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Fernández-Calvet A, Matilla-Cuenca L, Izco M, Navarro S, Serrano M, Ventura S, Blesa J, Herráiz M, Alkorta-Aranburu G, Galera S, Ruiz de Los Mozos I, Mansego ML, Toledo-Arana A, Alvarez-Erviti L, Valle J. Gut microbiota produces biofilm-associated amyloids with potential for neurodegeneration. Nat Commun 2024; 15:4150. [PMID: 38755164 PMCID: PMC11099085 DOI: 10.1038/s41467-024-48309-x] [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: 11/06/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
Age-related neurodegenerative diseases involving amyloid aggregation remain one of the biggest challenges of modern medicine. Alterations in the gastrointestinal microbiome play an active role in the aetiology of neurological disorders. Here, we dissect the amyloidogenic properties of biofilm-associated proteins (BAPs) of the gut microbiota and their implications for synucleinopathies. We demonstrate that BAPs are naturally assembled as amyloid-like fibrils in insoluble fractions isolated from the human gut microbiota. We show that BAP genes are part of the accessory genomes, revealing microbiome variability. Remarkably, the abundance of certain BAP genes in the gut microbiome is correlated with Parkinson's disease (PD) incidence. Using cultured dopaminergic neurons and Caenorhabditis elegans models, we report that BAP-derived amyloids induce α-synuclein aggregation. Our results show that the chaperone-mediated autophagy is compromised by BAP amyloids. Indeed, inoculation of BAP fibrils into the brains of wild-type mice promote key pathological features of PD. Therefore, our findings establish the use of BAP amyloids as potential targets and biomarkers of α-synucleinopathies.
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Affiliation(s)
- Ariadna Fernández-Calvet
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - Leticia Matilla-Cuenca
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - María Izco
- Laboratory of Molecular Neurobiology, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Miriam Serrano
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Javier Blesa
- HM CINAC (Centro Integral de Neurociencias Abarca Campal), Hospital Universitario HM Puerta del Sur, HM Hospitales, Madrid, Spain
- Instituto de Investigación Sanitaria, HM Hospitales, Madrid, Spain
| | - Maite Herráiz
- Department of Gastroenterology, Clínica Universitaria and Medical School, University of Navarra, Navarra, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Gorka Alkorta-Aranburu
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
- CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Sergio Galera
- Department of Personalized Medicine, NASERTIC, Government of Navarra, Pamplona, Spain
| | | | - María Luisa Mansego
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Alejandro Toledo-Arana
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - Lydia Alvarez-Erviti
- Laboratory of Molecular Neurobiology, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - Jaione Valle
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain.
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2
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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.
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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.
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3
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Böhning J, Tarafder AK, Bharat TA. The role of filamentous matrix molecules in shaping the architecture and emergent properties of bacterial biofilms. Biochem J 2024; 481:245-263. [PMID: 38358118 PMCID: PMC10903470 DOI: 10.1042/bcj20210301] [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: 09/18/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Numerous bacteria naturally occur within spatially organised, multicellular communities called biofilms. Moreover, most bacterial infections proceed with biofilm formation, posing major challenges to human health. Within biofilms, bacterial cells are embedded in a primarily self-produced extracellular matrix, which is a defining feature of all biofilms. The biofilm matrix is a complex, viscous mixture primarily composed of polymeric substances such as polysaccharides, filamentous protein fibres, and extracellular DNA. The structured arrangement of the matrix bestows bacteria with beneficial emergent properties that are not displayed by planktonic cells, conferring protection against physical and chemical stresses, including antibiotic treatment. However, a lack of multi-scale information at the molecular level has prevented a better understanding of this matrix and its properties. Here, we review recent progress on the molecular characterisation of filamentous biofilm matrix components and their three-dimensional spatial organisation within biofilms.
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Affiliation(s)
- Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Abul K. Tarafder
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Tanmay A.M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
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4
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Marijan D, Momchilova EA, Burns D, Chandhok S, Zapf R, Wille H, Potoyan DA, Audas TE. Protein thermal sensing regulates physiological amyloid aggregation. Nat Commun 2024; 15:1222. [PMID: 38336721 PMCID: PMC10858206 DOI: 10.1038/s41467-024-45536-0] [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: 05/24/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
To survive, cells must respond to changing environmental conditions. One way that eukaryotic cells react to harsh stimuli is by forming physiological, RNA-seeded subnuclear condensates, termed amyloid bodies (A-bodies). The molecular constituents of A-bodies induced by different stressors vary significantly, suggesting this pathway can tailor the cellular response by selectively aggregating a subset of proteins under a given condition. Here, we identify critical structural elements that regulate heat shock-specific amyloid aggregation. Our data demonstrates that manipulating structural pockets in constituent proteins can either induce or restrict their A-body targeting at elevated temperatures. We propose a model where selective aggregation within A-bodies is mediated by the thermal stability of a protein, with temperature-sensitive structural regions acting as an intrinsic form of post-translational regulation. This system would provide cells with a rapid and stress-specific response mechanism, to tightly control physiological amyloid aggregation or other cellular stress response pathways.
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Affiliation(s)
- Dane Marijan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Evgenia A Momchilova
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Daniel Burns
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Sahil Chandhok
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Richard Zapf
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, T6G 2M8, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Davit A Potoyan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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Kolodkin-Gal I, Parsek MR, Patrauchan MA. The roles of calcium signaling and calcium deposition in microbial multicellularity. Trends Microbiol 2023; 31:1225-1237. [PMID: 37429751 PMCID: PMC10772221 DOI: 10.1016/j.tim.2023.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/12/2023]
Abstract
Calcium signaling is an essential mediator of signal-controlling gene expression in most developmental systems. In addition, calcium has established extracellular functions as a structural component of biogenic minerals found in complex tissues. In bacteria, the formation of calcium carbonate structures is associated with complex colony morphology. Genes promoting the formation of biogenic minerals are essential for proper biofilm development and protection against antimicrobial solutes and toxins. Here we review recent findings on the role of calcium and calcium signaling as emerging regulators of biofilm formation in beneficial bacteria, as well as essential mediators of biofilm formation and virulence in human pathogens. The presented analysis concludes that the new understanding of calcium signaling may help to improve the performance of beneficial strains for sustainable agriculture, microbiome manipulation, and sustainable construction. Unraveling the roles of calcium may also promote the development of novel therapies against biofilm infections that target calcium uptake, calcium sensors, and calcium carbonate deposition.
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Affiliation(s)
- Ilana Kolodkin-Gal
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA, USA.
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
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6
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Guo Y, Mao Z, Ran F, Sun J, Zhang J, Chai G, Wang J. Nanotechnology-Based Drug Delivery Systems to Control Bacterial-Biofilm-Associated Lung Infections. Pharmaceutics 2023; 15:2582. [PMID: 38004561 PMCID: PMC10674810 DOI: 10.3390/pharmaceutics15112582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 11/26/2023] Open
Abstract
Airway mucus dysfunction and impaired immunological defenses are hallmarks of several lung diseases, including asthma, cystic fibrosis, and chronic obstructive pulmonary diseases, and are mostly causative factors in bacterial-biofilm-associated respiratory tract infections. Bacteria residing within the biofilm architecture pose a complex challenge in clinical settings due to their increased tolerance to currently available antibiotics and host immune responses, resulting in chronic infections with high recalcitrance and high rates of morbidity and mortality. To address these unmet clinical needs, potential anti-biofilm therapeutic strategies are being developed to effectively control bacterial biofilm. This review focuses on recent advances in the development and application of nanoparticulate drug delivery systems for the treatment of biofilm-associated respiratory tract infections, especially addressing the respiratory barriers of concern for biofilm accessibility and the various types of nanoparticles used to combat biofilms. Understanding the obstacles facing pulmonary drug delivery to bacterial biofilms and nanoparticle-based approaches to combatting biofilm may encourage researchers to explore promising treatment modalities for bacterial-biofilm-associated chronic lung infections.
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Affiliation(s)
- Yutong Guo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zeyuan Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Fang Ran
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jihong Sun
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Jingfeng Zhang
- The Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo 315000, China
| | - Guihong Chai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jian Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
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7
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Qin M, Li Y, Xu W, Gao W, Yin S, Hu X, Zhang R, Ding C. Spirooxindol alkaloids from Voacanga africana: Targeting biofilm of MBLs producing Escherichia coli. Bioorg Chem 2023; 140:106780. [PMID: 37579620 DOI: 10.1016/j.bioorg.2023.106780] [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: 06/10/2023] [Revised: 07/30/2023] [Accepted: 08/07/2023] [Indexed: 08/16/2023]
Abstract
Seven rarely spirooxindole alkaloids, voagafricines A-G (1-7) were isolated from the stem barks of Voacanga africana. Their structures were unambiguously elucidated by comprehensive spectroscopic data and electronic circular dichroism (ECD) analyses. 1 and 2 possess a unique indoleone system in conjugation with a 3,4'-decahydroquinoline spiral ring originating from seco-quinolhiddin core of the precursor, furthermore 1 undergo decarburization formed a novel C-3-nor monoterpenoid indole. All isolates were evaluated for their antibacterial activities against MBLs producing Escherichia coli strains. Compounds 1 and 7 were found to be potent inhibitors against E. coli 298 and 140 by targeting biofilm. Possible interaction sites of 1 and 7 with biofilm were preliminarily explored by means of molecular docking.
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Affiliation(s)
- Malong Qin
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Yupeng Li
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Wei Xu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Wen Gao
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Shanze Yin
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Xianguang Hu
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Rongping Zhang
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Resources, Yunnan University of Chinese Medicine, Kunming 650500, China.
| | - Caifeng Ding
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China.
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8
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Abd El-Hamid MI, El-Tarabili RM, Bahnass MM, Alshahrani MA, Saif A, Alwutayd KM, Safhi FA, Mansour AT, Alblwi NAN, Ghoneim MM, Elmaaty AA, Al-harthi HF, Bendary MM. Partnering essential oils with antibiotics: proven therapies against bovine Staphylococcus aureus mastitis. Front Cell Infect Microbiol 2023; 13:1265027. [PMID: 37790910 PMCID: PMC10542579 DOI: 10.3389/fcimb.2023.1265027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction There is an urgent need to develop therapeutic options for biofilm-producing Staphylococcus aureus (S. aureus). Therefore, the renewed interest in essential oils (EOs), especially carvacrol, linalool and eugenol, has attracted the attention of our research group. Methods Multidrug resistance and multivirulence profiles in addition to biofilm production of S. aureus strains isolated from cows with mastitis were evaluated using both phenotypic and genotypic methods. The antimicrobial and antibiofilm activities of EOs were tested using both in vitro and molecular docking studies. Moreover, the interactions between commonly used antibiotics and the tested EOs were detected using the checkerboard method. Results We found that all our isolates (n= 37) were biofilm methicillin resistant S. aureus (MRSA) producers and 40.5% were vancomycin resistant S. aureus (VRSA). Unfortunately, 73 and 43.2% of the recovered MRSA isolates showed multidrug resistant (MDR) and multivirulence patterns, respectively. The antimicrobial activities of the tested EOs matched with the phenotypic evaluation of the antibiofilm activities and molecular docking studies. Linalool showed the highest antimicrobial and antibiofilm activities, followed by carvacrol and eugenol EOs. Fortunately, synergistic interactions between the investigated EOs and methicillin or vancomycin were detected with fractional inhibitory concentration index (FICI) values ≤ 0.5. Moreover, the antimicrobial resistance patterns of 13 isolates changed to sensitive phenotypes after treatment with any of the investigated EOs. Treatment failure of bovine mastitis with resistant S. aureus can be avoided by combining the investigated EOs with available antimicrobial drugs. Conclusion We hope that our findings can be translated into a formulation of new pharmaceutical dosage forms against biofilm-producing S. aureus pathogens.
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Affiliation(s)
- Marwa I. Abd El-Hamid
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Reham M. El-Tarabili
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Mosa M. Bahnass
- Department of Animal Medicine (Infectious Diseases), Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
- Department of Clinical Laboratory Sciences, Applied Medical Sciences College, Najran University, Najran, Saudi Arabia
| | | | - Ahmed Saif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Khairiah Mubarak Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Abdallah Tageldein Mansour
- Animal and Fish Production Department, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
- Fish and Animal Production Department, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
| | | | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, Al Maarefa University, Riyadh, Saudi Arabia
| | - Ayman Abo Elmaaty
- Medicinal Chemistry Department, Faculty of Pharmacy, Port Said University, Port Said, Egypt
| | - Helal F. Al-harthi
- Biology Department, Turabah University College, Taif University, Taif, Saudi Arabia
| | - Mahmoud M. Bendary
- Department of Microbiology and Immunology, Faculty of Pharmacy, Port Said University, Port Said, Egypt
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9
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Collins MJ, Tomares DT, Nandana V, Schrader JM, Childers WS. RNase E biomolecular condensates stimulate PNPase activity. Sci Rep 2023; 13:12937. [PMID: 37558691 PMCID: PMC10412687 DOI: 10.1038/s41598-023-39565-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Bacterial Ribonucleoprotein bodies (BR-bodies) play an essential role in organizing RNA degradation via phase separation in the cytoplasm of bacteria. BR-bodies mediate multi-step mRNA decay through the concerted activity of the endoribonuclease RNase E coupled with the 3'-5' exoribonuclease Polynucleotide Phosphorylase (PNPase). In vivo, studies indicated that the loss of PNPase recruitment into BR-bodies led to a significant build-up of RNA decay intermediates in Caulobacter crescentus. However, it remained unclear whether this is due to a lack of colocalized PNPase and RNase E within BR-bodies or whether PNPase's activity is stimulated within the BR-body. We reconstituted RNase E's C-terminal domain with PNPase towards a minimal BR-body in vitro to distinguish these possibilities. We found that PNPase's catalytic activity is accelerated when colocalized within the RNase E biomolecular condensates, partly due to scaffolding and mass action effects. In contrast, disruption of the RNase E-PNPase protein-protein interaction led to a loss of PNPase recruitment into the RNase E condensates and a loss of ribonuclease rate enhancement. We also found that RNase E's unique biomolecular condensate environment tuned PNPase's substrate specificity for poly(A) over poly(U). Intriguingly, a critical PNPase reactant, phosphate, reduces RNase E phase separation both in vitro and in vivo. This regulatory feedback ensures that under limited phosphate resources, PNPase activity is enhanced by recruitment into RNase E's biomolecular condensates.
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Affiliation(s)
- Michael J Collins
- Department of Chemistry, University of Pittsburgh, Pittsburgh, 15260, USA
| | - Dylan T Tomares
- Department of Chemistry, University of Pittsburgh, Pittsburgh, 15260, USA
| | - Vidhyadhar Nandana
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, 15260, USA.
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10
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Buchanan JA, Varghese NR, Johnston CL, Sunde M. Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality. J Mol Biol 2023; 435:167919. [PMID: 37330295 DOI: 10.1016/j.jmb.2022.167919] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.
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Affiliation(s)
- Jessica A Buchanan
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Nikhil R Varghese
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Caitlin L Johnston
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
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11
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The Pga59 cell wall protein is an amyloid forming protein involved in adhesion and biofilm establishment in the pathogenic yeast Candida albicans. NPJ Biofilms Microbiomes 2023; 9:6. [PMID: 36697414 PMCID: PMC9877000 DOI: 10.1038/s41522-023-00371-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
The human commensal fungus Candida albicans can attach to epithelia or indwelling medical devices and form biofilms, that are highly tolerant to antifungal drugs and can evade the immune response. The cell surface protein Pga59 has been shown to influence adhesion and biofilm formation. Here, we present evidence that Pga59 displays amyloid properties. Using electron microscopy, staining with an amyloid fibre-specific dye and X-ray diffraction experiments, we showed that the predicted amyloid-forming region of Pga59 is sufficient to build up an amyloid fibre in vitro and that recombinant Pga59 can also adopt a cross-β amyloid fibre architecture. Further, mutations impairing Pga59 amyloid assembly led to diminished adhesion to substrates and reduced biofilm production. Immunogold labelling on amyloid structures extracted from C. albicans revealed that Pga59 is used by the fungal cell to assemble amyloids within the cell wall in response to adhesion. Altogether, our results suggest that Pga59 amyloid properties are used by the fungal cell to mediate cell-substrate interactions and biofilm formation.
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12
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Ravichandran S, Avatapalli S, Narasimhan Y, Kaushik KS, Yennamalli RM. 'Targeting' the search: An upgraded structural and functional repository of antimicrobial peptides for biofilm studies (B-AMP v2.0) with a focus on biofilm protein targets. Front Cell Infect Microbiol 2022; 12:1020391. [PMID: 36329825 PMCID: PMC9623296 DOI: 10.3389/fcimb.2022.1020391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/16/2022] [Indexed: 12/29/2022] Open
Abstract
Bacterial biofilms, often as multispecies communities, are recalcitrant to conventional antibiotics, making the treatment of biofilm infections a challenge. There is a push towards developing novel anti-biofilm approaches, such as antimicrobial peptides (AMPs), with activity against specific biofilm targets. In previous work, we developed Biofilm-AMP, a structural and functional repository of AMPs for biofilm studies (B-AMP v1.0) with more than 5000 structural models of AMPs and a vast library of AMP annotations to existing biofilm literature. In this study, we present an upgraded version of B-AMP, with a focus on existing and novel bacterial biofilm targets. B-AMP v2.0 hosts a curated collection of 2502 biofilm protein targets across 473 bacterial species, with structural protein models and functional annotations from PDB, UniProt, and PubMed databases. The biofilm targets can be searched for using the name of the source organism, and function and type of protein, and results include designated Target IDs (unique to B-AMP v2.0), UniProt IDs, 3D predicted protein structures, PDBQT files, pre-defined protein functions, and relevant scientific literature. To present an example of the combined applicability of both, the AMP and biofilm target libraries in the repository, we present two case studies. In the first case study, we expand an in silico pipeline to evaluate AMPs against a single biofilm target in the multidrug resistant, bacterial pathogen Corynebacterium striatum, using 3D protein-peptide docking models from previous work and Molecular Dynamics simulations (~1.2µs). In the second case study, we build an in silico pipeline to identify candidate AMPs (using AMPs with both anti-Gram positive and anti-Gram negative activity) against two biofilm targets with a common functional annotation in Pseudomonas aeruginosa and Staphylococcus aureus, widely-encountered bacterial co-pathogens. With its enhanced structural and functional capabilities, B-AMP v2.0 serves as a comprehensive resource for AMP investigations related to biofilm studies. B-AMP v2.0 is freely available at https://b-amp.karishmakaushiklab.com and will be regularly updated with structural models of AMPs and biofilm targets, as well as 3D protein-peptide interaction models for key biofilm-forming pathogens.
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Affiliation(s)
- Shashank Ravichandran
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | | | - Yatindrapravanan Narasimhan
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Karishma S. Kaushik
- Department of Biotechnology, Savitribai Phule Pune University, Pune, India,*Correspondence: Karishma S. Kaushik, ; Ragothaman M. Yennamalli,
| | - Ragothaman M. Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India,*Correspondence: Karishma S. Kaushik, ; Ragothaman M. Yennamalli,
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Amyloidogenic Peptides: New Class of Antimicrobial Peptides with the Novel Mechanism of Activity. Int J Mol Sci 2022; 23:ijms23105463. [PMID: 35628272 PMCID: PMC9140876 DOI: 10.3390/ijms23105463] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic-resistant bacteria are recognized as one of the leading causes of death in the world. We proposed and successfully tested peptides with a new mechanism of antimicrobial action “protein silencing” based on directed co-aggregation. The amyloidogenic antimicrobial peptide (AAMP) interacts with the target protein of model or pathogenic bacteria and forms aggregates, thereby knocking out the protein from its working condition. In this review, we consider antimicrobial effects of the designed peptides on two model organisms, E. coli and T. thermophilus, and two pathogenic organisms, P. aeruginosa and S. aureus. We compare the amino acid composition of proteomes and especially S1 ribosomal proteins. Since this protein is inherent only in bacterial cells, it is a good target for studying the process of co-aggregation. This review presents a bioinformatics analysis of these proteins. We sum up all the peptides predicted as amyloidogenic by several programs and synthesized by us. For the four organisms we studied, we show how amyloidogenicity correlates with antibacterial properties. Let us especially dwell on peptides that have demonstrated themselves as AMPs for two pathogenic organisms that cause dangerous hospital infections, and in which the minimal inhibitory concentration (MIC) turned out to be comparable to the MIC of gentamicin sulfate. All this makes our study encouraging for the further development of AAMP. The hybrid peptides may thus provide a starting point for the antibacterial application of amyloidogenic peptides.
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Song P, Zhang J, Li Y, Liu G, Li N. Solution Small-Angle Scattering in Soft Matter: Application and Prospective ※. ACTA CHIMICA SINICA 2022. [DOI: 10.6023/a21120624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Ma J, Cheng X, Xu Z, Zhang Y, Valle J, Fan S, Zuo X, Lasa I, Fang X. Structural mechanism for modulation of functional amyloid and biofilm formation by Staphylococcal Bap protein switch. EMBO J 2021; 40:e107500. [PMID: 34046916 PMCID: PMC8280801 DOI: 10.15252/embj.2020107500] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 12/24/2022] Open
Abstract
The Staphylococcal Bap proteins sense environmental signals (such as pH, [Ca2+ ]) to build amyloid scaffold biofilm matrices via unknown mechanisms. We here report the crystal structure of the aggregation-prone region of Staphylococcus aureus Bap which adopts a dumbbell-shaped fold. The middle module (MM) connecting the N-terminal and C-terminal lobes consists of a tandem of novel double-Ca2+ -binding motifs involved in cooperative interaction networks, which undergoes Ca2+ -dependent order-disorder conformational switches. The N-terminal lobe is sufficient to mediate amyloid aggregation through liquid-liquid phase separation and maturation, and subsequent biofilm formation under acidic conditions. Such processes are promoted by disordered MM at low [Ca2+ ] but inhibited by ordered MM stabilized by Ca2+ binding, with inhibition efficiency depending on structural integrity of the interaction networks. These studies illustrate a novel protein switch in pathogenic bacteria and provide insights into the mechanistic understanding of Bap proteins in modulation of functional amyloid and biofilm formation, which could be implemented in the anti-biofilm drug design.
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Affiliation(s)
- Junfeng Ma
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
| | - Xiang Cheng
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
| | - Zhonghe Xu
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
| | - Yikan Zhang
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
| | - Jaione Valle
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra‐Departamento de SaludIDISNAPamplonaSpain
| | - Shilong Fan
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
| | - Xiaobing Zuo
- X‐ray Science DivisionArgonne National LaboratoryLemontILUSA
| | - Iñigo Lasa
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra‐Departamento de SaludIDISNAPamplonaSpain
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijingChina
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