and to mimic their complex and delicate fabrication process and functions, the field of engineered living materials emerges at the interface of synthetic biology and materials science. Here, we review the recent efforts and discuss the challenges and future opportunities.
Collapse
Affiliation(s)
- Jiren Luo
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiangfeng Chen
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yaoge Huang
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Zhuojun Dai
- Materials Synthetic Biology Center, CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
15
|
Pirhaghi M, Najarzadeh Z, Moosavi-Movahedi F, Shafizadeh M, Mamashli F, Atarod D, Ghasemi A, Morshedi D, Meratan AA, Otzen DE, Saboury AA. The anti-platelet drug ticlopidine inhibits FapC fibrillation and biofilm production: Highlighting its antibiotic activity. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140883. [PMID: 36455808 DOI: 10.1016/j.bbapap.2022.140883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
Multidrug resistance of bacteria and persistent infections related to biofilms, as well as the low availability of new antibacterial drugs, make it urgent to develop new antibiotics. Here, we evaluate the antibacterial and anti-biofilm properties of ticlopidine (TP), an anti-platelet aggregation drug, TP showed antibacterial activity against both gram-positive (MRSA) and gram-negative (E. coli, and P. aeruginosa) bacteria over a long treatment period. TP significantly reduced the survival of gram-negative bacteria in human blood though impact on gram-positives was more limited. TP may cause death in MRSA by inhibiting staphyloxanthin pigment synthesis, leading to oxidative stress, while scanning electron microscopy imaging indicate a loss of membrane integrity, damage, and consequent death due to lysis in gram-negative bacteria. TP showed good anti-biofilm activity against P. aeruginosa and MRSA, and a stronger biofilm degradation activity on P. aeruginosa compared to MRSA. Measuring fluorescence of the amyloid-reporter Thioflavin T (ThT) in biofilm implicated inhibition of amyloid formation as part of TP activity. This was confirmed by assays on the purified protein in P. aeruginosa, FapC, whose fibrillation kinetics was inhibited by TP. TP prolonged the lag phase of aggregation and reduced the subsequent growth rate and prolonging the lag phase to very long times provides ample opportunity to exert TP's antibacterial effect. We conclude that TP shows activity as an antibiotic against both gram-positive and gram-negative bacteria thanks to a broad range of activities, targeting bacterial metabolic processes, cellular structures and the biofilm matrix.
Collapse
Affiliation(s)
- Mitra Pirhaghi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Zahra Najarzadeh
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | | | - Mahshid Shafizadeh
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Fatemeh Mamashli
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Deyhim Atarod
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Dina Morshedi
- Department of Bioprocess Engineering, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Ali Akbar Meratan
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| |
Collapse
|
16
|
Wei W, Wang S, Xu C, Zhou X, Lian X, He L, Li K. Gut microbiota, pathogenic proteins and neurodegenerative diseases. Front Microbiol 2022; 13:959856. [PMID: 36466655 PMCID: PMC9715766 DOI: 10.3389/fmicb.2022.959856] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/07/2022] [Indexed: 12/20/2023] Open
Abstract
As the world's population ages, neurodegenerative diseases (NDs) have brought a great burden to the world. However, effective treatment measures have not been found to alleviate the occurrence and development of NDs. Abnormal accumulation of pathogenic proteins is an important cause of NDs. Therefore, effective inhibition of the accumulation of pathogenic proteins has become a priority. As the second brain of human, the gut plays an important role in regulate emotion and cognition functions. Recent studies have reported that the disturbance of gut microbiota (GM) is closely related to accumulation of pathogenic proteins in NDs. On the one hand, pathogenic proteins directly produced by GM are transmitted from the gut to the central center via vagus nerve. On the other hand, The harmful substances produced by GM enter the peripheral circulation through intestinal barrier and cause inflammation, or cross the blood-brain barrier into the central center to cause inflammation, and cytokines produced by the central center cause the production of pathogenic proteins. These pathogenic proteins can produced by the above two aspects can cause the activation of central microglia and further lead to NDs development. In addition, certain GM and metabolites have been shown to have neuroprotective effects. Therefore, modulating GM may be a potential clinical therapeutic approach for NDs. In this review, we summarized the possible mechanism of NDs caused by abnormal accumulation of pathogenic proteins mediated by GM to induce the activation of central microglia, cause central inflammation and explore the therapeutic potential of dietary therapy and fecal microbiota transplantation (FMT) in NDs.
Collapse
Affiliation(s)
- Wei Wei
- The Mental Hospital of Yunnan Province, Mental Health Center Affiliated to Kunming Medical University, Kunming, China
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Shixu Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Chongchong Xu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xuemei Zhou
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xinqing Lian
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Lin He
- The Mental Hospital of Yunnan Province, Mental Health Center Affiliated to Kunming Medical University, Kunming, China
| | - Kuan Li
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| |
Collapse
|
17
|
Yarawsky AE, Hopkins JB, Chatzimagas L, Hub JS, Herr AB. Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap. J Mol Biol 2022; 434:167708. [PMID: 35777467 PMCID: PMC9615840 DOI: 10.1016/j.jmb.2022.167708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/20/2022] [Accepted: 06/25/2022] [Indexed: 11/16/2022]
Abstract
Staphylococcus epidermidis is a commensal bacterium on human skin that is also the leading cause of medical device-related infections. The accumulation-associated protein (Aap) from S. epidermidis is a critical factor for infection via its ability to mediate biofilm formation. The B-repeat superdomain of Aap is composed of 5 to 17 Zn2+-binding B-repeats, which undergo rapid, reversible assembly to form dimer and tetramer species. The tetramer can then undergo a conformational change and nucleate highly stable functional amyloid fibrils. In this study, multiple techniques including analytical ultracentrifugation (AUC) and small-angle X-ray scattering (SAXS) are used to probe a panel of B-repeat mutant constructs that assemble to distinct oligomeric states to define the structural characteristics of B-repeat dimer and tetramer species. The B-repeat region from Aap forms an extremely elongated conformation that presents several challenges for standard SAXS analyses. Specialized approaches, such as cross-sectional analyses, allowed for in-depth interpretation of data, while explicit-solvent calculations via WAXSiS allowed for accurate evaluation of atomistic models. The resulting models suggest mechanisms by which Aap functional amyloid fibrils form, illuminating an important contributing factor to recurrent staphylococcal infections.
Collapse
Affiliation(s)
- Alexander E Yarawsky
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL, USA
| | - Leonie Chatzimagas
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Andrew B Herr
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| |
Collapse
|
18
|
Novel Antibiofilm Inhibitor Ginkgetin as an Antibacterial Synergist against Escherichia coli. Int J Mol Sci 2022; 23:ijms23158809. [PMID: 35955943 PMCID: PMC9369100 DOI: 10.3390/ijms23158809] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 11/27/2022] Open
Abstract
As an opportunistic pathogen, Escherichia coli (E. coli) forms biofilm that increases the virulence of bacteria and antibiotic resistance, posing a serious threat to human and animal health. Recently, ginkgetin (Gin) has been discovered to have antiinflammatory, antioxidant, and antitumor properties. In the present study, we evaluated the antibiofilm and antibacterial synergist of Gin against E. coli. Additionally, Alamar Blue assay combined with confocal laser scanning microscope (CLSM) and crystal violet (CV) staining was used to evaluate the effect of antibiofilm and antibacterial synergist against E. coli. Results showed that Gin reduces biofilm formation, exopolysaccharide (EPS) production, and motility against E. coli without limiting its growth and metabolic activity. Furthermore, we identified the inhibitory effect of Gin on AI-2 signaling molecule production, which showed apparent anti-quorum sensing (QS) properties. The qRT-PCR also indicated that Gin reduced the transcription of curli-related genes (csgA, csgD), flagella-formation genes (flhC, flhD, fliC, fliM), and QS-related genes (luxS, lsrB, lsrK, lsrR). Moreover, Gin showed obvious antibacterial synergism to overcome antibiotic resistance in E. coli with marketed antibiotics, including gentamicin, colistin B, and colistin E. These results suggested the potent antibiofilm and novel antibacterial synergist effect of Gin for treating E. coli infections.
Collapse
|
19
|
Siemer AB. What makes functional amyloids work? Crit Rev Biochem Mol Biol 2022; 57:399-411. [PMID: 35997712 PMCID: PMC9588633 DOI: 10.1080/10409238.2022.2113030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/29/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Although first described in the context of disease, cross-β (amyloid) fibrils have also been found as functional entities in all kingdoms of life. However, what are the specific properties of the cross-β fibril motif that convey biological function, make them especially suited for their particular purpose, and distinguish them from other fibrils found in biology? This review approaches these questions by arguing that cross-β fibrils are highly periodic, stable, and self-templating structures whose formation is accompanied by substantial conformational change that leads to a multimerization of their core and framing sequences. A discussion of each of these properties is followed by selected examples of functional cross-β fibrils that show how function is usually achieved by leveraging many of these properties.
Collapse
Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
20
|
Seira Curto J, Surroca Lopez A, Casals Sanchez M, Tic I, Fernandez Gallegos MR, Sanchez de Groot N. Microbiome Impact on Amyloidogenesis. Front Mol Biosci 2022; 9:926702. [PMID: 35782871 PMCID: PMC9245625 DOI: 10.3389/fmolb.2022.926702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Our life is closely linked to microorganisms, either through a parasitic or symbiotic relationship. The microbiome contains more than 1,000 different bacterial species and outnumbers human genes by 150 times. Worryingly, during the last 10 years, it has been observed a relationship between alterations in microbiota and neurodegeneration. Several publications support the hypothesis that amyloid structures formed by microorganisms may trigger host proteins aggregation. In this review, we collect pieces of evidence supporting that the crosstalk between human and microbiota amyloid proteins could be feasible and, probably, a more common event than expected before. The combination of their outnumbers, the long periods of time that stay in our bodies, and the widespread presence of amyloid proteins in the bacteria Domain outline a worrying scenario. However, the identification of the exact microorganisms and the mechanisms through with they can influence human disease also opens the door to developing a new and diverse set of therapeutic strategies.
Collapse
|
21
|
Huyer C, Modafferi D, Aminzare M, Ferraro J, Abdali Z, Roy S, Saldanha DJ, Wasim S, Alberti J, Feng S, Cicoira F, Dorval Courchesne NM. Fabrication of Curli Fiber-PEDOT:PSS Biomaterials with Tunable Self-Healing, Mechanical, and Electrical Properties. ACS Biomater Sci Eng 2022; 9:2156-2169. [PMID: 35687654 DOI: 10.1021/acsbiomaterials.1c01180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Poly(3,4-ethylenedioxythiophene) polystyrenesulfonate (PEDOT:PSS) is a highly conductive, easily processable, self-healing polymer. It has been shown to be useful in bioelectronic applications, for instance, as a biointerfacing layer for studying brain activity, in biosensitive transistors, and in wearable biosensors. A green and biofriendly method for improving the mechanical properties, biocompatibility, and stability of PEDOT:PSS involves mixing the polymer with a biopolymer. Via structural changes and interactions with PEDOT:PSS, biopolymers have the potential to improve the self-healing ability, flexibility, and electrical conductivity of the composite. In this work, we fabricated novel protein-polymer multifunctional composites by mixing PEDOT:PSS with genetically programmable amyloid curli fibers produced byEscherichia coli bacteria. Curli fibers are among the stiffest protein polymers and, once isolated from bacterial biofilms, can form plastic-like thin films that heal with the addition of water. Curli-PEDOT:PSS composites containing 60% curli fibers exhibited a conductivity 4.5-fold higher than that of pristine PEDOT:PSS. The curli fibers imbued the biocomposites with an immediate water-induced self-healing ability. Further, the addition of curli fibers lowered the Young's and shear moduli of the composites, improving their compatibility for tissue-interfacing applications. Lastly, we showed that genetically engineered fluorescent curli fibers retained their ability to fluoresce within curli-PEDOT:PSS composites. Curli fibers thus allow to modulate a range of properties in conductive PEDOT:PSS composites, broadening the applications of this polymer in biointerfaces and bioelectronics.
Collapse
Affiliation(s)
- Catrina Huyer
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada.,Department of Chemical Engineering, Polytechnique Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Daniel Modafferi
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Masoud Aminzare
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Juliana Ferraro
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Zahra Abdali
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Sophia Roy
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Dalia Jane Saldanha
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Saadia Wasim
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada
| | - Johan Alberti
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada.,Department of Chemical Engineering, Polytechnique Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Shurui Feng
- Department of Chemical Engineering, McGill University, Montreal, Quebec H3A 0C5, Canada.,Department of Chemical Engineering, Polytechnique Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Fabio Cicoira
- Department of Chemical Engineering, Polytechnique Montreal, Montreal, Quebec H3C 3J7, Canada
| | | |
Collapse
|
22
|
Bhoite SS, Han Y, Ruotolo BT, Chapman MR. Mechanistic insights into accelerated α-synuclein aggregation mediated by human microbiome-associated functional amyloids. J Biol Chem 2022; 298:102088. [PMID: 35654142 PMCID: PMC9253359 DOI: 10.1016/j.jbc.2022.102088] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 01/31/2023] Open
Abstract
The gut microbiome has been shown to have key implications in the pathogenesis of Parkinson's disease (PD). The Escherichia coli functional amyloid CsgA is known to accelerate α-synuclein aggregation in vitro and induce PD symptoms in mice. However, the mechanism governing CsgA-mediated acceleration of α-synuclein aggregation is unclear. Here, we show that CsgA can form stable homodimeric species that correlate with faster α-synuclein amyloid aggregation. Furthermore, we identify and characterize new CsgA homologs encoded by bacteria present in the human microbiome. These CsgA homologs display diverse aggregation kinetics, and they differ in their ability to modulate α-synuclein aggregation. Remarkably, we demonstrate that slowing down CsgA aggregation leads to an increased acceleration of α-synuclein aggregation, suggesting that the intrinsic amyloidogenicity of gut bacterial CsgA homologs affects their ability to accelerate α-synuclein aggregation. Finally, we identify a complex between CsgA and α-synuclein that functions as a platform to accelerate α-synuclein aggregation. Taken together, our work reveals complex interplay between bacterial amyloids and α-synuclein that better informs our understanding of PD causation.
Collapse
Affiliation(s)
- Sujeet S. Bhoite
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA,For correspondence: Matthew R. Chapman; Brandon T. Ruotolo
| | - Matthew R. Chapman
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA,For correspondence: Matthew R. Chapman; Brandon T. Ruotolo
| |
Collapse
|
23
|
Wiatrak B, Balon K, Jawień P, Bednarz D, Jęśkowiak I, Szeląg A. The Role of the Microbiota-Gut-Brain Axis in the Development of Alzheimer's Disease. Int J Mol Sci 2022; 23:ijms23094862. [PMID: 35563253 PMCID: PMC9104401 DOI: 10.3390/ijms23094862] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/16/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023] Open
Abstract
Along with the increase in life expectancy in the populations of developed and developing countries resulting from better access and improved health care, the number of patients with dementia, including Alzheimer’s disease (AD), is growing. The disease was first diagnosed and described at the beginning of the 20th century. However, to this day, there is no effective causal therapy, and symptomatic treatment often improves patients’ quality of life only for a short time. The current pharmacological therapies are based mainly on the oldest hypotheses of the disease—cholinergic (drugs affecting the cholinergic system are available), the hypothesis of amyloid-β aggregation (an anti-amyloid drug was conditionally approved by the FDA in 2020), and one drug is an N-methyl-D-aspartate receptor (NMDAR) antagonist (memantine). Hypotheses about AD pathogenesis focus on the nervous system and the brain. As research progresses, it has become known that AD can be caused by diseases that have been experienced over the course of a lifetime, which could also affect other organs. In this review, we focus on the potential association of AD with the digestive system, primarily the gut microbiota. The role of diet quality in preventing and alleviating Alzheimer’s disease is also discussed. The problem of neuroinflammation, which may be the result of microbiota disorders, is also described. An important aspect of the work is the chapter on the treatment strategies for changing the microbiota, potentially protecting against the disease and alleviating its course in the initial stages.
Collapse
Affiliation(s)
- Benita Wiatrak
- Department of Pharmacology, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (D.B.); (I.J.); (A.S.)
- Correspondence: (B.W.); (P.J.)
| | - Katarzyna Balon
- Laboratory of Genomics & Bioinformatics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland;
| | - Paulina Jawień
- Department of Biostructure and Animal Physiology, Wroclaw University of Environmental and Life Sciences, Norwida 25/27, 50-375 Wroclaw, Poland
- Correspondence: (B.W.); (P.J.)
| | - Dominika Bednarz
- Department of Pharmacology, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (D.B.); (I.J.); (A.S.)
| | - Izabela Jęśkowiak
- Department of Pharmacology, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (D.B.); (I.J.); (A.S.)
| | - Adam Szeląg
- Department of Pharmacology, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (D.B.); (I.J.); (A.S.)
| |
Collapse
|
24
|
Ibacache-Quiroga C, González-Pizarro K, Charifeh M, Canales C, Díaz-Viciedo R, Schmachtenberg O, Dinamarca MA. Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors. Foods 2022; 11:foods11070900. [PMID: 35406987 PMCID: PMC8997647 DOI: 10.3390/foods11070900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Kefir beverage is a probiotic food associated with health benefits, containing probiotic microorganisms and biomolecules produced during fermentation. The microbial composition of these beverages varies among countries, geographical regions, and the substrates, therefore, the characterization of kefir beverages is of great relevance in understanding their potential health-promoting and biotechnological applications. Therefore, this study presents the metagenomic and functional characterization of two Chilean kefir beverages, K02 and K03, through shotgun and amplicon-based metagenomic, microbiological, chemical, and biochemical studies. Results show that both beverages’ microbiota were mainly formed by Bacteria (>98%), while Eukarya represented less than 2%. Regarding Bacteria, the most abundant genera were Acetobacter (93.43% in K02 and 80.99% in K03) and Lactobacillus (5.72% in K02 and 16.75% in K03), while Kazachstania was the most abundant genus from Eukarya (42.55% and 36.08% in K02 and K03). Metagenomic analyses revealed metabolic pathways for lactose and casein assimilation, biosynthesis of health-promoting biomolecules, and clusters for antibiotic resistance, quorum sensing communication, and biofilm formation. Enzymatic activities, microbial β-amyloids, and short-chain fatty acids (acetic acid and propionic acid) were also detected in these beverages. Likewise, both kefir beverages inhibited biofilm formation of the opportunistic pathogen Pseudomonas aeruginosa.
Collapse
Affiliation(s)
- Claudia Ibacache-Quiroga
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Correspondence: (C.I.-Q.); (M.A.D.); Tel.: +56-322-508-440 (C.I.-Q.); +56-322-508-442 (M.A.D.)
| | - Karoll González-Pizarro
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
| | - Mariam Charifeh
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
| | - Christian Canales
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción 4080871, Chile;
| | - Rodrigo Díaz-Viciedo
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
| | - Oliver Schmachtenberg
- Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2360102, Chile;
- Centro Interdisciplinario de Neurociencias (CINV), Universidad de Valparaíso, Valparaíso 2381850, Chile
| | - M. Alejandro Dinamarca
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Correspondence: (C.I.-Q.); (M.A.D.); Tel.: +56-322-508-440 (C.I.-Q.); +56-322-508-442 (M.A.D.)
| |
Collapse
|
25
|
Abdali Z, Renner-Rao M, Chow A, Cai A, Harrington MJ, Dorval Courchesne NM. Extracellular Secretion and Simple Purification of Bacterial Collagen from Escherichia coli. Biomacromolecules 2022; 23:1557-1568. [PMID: 35258298 DOI: 10.1021/acs.biomac.1c01191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Because of structural similarities with type-I animal collagen, recombinant bacterial collagen-like proteins have been progressively used as a source of collagen for biomaterial applications. However, the intracellular expression combined with current costly and time-consuming chromatography methods for purification makes the large-scale production of recombinant bacterial collagen challenging. Here, we report the use of an adapted secretion pathway, used natively byEscherichia colito secrete curli fibers, for extracellular secretion of the bacterial collagen. We confirmed that a considerable fraction of expressed collagen (∼70%) is being secreted freely into the extracellular medium, with an initial purity of ∼50% in the crude culture supernatant. To simplify the purification of extracellular collagen, we avoided cell lysis and used cross-flow filtration or acid precipitation to concentrate the voluminous supernatant and separate the collagen from impurities. We confirmed that the secreted collagen forms triple helical structures, using Sirius Red staining and circular dichroism. We also detected collagen biomarkers via Raman spectroscopy, further supporting that the recombinant collagen forms a stable triple helical conformation. We further studied the effect of the isolation methods on the morphology and secondary structure, concluding that the final collagen structure is process-dependent. Overall, we show that the curli secretion system can be adapted for extracellular secretion of the bacterial collagen, eliminating the need for cell lysis, which simplifies the collagen isolation process and enables a simple cost-effective method with potential for scale-up.
Collapse
Affiliation(s)
- Zahra Abdali
- Department of Chemical Engineering, McGill University, Montreal H3A 0C5, Quebec, Canada
| | - Max Renner-Rao
- Department of Chemistry, McGill University, Montreal H3A 0C5, Quebec, Canada
| | - Amy Chow
- Department of Chemical Engineering, McGill University, Montreal H3A 0C5, Quebec, Canada
| | - Anqi Cai
- Department of Chemical Engineering, McGill University, Montreal H3A 0C5, Quebec, Canada
| | | | | |
Collapse
|
26
|
Hassan MN, Nabi F, Khan AN, Hussain M, Siddiqui WA, Uversky VN, Khan RH. The amyloid state of proteins: A boon or bane? Int J Biol Macromol 2022; 200:593-617. [PMID: 35074333 DOI: 10.1016/j.ijbiomac.2022.01.115] [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] [Received: 12/13/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/05/2022]
Abstract
Proteins and their aggregation is significant field of research due to their association with various conformational maladies including well-known neurodegenerative diseases like Alzheimer's (AD), Parkinson's (PD), and Huntington's (HD) diseases. Amyloids despite being given negative role for decades are also believed to play a functional role in bacteria to humans. In this review, we discuss both facets of amyloid. We have shed light on AD, which is one of the most common age-related neurodegenerative disease caused by accumulation of Aβ fibrils as extracellular senile plagues. We also discuss PD caused by the aggregation and deposition of α-synuclein in form of Lewy bodies and neurites. Other amyloid-associated diseases such as HD and amyotrophic lateral sclerosis (ALS) are also discussed. We have also reviewed functional amyloids that have various biological roles in both prokaryotes and eukaryotes that includes formation of biofilm and cell attachment in bacteria to hormone storage in humans, We discuss in detail the role of Curli fibrils' in biofilm formation, chaplins in cell attachment to peptide hormones, and Pre-Melansomal Protein (PMEL) roles. The disease-related and functional amyloids are compared with regard to their structural integrity, variation in regulation, and speed of forming aggregates and elucidate how amyloids have turned from foe to friend.
Collapse
Affiliation(s)
- Md Nadir Hassan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Murtaza Hussain
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Waseem A Siddiqui
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 10 Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy 11 of Sciences", Pushchino, Moscow Region 142290, Russia; Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College 13 of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
| |
Collapse
|
27
|
Wollanke B, Gerhards H, Ackermann K. Infectious Uveitis in Horses and New Insights in Its Leptospiral Biofilm-Related Pathogenesis. Microorganisms 2022; 10:387. [PMID: 35208842 PMCID: PMC8875353 DOI: 10.3390/microorganisms10020387] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/17/2022] Open
Abstract
Uveitis is a sight-threatening eye disease in equids known worldwide that leads to considerable pain and suffering. By far the most common type of uveitis in Germany and neighboring countries is classical equine recurrent uveitis (ERU), which is caused by chronic intraocular leptospiral infection and is the main cause of infectious uveitis in horses. Other infectious causes are extremely rare and are usually clinically distinguishable from ERU. ERU can be treated very effectively by vitreous cavity lavage (vitrectomy). For proper indications of this demanding surgery, it is necessary to differentiate ERU from other types of uveitis in which vitrectomy is not helpful. This can be conducted on the basis of anamnesis in combination with ophthalmologic findings and by aqueous humor examination. During vitrectomy, vitreous material is obtained. These vitreous samples have historically been used for numerous etiologic studies. In this way, a chronic intraocular leptospiral infection has been shown to be the cause of typical ERU and, among other findings, ERU has also been recognized as a biofilm infection, providing new insights into the pathogenesis of ERU and explaining some thus far unexplainable phenomena of ERU. ERU may not only have transmissible aspects to some types of uveitis in humans but may also serve as a model for a spontaneously occurring biofilm infection. Vitreous material obtained during therapeutically indicated vitrectomy can be used for further studies on in vivo biofilm formation, biofilm composition and possible therapeutic approaches.
Collapse
Affiliation(s)
- Bettina Wollanke
- Equine Clinic, Ludwig-Maximilians-University, 80539 Munich, Germany; (H.G.); (K.A.)
| | | | | |
Collapse
|
28
|
Li Z, Wang X, Wang J, Yuan X, Jiang X, Wang Y, Zhong C, Xu D, Gu T, Wang F. Bacterial biofilms as platforms engineered for diverse applications. Biotechnol Adv 2022; 57:107932. [DOI: 10.1016/j.biotechadv.2022.107932] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 12/23/2022]
|
29
|
Pan Q, Guo F, Huang Y, Li A, Chen S, Chen J, Liu HF, Pan Q. Gut Microbiota Dysbiosis in Systemic Lupus Erythematosus: Novel Insights into Mechanisms and Promising Therapeutic Strategies. Front Immunol 2021; 12:799788. [PMID: 34925385 PMCID: PMC8677698 DOI: 10.3389/fimmu.2021.799788] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that was traditionally thought to be closely related to genetic and environmental risk factors. Although treatment options for SLE with hormones, immunosuppressants, and biologic drugs are now available, the rates of clinical response and functional remission of these drugs are still not satisfactory. Currently, emerging evidence suggests that gut microbiota dysbiosis may play crucial roles in the occurrence and development of SLE, and manipulation of targeting the gut microbiota holds great promises for the successful treatment of SLE. The possible mechanisms of gut microbiota dysbiosis in SLE have not yet been well identified to date, although they may include molecular mimicry, impaired intestinal barrier function and leaky gut, bacterial biofilms, intestinal specific pathogen infection, gender bias, intestinal epithelial cells autophagy, and extracellular vesicles and microRNAs. Potential therapies for modulating gut microbiota in SLE include oral antibiotic therapy, fecal microbiota transplantation, glucocorticoid therapy, regulation of intestinal epithelial cells autophagy, extracellular vesicle-derived miRNA therapy, mesenchymal stem cell therapy, and vaccination. This review summarizes novel insights into the mechanisms of microbiota dysbiosis in SLE and promising therapeutic strategies, which may help improve our understanding of the pathogenesis of SLE and provide novel therapies for SLE.
Collapse
Affiliation(s)
- Quanren Pan
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Fengbiao Guo
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yanyan Huang
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Aifen Li
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Shuxian Chen
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jiaxuan Chen
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Hua-Feng Liu
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Qingjun Pan
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| |
Collapse
|
30
|
Chen Y, Cui G, Cui Y, Chen D, Lin H. Small molecule targeting amyloid fibrils inhibits Streptococcus mutans biofilm formation. AMB Express 2021; 11:171. [PMID: 34919191 PMCID: PMC8683520 DOI: 10.1186/s13568-021-01333-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/11/2021] [Indexed: 11/10/2022] Open
Abstract
Amyloid fibrils are important scaffold in bacterial biofilms. Streptococcus mutans is an established cariogenic bacteria dwelling within biofilms, and C123 segment of P1 protein is known to form amyloid fibrils in S. mutans biofilms, among which C3 segment could serve as a promising anti-amyloid target due to its critical role in C123-P1 interactions. Recently, small molecules have been found to successfully inhibit biofilms by targeting amyloid fibrils. Thus, our study aimed to screen small molecules targeting C3 segment with the capacity to influence amyloid fibrils and S. mutans biofilms. In silico screening was utilized to discover promising small molecules, which were evaluated for their effects on bacterial cells and amyloid fibrils. We selected 99 small molecules and enrolled 55 small molecules named D1-D55 for crystal violet staining. Notably, D25 selectively inhibit S. mutans biofilms but had no significant influence on biofilms formed by Streptococcus gordonii and Streptococcus sanguinis, and D25 showed no bactericidal effects and low cytotoxicity. In addition, amyloid fibrils in free-floating bacteria, biofilms and purified C123 were quantified with ThT assays, and the differences were not statistically significant in the presence or absence of D25. Morphological changes of amyloid fibrils were visualized with TEM images, where amorphous aggregates were obvious coupled with long and atypical amyloid fibrils. Moreover, amyloid-related genes were upregulated in response to D25. In conclusion, D25 is a promising antimicrobial agent with the capacity to influence amyloid fibrils and inhibit S. mutans biofilms.
Collapse
Affiliation(s)
- Yuanyuan Chen
- Department of Preventive Dentistry, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Guxin Cui
- Department of Preventive Dentistry, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Yuqi Cui
- Department of Preventive Dentistry, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Dongru Chen
- Department of Orthodontics, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Huancai Lin
- Department of Preventive Dentistry, Hospital of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, Guangdong China
| |
Collapse
|
31
|
Liu Y, Zhang Y, Sun Y, Ding F. A buried glutamate in the cross-β core renders β-endorphin fibrils reversible. NANOSCALE 2021; 13:19593-19603. [PMID: 34812835 PMCID: PMC8674924 DOI: 10.1039/d1nr05679d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Functional amyloids are abundant in living organisms from prokaryotes to eukaryotes playing diverse biological roles. In contrast to the irreversible aggregation of most known pathological amyloids, we postulate that naturally-occurring functional amyloids are reversible under evolutionary pressure to be able to modulate the fibrillization process, reuse the composite peptides, or perform their biological functions. β-Endorphin, an endogenous opioid peptide hormone, forms such kinds of reversible amyloid fibrils in secretory granules for efficient storage and returns to the functional state of monomers upon release into the blood. The environmental change between low pH in secretory granules and neutral pH in extracellular spaces is believed to drive the reversible fibrillization of β-endorphin. Here, we investigate the critical role of a buried glutamate, Glu8, in the pH-responsive disassembly of β-endorphin fibrils using all-atom molecular dynamics simulations along with structure-based pKa prediction. The fibril was stable at pH 5.5 or lower with all the buried Glu8 residues protonated and neutrally charged. After switching to neutral pH, the Glu8 residues of peptides at the outer layers of the ordered fibrils became deprotonated due to partial solvent exposure, causing sheet-to-coil conformational changes and subsequent exposure of adjacent Glu8 residues in the inner chains. Via iterative deprotonation of Glu8 and induced structural disruption, all Glu8 residues would be progressively deprotonated. Electrostatic repulsion between deprotonated Glu8 residues along with their high solvation tendency disrupted the hydrogen bonding between the β1 strands and increased the solvent exposure of those otherwise buried residues in the cross-β core. Overall, our computational study reveals that the strategic positioning of ionizable residues into the cross-β core is a potential approach for designing reversible amyloid fibrils as pH-responsive smart bio-nanomaterials.
Collapse
Affiliation(s)
- Yuying Liu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yu Zhang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.
| |
Collapse
|
32
|
Evstigneeva SS, Telesheva EM, Mokeev DI, Borisov IV, Petrova LP, Shelud’ko AV. Response of Bacteria to Mechanical Stimuli. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Abstract—
Bacteria adapt rapidly to changes in ambient conditions, constantly inspecting their surroundings by means of their sensor systems. These systems are often thought to respond only to signals of a chemical nature. Yet, bacteria are often affected by mechanical forces, e.g., during transition from planktonic to sessile state. Mechanical stimuli, however, have seldom been considered as the signals bacteria can sense and respond to. Nonetheless, bacteria perceive mechanical stimuli, generate signals, and develop responses. This review analyzes the information on the way bacteria respond to mechanical stimuli and outlines how bacteria convert incoming signals into appropriate responses.
Collapse
|
33
|
Liu M, Han P, Zhang L, Zhong C, You C. Biofilm-Mediated Immobilization of a Multienzyme Complex for Accelerating Inositol Production from Starch. Bioconjug Chem 2021; 32:2032-2042. [PMID: 34469136 DOI: 10.1021/acs.bioconjchem.1c00338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Bacterial biofilm, as a natural and renewable material, is a promising architecture for enzyme immobilization. In this study, we have demonstrated the feasibility of an Escherichia coli biofilm to immobilize a self-assembly multienzyme complex by the covalent interaction between a peptide SpyTag and its protein partner SpyCatcher. The SpyTag-labeled biofilm is displayed on the surface of E. coli by overexpressing the recombinant CsgA-SpyTag, in which CsgA is capable of forming biofilms. This SpyTag bearing biofilm is used to bind with SpyCatcher bearing synthetic mini-scaffoldin, which also contains a carbohydrate-binding module 3 (CBM3), and four different cohesins from different microorganisms. CBM3 was used to bind with cellulose, while the four different cohesins were used to recruit four dockerin-containing cascade enzymes, which were subsequently applied to convert starch to myo-inositol. Compared to the free enzyme mixture, the biofilm-immobilized enzyme complex exhibited a 4.28 times increase in initial reaction rate in producing myo-inositol from 10 g/L maltodextrin (a derivative of starch). Additionally, this biofilm-immobilized enzyme complex showed much higher recycle ability than the enzyme complex which was immobilized on a regenerated amorphous cellulose (RAC) system. In conclusion, the biofilm-mediated immobilization of the enzymatic biosystem provides a promising strategy to increase the reaction rate and enhance the stability of an in vitro enzymatic biosystem, exhibiting high potential to improve the efficiency of an in vitro biosystem.
Collapse
Affiliation(s)
- Meixia Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Pingping Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lingling Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chao Zhong
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chun You
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.,Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin, 300308, China
| |
Collapse
|
34
|
The Way forward for the Origin of Life: Prions and Prion-Like Molecules First Hypothesis. Life (Basel) 2021; 11:life11090872. [PMID: 34575021 PMCID: PMC8467930 DOI: 10.3390/life11090872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/11/2021] [Accepted: 08/22/2021] [Indexed: 11/18/2022] Open
Abstract
In this paper the hypothesis that prions and prion-like molecules could have initiated the chemical evolutionary process which led to the eventual emergence of life is reappraised. The prions first hypothesis is a specific application of the protein-first hypothesis which asserts that protein-based chemical evolution preceded the evolution of genetic encoding processes. This genetics-first hypothesis asserts that an “RNA-world era” came before protein-based chemical evolution and rests on a singular premise that molecules such as RNA, acetyl-CoA, and NAD are relics of a long line of chemical evolutionary processes preceding the Last Universal Common Ancestor (LUCA). Nevertheless, we assert that prions and prion-like molecules may also be relics of chemical evolutionary processes preceding LUCA. To support this assertion is the observation that prions and prion-like molecules are involved in a plethora of activities in contemporary biology in both complex (eukaryotes) and primitive life forms. Furthermore, a literature survey reveals that small RNA virus genomes harbor information about prions (and amyloids). If, as has been presumed by proponents of the genetics-first hypotheses, small viruses were present during an RNA world era and were involved in some of the earliest evolutionary processes, this places prions and prion-like molecules potentially at the heart of the chemical evolutionary process whose eventual outcome was life. We deliberate on the case for prions and prion-like molecules as the frontier molecules at the dawn of evolution of living systems.
Collapse
|
35
|
Lipke PN, Mathelié-Guinlet M, Viljoen A, Dufrêne YF. A New Function for Amyloid-Like Interactions: Cross-Beta Aggregates of Adhesins form Cell-to-Cell Bonds. Pathogens 2021; 10:pathogens10081013. [PMID: 34451476 PMCID: PMC8398270 DOI: 10.3390/pathogens10081013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 12/30/2022] Open
Abstract
Amyloid structures assemble through a repeating type of bonding called "cross-β", in which identical sequences in many protein molecules form β-sheets that interdigitate through side chain interactions. We review the structural characteristics of such bonds. Single cell force microscopy (SCFM) shows that yeast expressing Als5 adhesin from Candida albicans demonstrate the empirical characteristics of cross-β interactions. These properties include affinity for amyloid-binding dyes, birefringence, critical concentration dependence, repeating structure, and inhibition by anti-amyloid agents. We present a model for how cross-β bonds form in trans between two adhering cells. These characteristics also apply to other fungal adhesins, so the mechanism appears to be an example of a new type of cell-cell adhesion.
Collapse
Affiliation(s)
- Peter N. Lipke
- Biology Department, Brooklyn College of City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Correspondence: ; Tel.: +1-(917)-696-4862
| | - Marion Mathelié-Guinlet
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium; (M.M.-G.); (A.V.); (Y.F.D.)
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium; (M.M.-G.); (A.V.); (Y.F.D.)
| | - Yves F. Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium; (M.M.-G.); (A.V.); (Y.F.D.)
| |
Collapse
|
36
|
Takács K, Grolmusz V. On the border of the amyloidogenic sequences: prefix analysis of the parallel beta sheets in the PDB_Amyloid collection. J Integr Bioinform 2021; 19:jib-2020-0043. [PMID: 34303324 PMCID: PMC9069647 DOI: 10.1515/jib-2020-0043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/28/2021] [Indexed: 01/04/2023] Open
Abstract
The Protein Data Bank (PDB) today contains more than 174,000 entries with the 3-dimensional structures of biological macromolecules. Using the rich resources of this repository, it is possible identifying subsets with specific, interesting properties for different applications. Our research group prepared an automatically updated list of amyloid- and probably amyloidogenic molecules, the PDB_Amyloid collection, which is freely available at the address http://pitgroup.org/amyloid. This resource applies exclusively the geometric properties of the steric structures for identifying amyloids. In the present contribution, we analyze the starting (i.e., prefix) subsequences of the characteristic, parallel beta-sheets of the structures in the PDB_Amyloid collection, and identify further appearances of these length-5 prefix subsequences in the whole PDB data set. We have identified this way numerous proteins, whose normal or irregular functions involve amyloid formation, structural misfolding, or anti-coagulant properties, simply by containing these prefixes: including the T-cell receptor (TCR), bound with the major histocompatibility complexes MHC-1 and MHC-2; the p53 tumor suppressor protein; a mycobacterial RNA polymerase transcription initialization complex; the human bridging integrator protein BIN-1; and the tick anti-coagulant peptide TAP.
Collapse
Affiliation(s)
- Kristóf Takács
- PIT Bioinformatics Group, Eötvös University, BudapestH-1117, Hungary
| | - Vince Grolmusz
- PIT Bioinformatics Group, Eötvös University, BudapestH-1117, Hungary.,Uratim Ltd., BudapestH-1118, Hungary
| |
Collapse
|
37
|
Exploiting pilus-mediated bacteria-host interactions for health benefits. Mol Aspects Med 2021; 81:100998. [PMID: 34294411 DOI: 10.1016/j.mam.2021.100998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/30/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023]
Abstract
Surface pili (or fimbriae) are an important but conspicuous adaptation of several genera and species of Gram-negative and Gram-positive bacteria. These long and non-flagellar multi-subunit adhesins mediate the initial contact that a bacterium has with a host or environment, and thus have come to be regarded as a key colonization factor for virulence activity in pathogens or niche adaptation in commensals. Pili in pathogenic bacteria are well recognized for their roles in the adhesion to host cells, colonization of tissues, and establishment of infection. As an 'anti-adhesive' ploy, targeting pilus-mediated attachment for disruption has become a potentially effective alternative to using antibiotics. In this review, we give a description of the several structurally distinct bacterial pilus types thus far characterized, and as well offer details about the intricacy of their individual structure, assembly, and function. With a molecular understanding of pilus biogenesis and pilus-mediated host interactions also provided, we go on to describe some of the emerging new approaches and compounds that have been recently developed to prevent the adhesion, colonization, and infection of piliated bacterial pathogens.
Collapse
|
38
|
Masrati G, Landau M, Ben-Tal N, Lupas A, Kosloff M, Kosinski J. Integrative Structural Biology in the Era of Accurate Structure Prediction. J Mol Biol 2021; 433:167127. [PMID: 34224746 DOI: 10.1016/j.jmb.2021.167127] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022]
Abstract
Characterizing the three-dimensional structure of macromolecules is central to understanding their function. Traditionally, structures of proteins and their complexes have been determined using experimental techniques such as X-ray crystallography, NMR, or cryo-electron microscopy-applied individually or in an integrative manner. Meanwhile, however, computational methods for protein structure prediction have been improving their accuracy, gradually, then suddenly, with the breakthrough advance by AlphaFold2, whose models of monomeric proteins are often as accurate as experimental structures. This breakthrough foreshadows a new era of computational methods that can build accurate models for most monomeric proteins. Here, we envision how such accurate modeling methods can combine with experimental structural biology techniques, enhancing integrative structural biology. We highlight the challenges that arise when considering multiple structural conformations, protein complexes, and polymorphic assemblies. These challenges will motivate further developments, both in modeling programs and in methods to solve experimental structures, towards better and quicker investigation of structure-function relationships.
Collapse
Affiliation(s)
- Gal Masrati
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Andrei Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Mickey Kosloff
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838 Haifa, Israel.
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Hamburg 22607, Germany; Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| |
Collapse
|
39
|
Matilla-Cuenca L, Toledo-Arana A, Valle J. Anti-Biofilm Molecules Targeting Functional Amyloids. Antibiotics (Basel) 2021; 10:antibiotics10070795. [PMID: 34210036 PMCID: PMC8300730 DOI: 10.3390/antibiotics10070795] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
The choice of an effective therapeutic strategy in the treatment of biofilm-related infections is a significant issue. Amyloids, which have been historically related to human diseases, are now considered to be prevailing structural components of the biofilm matrix in a wide range of bacteria. This assumption creates the potential for an exciting research area, in which functional amyloids are considered to be attractive targets for drug development to dissemble biofilm structures. The present review describes the best-characterized bacterial functional amyloids and focuses on anti-biofilm agents that target intrinsic and facultative amyloids. This study provides a better understanding of the different modes of actions of the anti-amyloid molecules to inhibit biofilm formation. This information can be further exploited to improve the therapeutic strategies to combat biofilm-related infections.
Collapse
|
40
|
Overstreet AMC, Grayson BE, Boger A, Bakke D, Carmody EM, Bales CE, Paski SC, Murphy SF, Dethlefs CR, Shannon KJ, Adlaka KR, Wolford CE, Campiti VJ, Raghunandan CV, Seeley RJ, Boone DL. Gastrokine-1, an anti-amyloidogenic protein secreted by the stomach, regulates diet-induced obesity. Sci Rep 2021; 11:9477. [PMID: 33947892 PMCID: PMC8096951 DOI: 10.1038/s41598-021-88928-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/19/2021] [Indexed: 12/27/2022] Open
Abstract
Obesity and its sequelae have a major impact on human health. The stomach contributes to obesity in ways that extend beyond its role in digestion, including through effects on the microbiome. Gastrokine-1 (GKN1) is an anti-amyloidogenic protein abundantly and specifically secreted into the stomach lumen. We examined whether GKN1 plays a role in the development of obesity and regulation of the gut microbiome. Gkn1-/- mice were resistant to diet-induced obesity and hepatic steatosis (high fat diet (HFD) fat mass (g) = 10.4 ± 3.0 (WT) versus 2.9 ± 2.3 (Gkn1-/-) p < 0.005; HFD liver mass (g) = 1.3 ± 0.11 (WT) versus 1.1 ± 0.07 (Gkn1-/-) p < 0.05). Gkn1-/- mice also exhibited increased expression of the lipid-regulating hormone ANGPTL4 in the small bowel. The microbiome of Gkn1-/- mice exhibited reduced populations of microbes implicated in obesity, namely Firmicutes of the class Erysipelotrichia. Altered metabolism consistent with use of fat as an energy source was evident in Gkn1-/- mice during the sleep period. GKN1 may contribute to the effects of the stomach on the microbiome and obesity. Inhibition of GKN1 may be a means to prevent obesity.
Collapse
Affiliation(s)
- Anne-Marie C Overstreet
- Department of Microbiology and Immunology, Indiana University School of Medicine-South Bend, RCH122, 1234 N. Notre Dame Ave., South Bend, IN, 46617, USA
| | - Bernadette E Grayson
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
- Department of Neurobiology and Anatomical Sciences, University of Mississippi Medical Center, Jackson, MS, USA
| | - Antonia Boger
- Department of Microbiology and Immunology, Indiana University School of Medicine-South Bend, RCH122, 1234 N. Notre Dame Ave., South Bend, IN, 46617, USA
| | - Danika Bakke
- Department of Microbiology and Immunology, Indiana University School of Medicine-South Bend, RCH122, 1234 N. Notre Dame Ave., South Bend, IN, 46617, USA
| | - Erin M Carmody
- Department of Biology, University of Notre Dame, South Bend, IN, USA
| | - Cayla E Bales
- Department of Biology, University of Notre Dame, South Bend, IN, USA
| | | | - Stephen F Murphy
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Kara J Shannon
- Department of Biology, University of Notre Dame, South Bend, IN, USA
| | - Katie R Adlaka
- Department of Biology, University of Notre Dame, South Bend, IN, USA
| | - Claire E Wolford
- Department of Biology, University of Notre Dame, South Bend, IN, USA
| | - Vincent J Campiti
- Department of Microbiology and Immunology, Indiana University School of Medicine-South Bend, RCH122, 1234 N. Notre Dame Ave., South Bend, IN, 46617, USA
| | - Christina V Raghunandan
- Department of Microbiology and Immunology, Indiana University School of Medicine-South Bend, RCH122, 1234 N. Notre Dame Ave., South Bend, IN, 46617, USA
| | - Randy J Seeley
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
- Department of Surgery, University of Michigan Health System, Ann Arbor, MI, USA
| | - David L Boone
- Department of Microbiology and Immunology, Indiana University School of Medicine-South Bend, RCH122, 1234 N. Notre Dame Ave., South Bend, IN, 46617, USA.
- Department of Biology, University of Notre Dame, South Bend, IN, USA.
| |
Collapse
|
41
|
Gilbert C, Tang TC, Ott W, Dorr BA, Shaw WM, Sun GL, Lu TK, Ellis T. Living materials with programmable functionalities grown from engineered microbial co-cultures. NATURE MATERIALS 2021; 20:691-700. [PMID: 33432140 DOI: 10.1038/s41563-020-00857-5] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/14/2020] [Indexed: 05/14/2023]
Abstract
Biological systems assemble living materials that are autonomously patterned, can self-repair and can sense and respond to their environment. The field of engineered living materials aims to create novel materials with properties similar to those of natural biomaterials using genetically engineered organisms. Here, we describe an approach to fabricating functional bacterial cellulose-based living materials using a stable co-culture of Saccharomyces cerevisiae yeast and bacterial cellulose-producing Komagataeibacter rhaeticus bacteria. Yeast strains can be engineered to secrete enzymes into bacterial cellulose, generating autonomously grown catalytic materials and enabling DNA-encoded modification of bacterial cellulose bulk properties. Alternatively, engineered yeast can be incorporated within the growing cellulose matrix, creating living materials that can sense and respond to chemical and optical stimuli. This symbiotic culture of bacteria and yeast is a flexible platform for the production of bacterial cellulose-based engineered living materials with potential applications in biosensing and biocatalysis.
Collapse
Affiliation(s)
- Charlie Gilbert
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Tzu-Chieh Tang
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Mediated Matter Group, Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wolfgang Ott
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Brandon A Dorr
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William M Shaw
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - George L Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Timothy K Lu
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
- Department of Bioengineering, Imperial College London, London, UK.
| |
Collapse
|
42
|
Huang Y, Liao J, Liu X, Zhong Y, Cai X, Long L. Review: The Role of Intestinal Dysbiosis in Parkinson's Disease. Front Cell Infect Microbiol 2021; 11:615075. [PMID: 33968794 PMCID: PMC8100321 DOI: 10.3389/fcimb.2021.615075] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
Several studies have highlighted the roles played by the gut microbiome in central nervous system diseases. Clinical symptoms and neuropathology have suggested that Parkinson’s disease may originate in the gut, which is home to approximately 100 trillion microbes. Alterations in the gastrointestinal microbiota populations may promote the development and progression of Parkinson’s disease. Here, we reviewed existing studies that have explored the role of intestinal dysbiosis in Parkinson’s disease, focusing on the roles of microbiota, their metabolites, and components in inflammation, barrier failure, microglial activation, and α-synuclein pathology. We conclude that there are intestinal dysbiosis in Parkinson’s disease. Intestinal dysbiosis is likely involved in the pathogenesis of Parkinson’s disease through mechanisms that include barrier destruction, inflammation and oxidative stress, decreased dopamine production, and molecular mimicry. Additional studies remain necessary to explore and verify the mechanisms through which dysbiosis may cause or promote Parkinson’s disease. Preclinical studies have shown that gastrointestinal microbial therapy may represent an effective and novel treatment for Parkinson’s disease; however, more studies, especially clinical studies, are necessary to explore the curative effects of microbial therapy in Parkinson’s disease.
Collapse
Affiliation(s)
- Yiying Huang
- Department of Neurology, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jinchi Liao
- Department of Neurology, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xu Liu
- Department of Neurology, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yunxiao Zhong
- Department of Neurology, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaodong Cai
- Department of Neurology, Sixth Affiliated Hospital, Sun Yat-Sen University (Guangdong Gastrointestinal and Anal Hospital), Guangzhou, China
| | - Ling Long
- Department of Neurology, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| |
Collapse
|
43
|
Malishev R, Salinas N, Gibson J, Eden AB, Mieres-Perez J, Ruiz-Blanco YB, Malka O, Kolusheva S, Klärner FG, Schrader T, Sanchez-Garcia E, Wang C, Landau M, Bitan G, Jelinek R. Inhibition of Staphylococcus aureus biofilm-forming functional amyloid by molecular tweezers. Cell Chem Biol 2021; 28:1310-1320.e5. [PMID: 33852903 DOI: 10.1016/j.chembiol.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/19/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023]
Abstract
Biofilms are rigid and largely impenetrable three-dimensional matrices constituting virulence determinants of various pathogenic bacteria. Here, we demonstrate that molecular tweezers, unique supramolecular artificial receptors, modulate biofilm formation of Staphylococcus aureus. In particular, the tweezers affect the structural and assembly properties of phenol-soluble modulin α1 (PSMα1), a biofilm-scaffolding functional amyloid peptide secreted by S. aureus. The data reveal that CLR01, a diphosphate tweezer, exhibits significant S. aureus biofilm inhibition and disrupts PSMα1 self-assembly and fibrillation, likely through inclusion of lysine side chains of the peptide. In comparison, different peptide binding occurs in the case of CLR05, a tweezer containing methylenecarboxylate units, which exhibits lower affinity for the lysine residues yet disrupts S. aureus biofilm more strongly than CLR01. Our study points to a possible role for molecular tweezers as potent biofilm inhibitors and antibacterial agents, particularly against untreatable biofilm-forming and PSM-producing bacteria, such as methicillin-resistant S. aureus.
Collapse
Affiliation(s)
- Ravit Malishev
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Nir Salinas
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - James Gibson
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Angela Bailey Eden
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Orit Malka
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | | | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Elsa Sanchez-Garcia
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), 22607 Hamburg, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Raz Jelinek
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel.
| |
Collapse
|
44
|
Michiels E, Liu S, Gallardo R, Louros N, Mathelié-Guinlet M, Dufrêne Y, Schymkowitz J, Vorberg I, Rousseau F. Entropic Bristles Tune the Seeding Efficiency of Prion-Nucleating Fragments. Cell Rep 2021; 30:2834-2845.e3. [PMID: 32101755 PMCID: PMC7043027 DOI: 10.1016/j.celrep.2020.01.098] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/07/2020] [Accepted: 01/28/2020] [Indexed: 01/04/2023] Open
Abstract
Prions of lower eukaryotes are self-templating protein aggregates with cores formed by parallel in-register beta strands. Short aggregation-prone glutamine (Q)- and asparagine (N)-rich regions embedded in longer disordered domains have been proposed to act as nucleation sites that initiate refolding of soluble prion proteins into highly ordered fibrils, termed amyloid. We demonstrate that a short Q/N-rich peptide corresponding to a proposed nucleation site in the prototype Saccharomyces cerevisiae prion protein Sup35 is sufficient to induce infectious cytosolic prions in mouse neuroblastoma cells ectopically expressing the soluble Sup35 NM prion domain. Embedding this nucleating core in a non-native N-rich sequence that does not form amyloid but acts as an entropic bristle quadruples seeding efficiency. Our data suggest that large disordered sequences flanking an aggregation core in prion proteins act as not only solubilizers of the monomeric protein but also breakers of the formed amyloid fibrils, enhancing infectivity of the prion seeds. A short peptide derived from Sup35 (p103–113) forms rigid amyloid fibrils p103–113 fibrils can induce infectious Sup35 NM prions in mammalian cells Embedding p103–113 in an N-rich sequence increases fibril brittleness Increased fibril brittleness enhances prion-inducing capacity
Collapse
Affiliation(s)
- Emiel Michiels
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, 3000 Leuven, Belgium
| | - Shu Liu
- German Center for Neurodegenerative Diseases Bonn (DZNE e.V.), Venusberg-Campus 1, Building 99, 53127 Bonn, Germany
| | - Rodrigo Gallardo
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, 3000 Leuven, Belgium
| | - Nikolaos Louros
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, 3000 Leuven, Belgium
| | - Marion Mathelié-Guinlet
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.06, 1348 Louvain-la-Neuve, Belgium
| | - Yves Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du Sud, 4-5, bte L7.07.06, 1348 Louvain-la-Neuve, Belgium; Walloon Excellence in Life Sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
| | - Joost Schymkowitz
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, 3000 Leuven, Belgium.
| | - Ina Vorberg
- German Center for Neurodegenerative Diseases Bonn (DZNE e.V.), Venusberg-Campus 1, Building 99, 53127 Bonn, Germany; Rheinische Friedrich-Wilhelms-Universität Bonn, Siegmund-Freud-Str. 25, 53127 Bonn, Germany.
| | - Frederic Rousseau
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KULeuven, 3000 Leuven, Belgium.
| |
Collapse
|
45
|
Jakubovics NS, Goodman SD, Mashburn-Warren L, Stafford GP, Cieplik F. The dental plaque biofilm matrix. Periodontol 2000 2021; 86:32-56. [PMID: 33690911 PMCID: PMC9413593 DOI: 10.1111/prd.12361] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Steven D Goodman
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Lauren Mashburn-Warren
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Graham P Stafford
- Integrated Biosciences, School of Clinical Dentistry, University of Sheffield, Sheffield, UK
| | - Fabian Cieplik
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| |
Collapse
|
46
|
Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Amyloid and Amyloid-Like Aggregates: Diversity and the Term Crisis. BIOCHEMISTRY (MOSCOW) 2021; 85:1011-1034. [PMID: 33050849 DOI: 10.1134/s0006297920090035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Active accumulation of the data on new amyloids continuing nowadays dissolves boundaries of the term "amyloid". Currently, it is most often used to designate aggregates with cross-β structure. At the same time, amyloids also exhibit a number of other unusual properties, such as: detergent and protease resistance, interaction with specific dyes, and ability to induce transition of some proteins from a soluble form to an aggregated one. The same features have been also demonstrated for the aggregates lacking cross-β structure, which are commonly called "amyloid-like" and combined into one group, although they are very diverse. We have collected and systematized information on the properties of more than two hundred known amyloids and amyloid-like proteins with emphasis on conflicting examples. In particular, a number of proteins in membraneless organelles form aggregates with cross-β structure that are morphologically indistinguishable from the other amyloids, but they can be dissolved in the presence of detergents, which is not typical for amyloids. Such paradoxes signify the need to clarify the existing definition of the term amyloid. On the other hand, the demonstrated structural diversity of the amyloid-like aggregates shows the necessity of their classification.
Collapse
Affiliation(s)
- A B Matiiv
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - N P Trubitsina
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - A G Matveenko
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Y A Barbitoff
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Bioinformatics Institute, St. Petersburg, 197342, Russia
| | - G A Zhouravleva
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - S A Bondarev
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia. .,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| |
Collapse
|
47
|
Kurbasic M, Parisi E, Garcia AM, Marchesan S. Self-Assembling, Ultrashort Peptide Gels as Antimicrobial Biomaterials. Curr Top Med Chem 2021; 20:1300-1309. [PMID: 32178611 DOI: 10.2174/1568026620666200316150221] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/09/2020] [Accepted: 02/17/2020] [Indexed: 12/25/2022]
Abstract
Supramolecular antimicrobial hydrogels based on peptides are attractive soft materials for the treatment of infections, considering their ease of preparation and benign fate in biological settings and in the environment. In particular, stimuli-responsive systems that can be assembled/disassembled ad hoc could offer the opportunity to switch on/off their bioactivity as needed. Besides, the shorter is the peptide, the lower its cost of production. However, a structure-to-function relationship is yet to be defined and reported activities are generally not yet competitive relative to traditional antibiotics. Inspiration for their design can be found in host defense peptides (HDPs), which can self-assemble to exert their function. This article reviews research developments in this emerging area, and it examines features, differences and similarities between antimicrobial and amyloid peptides to open the avenue towards the next generation of supramolecular antimicrobial peptides as innovative therapeutic materials.
Collapse
Affiliation(s)
- Marina Kurbasic
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Evelina Parisi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Ana M Garcia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Silvia Marchesan
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| |
Collapse
|
48
|
Hou Q, Keren-Paz A, Korenblum E, Oved R, Malitsky S, Kolodkin-Gal I. Weaponizing volatiles to inhibit competitor biofilms from a distance. NPJ Biofilms Microbiomes 2021; 7:2. [PMID: 33402677 PMCID: PMC7785731 DOI: 10.1038/s41522-020-00174-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/19/2020] [Indexed: 01/29/2023] Open
Abstract
The soil bacterium Bacillus subtilis forms beneficial biofilms that induce plant defences and prevent the growth of pathogens. It is naturally found in the rhizosphere, where microorganisms coexist in an extremely competitive environment, and thus have evolved a diverse arsenal of defence mechanisms. In this work, we found that volatile compounds produced by B. subtilis biofilms inhibited the development of competing biofilm colonies, by reducing extracellular matrix gene expression, both within and across species. This effect was dose-dependent, with the structural defects becoming more pronounced as the number of volatile-producing colonies increased. This inhibition was mostly mediated by organic volatiles, and we identified the active molecules as 3-methyl-1-butanol and 1-butanol. Similar results were obtained with biofilms formed by phylogenetically distinct bacterium sharing the same niche, Escherichia coli, which produced the biofilm-inhibiting 3-methyl-1-butanol and 2-nonanon. The ability of established biofilms to inhibit the development and spreading of new biofilms from afar might be a general mechanism utilized by bacterial biofilms to protect an occupied niche from the invasion of competing bacteria.
Collapse
Affiliation(s)
- Qihui Hou
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alona Keren-Paz
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Elisa Korenblum
- grid.13992.300000 0004 0604 7563Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rela Oved
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- grid.13992.300000 0004 0604 7563Metabolic Profiling Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
49
|
Abdali Z, Aminzare M, Zhu X, DeBenedictis E, Xie O, Keten S, Dorval Courchesne NM. Curli-Mediated Self-Assembly of a Fibrous Protein Scaffold for Hydroxyapatite Mineralization. ACS Synth Biol 2020; 9:3334-3343. [PMID: 33237760 DOI: 10.1021/acssynbio.0c00415] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nanostructures formed by self-assembled peptides have been increasingly exploited as functional materials for a wide variety of applications, from biotechnology to energy. However, it is sometimes challenging to assemble free short peptides into functional supramolecular structures, since not all peptides have the ability to self-assemble. Here, we report a self-assembly mechanism for short functional peptides that we derived from a class of fiber-forming amyloid proteins called curli. CsgA, the major subunit of curli fibers, is a self-assembling β-helical subunit composed of five pseudorepeats (R1-R5). We first deleted the internal repeats (R2, R3, R4), known to be less essential for the aggregation of CsgA monomers into fibers, forming a truncated CsgA variant (R1/R5). As a proof-of-concept to introduce functionality in the fibers, we then genetically substituted the internal repeats by a hydroxyapatite (HAP)-binding peptide, resulting in a R1/HAP/R5 construct. Our method thus utilizes the R1/R5-driven self-assembly mechanism to assemble the HAP-binding peptide and form hydrogel-like materials in macroscopic quantities suitable for biomineralization. We confirmed the expression and fibrillar morphology of the truncated and HAP-containing curli-like amyloid fibers. X-ray diffraction and TEM showed the functionality of the HAP-binding peptide for mineralization and formation of nanocrystalline HAP. Overall, we show that fusion to the R1 and R5 repeats of CsgA enables the self-assembly of functional peptides into micron long fibers. Further, the mineral-templating ability that the R1/HAP/R5 fibers possesses opens up broader applications for curli proteins in the tissue engineering and biomaterials fields.
Collapse
Affiliation(s)
- Zahra Abdali
- Department of Chemical Engineering, McGill University, Montréal, Québec H3A 0C5, Canada
| | - Masoud Aminzare
- Department of Chemical Engineering, McGill University, Montréal, Québec H3A 0C5, Canada
| | - Xiaodan Zhu
- Department of Chemical Engineering, McGill University, Montréal, Québec H3A 0C5, Canada
| | - Elizabeth DeBenedictis
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States of America
| | - Oliver Xie
- Department of Chemical Engineering, McGill University, Montréal, Québec H3A 0C5, Canada
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States of America
| | | |
Collapse
|
50
|
Chen P, Ding F, Cai R, Javed I, Yang W, Zhang Z, Li Y, Davis TP, Ke PC, Chen C. Amyloidosis Inhibition, a New Frontier of the Protein Corona. NANO TODAY 2020; 35:100937. [PMID: 32728376 PMCID: PMC7388636 DOI: 10.1016/j.nantod.2020.100937] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The protein corona has served as a central dogma and a nuisance to the applications of nanomedicine and nanobiotechnology for well over a decade. Here we introduce the emerging field of amyloidosis inhibition, which aims to understand and harness the interfacial phenomena associated with a nanoparticle interacting with pathogenic amyloid proteins. Much of this interaction correlates with our understanding of the protein corona, and yet much differs, as elaborated for the first time in this Perspective. Specifically, we examine the in vitro, in silico and in vivo features of the new class of "amyloid protein corona", and discuss how the interactions with nanoparticles may halt the self-assembly of amyloid proteins. As amyloidosis is driven off pathway by the nanoparticles, the oligomeric and protofibrillar populations are suppressed to ameliorate their cytotoxicity. Furthermore, as amyloid proteins spread via the transport of bodily fluids or cross seeding, amyloidosis is inherently associated with dynamic proteins and ligands to evoke the immune system. Accordingly, we ponder the structural and medical implications of the amyloid protein corona in the presence of their stimulated cytokines. Understanding and exploiting the amyloid protein corona may facilitate the development of new theranostics against a range of debilitating amyloid diseases.
Collapse
Affiliation(s)
- Pengyu Chen
- Materials Research and Education Center, Auburn University, Auburn, AL 36849, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Rong Cai
- CAS Center for Excellence in Nanoscience and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
- Research Unit of Nanoscience and Technology, Chinese Academy of Medical Sciences, Beijing 100039, China
| | - Ibrahim Javed
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Wen Yang
- Materials Research and Education Center, Auburn University, Auburn, AL 36849, United States
| | - Zhenzhen Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yuhuan Li
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, China
| | - Thomas P. Davis
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Pu Chun Ke
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, China
| | - Chunying Chen
- CAS Center for Excellence in Nanoscience and CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
- Research Unit of Nanoscience and Technology, Chinese Academy of Medical Sciences, Beijing 100039, China
| |
Collapse
|