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Suleman M, Yaseen AR, Ahmed S, Khan Z, Irshad A, Pervaiz A, Rahman HH, Azhar M. Pyocins and Beyond: Exploring the World of Bacteriocins in Pseudomonas aeruginosa. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10322-3. [PMID: 39023701 DOI: 10.1007/s12602-024-10322-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
Abstract
Pseudomonas aeruginosa significantly induces health-associated infections in a variety of species other than humans. Over the years, the opportunistic pathogen has developed resistance against commonly used antibiotics. Since most P. aeruginosa strains are multi-drug resistant, regular antibiotic treatment of its infections is becoming a dire concern, shifting the global focus towards the development of alternate antimicrobial approaches. Pyocins are one of the most diverse antimicrobial peptide combinations produced by bacteria. They have potent antimicrobial properties, mainly against bacteria from the same phylogenetic group. P. aeruginosa, whether from clinical or environmental origins, produce several different pyocins that show inhibitory activity against other multi-drug-resistant strains of P. aeruginosa. They are, therefore, good candidates for alternate therapeutic antimicrobials because they have a unique mode of action that kills antibiotic-resistant bacteria by attacking their biofilms. Here, we review pseudomonas-derived antimicrobial pyocins with great therapeutic potential against multi-drug-resistant P. aeruginosa.
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Affiliation(s)
- Muhammad Suleman
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Allah Rakha Yaseen
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Shahbaz Ahmed
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Zoha Khan
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
| | - Asma Irshad
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
| | - Afsah Pervaiz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Hafiza Hiba Rahman
- Department of Pathology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muteeba Azhar
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
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Zhao X, Wang W, Zeng X, Xu R, Yuan B, Yu W, Wang M, Jia R, Chen S, Zhu D, Liu M, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Sun D, Cheng A. Klebicin E, a pore-forming bacteriocin of Klebsiella pneumoniae, exploits the porin OmpC and the Ton system for translocation. J Biol Chem 2024; 300:105694. [PMID: 38301890 PMCID: PMC10906532 DOI: 10.1016/j.jbc.2024.105694] [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: 09/21/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriocins, which have narrow-spectrum activity and limited adverse effects, are promising alternatives to antibiotics. In this study, we identified klebicin E (KlebE), a small bacteriocin derived from Klebsiella pneumoniae. KlebE exhibited strong efficacy against multidrug-resistant K. pneumoniae isolates and conferred a significant growth advantage to the producing strain during intraspecies competition. A giant unilamellar vesicle leakage assay demonstrated the unique membrane permeabilization effect of KlebE, suggesting that it is a pore-forming toxin. In addition to a C-terminal toxic domain, KlebE also has a disordered N-terminal domain and a globular central domain. Pulldown assays and soft agar overlay experiments revealed the essential role of the outer membrane porin OmpC and the Ton system in KlebE recognition and cytotoxicity. Strong binding between KlebE and both OmpC and TonB was observed. The TonB-box, a crucial component of the toxin-TonB interaction, was identified as the 7-amino acid sequence (E3ETLTVV9) located in the N-terminal region. Further studies showed that a region near the bottom of the central domain of KlebE plays a primary role in recognizing OmpC, with eight residues surrounding this region identified as essential for KlebE toxicity. Finally, based on the discrepancies in OmpC sequences between the KlebE-resistant and sensitive strains, it was found that the 91st residue of OmpC, an aspartic acid residue, is a key determinant of KlebE toxicity. The identification and characterization of this toxin will facilitate the development of bacteriocin-based therapies targeting multidrug-resistant K. pneumoniae infections.
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Affiliation(s)
- Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Wenyu Wang
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Zeng
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Rong Xu
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Wenyao Yu
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China.
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Avizemer Z, Martí-Gómez C, Hoch SY, McCandlish DM, Fleishman SJ. Evolutionary paths that link orthogonal pairs of binding proteins. RESEARCH SQUARE 2023:rs.3.rs-2836905. [PMID: 37131620 PMCID: PMC10153392 DOI: 10.21203/rs.3.rs-2836905/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Some protein binding pairs exhibit extreme specificities that functionally insulate them from homologs. Such pairs evolve mostly by accumulating single-point mutations, and mutants are selected if their affinity exceeds the threshold required for function1-4. Thus, homologous and high-specificity binding pairs bring to light an evolutionary conundrum: how does a new specificity evolve while maintaining the required affinity in each intermediate5,6? Until now, a fully functional single-mutation path that connects two orthogonal pairs has only been described where the pairs were mutationally close thus enabling experimental enumeration of all intermediates2. We present an atomistic and graph-theoretical framework for discovering low molecular strain single-mutation paths that connect two extant pairs, enabling enumeration beyond experimental capability. We apply it to two orthogonal bacterial colicin endonuclease-immunity pairs separated by 17 interface mutations7. We were not able to find a strain-free and functional path in the sequence space defined by the two extant pairs. But including mutations that bridge amino acids that cannot be exchanged through single-nucleotide mutations led us to a strain-free 19-mutation trajectory that is completely viable in vivo. Our experiments show that the specificity switch is remarkably abrupt, resulting from only one radical mutation on each partner. Furthermore, each of the critical specificity-switch mutations increases fitness, demonstrating that functional divergence could be driven by positive Darwinian selection. These results reveal how even radical functional changes in an epistatic fitness landscape may evolve.
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Affiliation(s)
- Ziv Avizemer
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Carlos Martí-Gómez
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Shlomo Yakir Hoch
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - David M. McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
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Bosch DE, Abbasian R, Parajuli B, Peterson SB, Mougous JD. Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales. mBio 2023; 14:e0103923. [PMID: 37345922 PMCID: PMC10470768 DOI: 10.1128/mbio.01039-23] [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: 04/25/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023] Open
Abstract
Bacteroidales use type VI secretion systems (T6SS) to competitively colonize and persist in the colon. We identify a horizontally transferred T6SS with Ntox15 family nuclease effector (Tde1) that mediates interbacterial antagonism among Bacteroidales, including several derived from a single human donor. Expression of cognate (Tdi1) or orphan immunity proteins in acquired interbacterial defense systems protects against Tde1-dependent attack. We find that immunity protein interaction induces a large effector conformational change in Tde nucleases, disrupting the active site and altering the DNA-binding site. Crystallographic snapshots of isolated Tde1, the Tde1/Tdi1 complex, and homologs from Phocaeicola vulgatus (Tde2/Tdi2) illustrate a conserved mechanism of immunity inserting into the central core of Tde, splitting the nuclease fold into two subdomains. The Tde/Tdi interface and immunity mechanism are distinct from all other polymorphic toxin-immunity interactions of known structure. Bacteroidales abundance has been linked to inflammatory bowel disease activity in prior studies, and we demonstrate that Tde and T6SS structural genes are each enriched in fecal metagenomes from ulcerative colitis subjects. Genetically mobile Tde1-encoding T6SS in Bacteroidales mediate competitive growth and may be involved in inflammatory bowel disease. Broad immunity is conferred by Tdi1 homologs through a fold-disrupting mechanism unique among polymorphic effector-immunity pairs of known structure. IMPORTANCE Bacteroidales are related to inflammatory bowel disease severity and progression. We identify type VI secretion system (T6SS) nuclease effectors (Tde) which are enriched in ulcerative colitis and horizontally transferred on mobile genetic elements. Tde-encoding T6SSs mediate interbacterial competition. Orphan and cognate immunity proteins (Tdi) prevent intoxication by multiple Tde through a new mechanism among polymorphic toxin systems. Tdi inserts into the effector central core, splitting Ntox15 into two subdomains and disrupting the active site. This mechanism may allow for evolutionary diversification of the Tde/Tdi interface as observed in colicin nuclease-immunity interactions, promoting broad neutralization of Tde by orphan Tdi. Tde-dependent T6SS interbacterial antagonism may contribute to Bacteroidales diversity in the context of ulcerative colitis.
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Affiliation(s)
- Dustin E. Bosch
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Romina Abbasian
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Bishal Parajuli
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - S. Brook Peterson
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Joseph D. Mougous
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, Washington, USA
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5
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Nafaee ZH, Hajdu B, Hunyadi-Gulyás É, Gyurcsik B. Hydrolytic Mechanism of a Metalloenzyme Is Modified by the Nature of the Coordinated Metal Ion. Molecules 2023; 28:5511. [PMID: 37513383 PMCID: PMC10386286 DOI: 10.3390/molecules28145511] [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: 06/06/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The nuclease domain of colicin E7 cleaves double-strand DNA non-specifically. Zn2+ ion was shown to be coordinated by the purified NColE7 as its native metal ion. Here, we study the structural and catalytic aspects of the interaction with Ni2+, Cu2+ and Cd2+ non-endogenous metal ions and the consequences of their competition with Zn2+ ions, using circular dichroism spectroscopy and intact protein mass spectrometry. An R447G mutant exerting decreased activity allowed for the detection of nuclease action against pUC119 plasmid DNA via agarose gel electrophoresis in the presence of comparable metal ion concentrations. It was shown that all of the added metal ions could bind to the apoprotein, resulting in a minor secondary structure change, but drastically shifting the charge distribution of the protein. Zn2+ ions could not be replaced by Ni2+, Cu2+ and Cd2+. The nuclease activity of the Ni2+-bound enzyme was extremely high in comparison with the other metal-bound forms, and could not be inhibited by the excess of Ni2+ ions. At the same time, this activity was significantly decreased in the presence of equivalent Zn2+, independent of the order of addition of each component of the mixture. We concluded that the Ni2+ ions promoted the DNA cleavage of the enzyme through a more efficient mechanism than the native Zn2+ ions, as they directly generate the nucleophilic OH- ion.
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Affiliation(s)
- Zeyad H Nafaee
- Department of Inorganic, Organic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
- College of Pharmacy, University of Babylon, Hillah 51001, Iraq
| | - Bálint Hajdu
- Department of Inorganic, Organic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Eötvös Loránd Research Network, Temesvári krt. 62, H-6726 Szeged, Hungary
| | - Béla Gyurcsik
- Department of Inorganic, Organic and Analytical Chemistry, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
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Dini I, De Biasi MG, Mancusi A. An Overview of the Potentialities of Antimicrobial Peptides Derived from Natural Sources. Antibiotics (Basel) 2022; 11:1483. [PMID: 36358138 PMCID: PMC9686932 DOI: 10.3390/antibiotics11111483] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial peptides (AMPs) are constituents of the innate immune system in every kind of living organism. They can act by disrupting the microbial membrane or without affecting membrane stability. Interest in these small peptides stems from the fear of antibiotics and the emergence of microorganisms resistant to antibiotics. Through membrane or metabolic disruption, they defend an organism against invading bacteria, viruses, protozoa, and fungi. High efficacy and specificity, low drug interaction and toxicity, thermostability, solubility in water, and biological diversity suggest their applications in food, medicine, agriculture, animal husbandry, and aquaculture. Nanocarriers can be used to protect, deliver, and improve their bioavailability effectiveness. High cost of production could limit their use. This review summarizes the natural sources, structures, modes of action, and applications of microbial peptides in the food and pharmaceutical industries. Any restrictions on AMPs' large-scale production are also taken into consideration.
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Affiliation(s)
- Irene Dini
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | | | - Andrea Mancusi
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy
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Lopes BS, Hanafiah A, Nachimuthu R, Muthupandian S, Md Nesran ZN, Patil S. The Role of Antimicrobial Peptides as Antimicrobial and Antibiofilm Agents in Tackling the Silent Pandemic of Antimicrobial Resistance. Molecules 2022; 27:molecules27092995. [PMID: 35566343 PMCID: PMC9105241 DOI: 10.3390/molecules27092995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/11/2023] Open
Abstract
Just over a million people died globally in 2019 due to antibiotic resistance caused by ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). The World Health Organization (WHO) also lists antibiotic-resistant Campylobacter and Helicobacter as bacteria that pose the greatest threat to human health. As it is becoming increasingly difficult to discover new antibiotics, new alternatives are needed to solve the crisis of antimicrobial resistance (AMR). Bacteria commonly found in complex communities enclosed within self-produced matrices called biofilms are difficult to eradicate and develop increased stress and antimicrobial tolerance. This review summarises the role of antimicrobial peptides (AMPs) in combating the silent pandemic of AMR and their application in clinical medicine, focusing on both the advantages and disadvantages of AMPs as antibiofilm agents. It is known that many AMPs display broad-spectrum antimicrobial activities, but in a variety of organisms AMPs are not stable (short half-life) or have some toxic side effects. Hence, it is also important to develop new AMP analogues for their potential use as drug candidates. The use of one health approach along with developing novel therapies using phages and breakthroughs in novel antimicrobial peptide synthesis can help us in tackling the problem of AMR.
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Affiliation(s)
- Bruno S. Lopes
- Department of Medical Microbiology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
- Correspondence: (B.S.L.); (A.H.)
| | - Alfizah Hanafiah
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia;
- Correspondence: (B.S.L.); (A.H.)
| | - Ramesh Nachimuthu
- Antibiotic Resistance and Phage Therapy Laboratory, Department of Biomedical Sciences, Vellore Institute of Technology, School of Bioscience and Technology, Vellore 632014, India;
| | - Saravanan Muthupandian
- AMR and Nanotherapeutics Laboratory, Department of Pharmacology, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College, Chennai 600077, India;
| | - Zarith Nameyrra Md Nesran
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia;
| | - Sandip Patil
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, China;
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Cuthbert BJ, Hayes CS, Goulding CW. Functional and Structural Diversity of Bacterial Contact-Dependent Growth Inhibition Effectors. Front Mol Biosci 2022; 9:866854. [PMID: 35558562 PMCID: PMC9086364 DOI: 10.3389/fmolb.2022.866854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/25/2022] Open
Abstract
Bacteria live in complex communities and environments, competing for space and nutrients. Within their niche habitats, bacteria have developed various inter-bacterial mechanisms to compete and communicate. One such mechanism is contact-dependent growth inhibition (CDI). CDI is found in many Gram-negative bacteria, including several pathogens. These CDI+ bacteria encode a CdiB/CdiA two-partner secretion system that delivers inhibitory toxins into neighboring cells upon contact. Toxin translocation results in the growth inhibition of closely related strains and provides a competitive advantage to the CDI+ bacteria. CdiB, an outer-membrane protein, secretes CdiA onto the surface of the CDI+ bacteria. When CdiA interacts with specific target-cell receptors, CdiA delivers its C-terminal toxin region (CdiA-CT) into the target-cell. CdiA-CT toxin proteins display a diverse range of toxic functions, such as DNase, RNase, or pore-forming toxin activity. CDI+ bacteria also encode an immunity protein, CdiI, that specifically binds and neutralizes its cognate CdiA-CT, protecting the CDI+ bacteria from auto-inhibition. In Gram-negative bacteria, toxin/immunity (CdiA-CT/CdiI) pairs have highly variable sequences and functions, with over 130 predicted divergent toxin/immunity complex families. In this review, we will discuss biochemical and structural advances made in the characterization of CDI. This review will focus on the diverse array of CDI toxin/immunity complex structures together with their distinct toxin functions. Additionally, we will discuss the most recent studies on target-cell recognition and toxin entry, along with the discovery of a new member of the CDI loci. Finally, we will offer insights into how these diverse toxin/immunity complexes could be harnessed to fight human diseases.
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Affiliation(s)
- Bonnie J. Cuthbert
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Christopher S. Hayes
- Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Celia W. Goulding
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, United States
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Sudhakari PA, Ramisetty BCM. Modeling endonuclease colicin-like bacteriocin operons as 'genetic arms' in plasmid-genome conflicts. Mol Genet Genomics 2022; 297:763-777. [PMID: 35320397 DOI: 10.1007/s00438-022-01884-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/06/2022] [Indexed: 11/28/2022]
Abstract
Plasmids are acellular propagating entities that depend on bacteria, as molecular parasites, for propagation. A 'tussle' between bacteria and plasmid ensues; bacteria for riddance of the plasmid and plasmid for persistence within a live host. Plasmid-maintenance systems such as endonuclease Colicin-Like Bacteriocins (CLBs) ensure plasmid propagation within the population; (i) the plasmid-cured cells are killed by the CLBs; (ii) damaged cells lyse and release the CLBs that eliminate the competitors, and (iii) the released plasmids invade new bacteria. Surprisingly, endonuclease CLB operons occur on bacterial genomes whose significance is unknown. Here, we study genetics, eco-evolutionary drive, and physiological relevance of genomic endonuclease CLB operons. We investigated plasmidic and genomic endonuclease CLB operons using sequence analyses from an eco-evolutionary perspective. We found 1266 genomic and plasmidic endonuclease CLB operons across 30 bacterial genera. Although 51% of the genomes harbor endonuclease CLB operons, the majority of the genomic endonuclease CLB operons lacked a functional lysis gene, suggesting the negative selection of lethal genes. The immunity gene of the endonuclease CLB operon protects the plasmid-cured host, eliminating the metabolic burden. We show mutual exclusivity of endonuclease CLB operons on genomes and plasmids. We propose an anti-addiction hypothesis for genomic endonuclease CLB operons. Using a stochastic hybrid agent-based model, we show that the endonuclease CLB operons on genomes confer an advantage to the host genome in terms of immunity to the toxin and elimination of plasmid burden. The conflict between bacterial genome and plasmids allows the emergence of 'genetic arms' such as CLB operons that regulate the ecological interplay of bacterial genomes and plasmids.
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Affiliation(s)
- Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India.
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10
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Garcia Gonzalez J, Hernandez FJ. Nuclease activity: an exploitable biomarker in bacterial infections. Expert Rev Mol Diagn 2022; 22:265-294. [PMID: 35240900 DOI: 10.1080/14737159.2022.2049249] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION In the increasingly challenging field of clinical microbiology, diagnosis is a cornerstone whose accuracy and timing are crucial for the successful management, therapy, and outcome of infectious diseases. Currently employed biomarkers of infectious diseases define the scope and limitations of diagnostic techniques. As such, expanding the biomarker catalog is crucial to address unmet needs and bring about novel diagnostic functionalities and applications. AREAS COVERED This review describes the extracellular nucleases of 15 relevant bacterial pathogens and discusses the potential use of nuclease activity as a diagnostic biomarker. Articles were searched for in PubMed using terms: "nuclease", "bacteria", "nuclease activity" or "biomarker". For overview sections, original and review articles between 2000 and 2019 were searched for using terms: "infections", "diagnosis", "bacterial", "burden", "challenges". Informative articles were selected. EXPERT OPINION Using the catalytic activity of nucleases offers new possibilities compared to established biomarkers. Nucleic acid activatable reporters in combination with different transduction platforms and delivery methods can be used to detect disease-associated nuclease activity patterns in vitro and in vivo for prognostic and diagnostic applications. Even when these patterns are not obvious or of unknown etiology, screening platforms could be used to identify new disease reporters.
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Affiliation(s)
- Javier Garcia Gonzalez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
| | - Frank J Hernandez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
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11
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Calcuttawala F, Pal A, Nath P, Kar R, Hazra D, Pal R. Structural and functional insights into colicin: a new paradigm in drug discovery. Arch Microbiol 2021; 204:37. [PMID: 34928429 DOI: 10.1007/s00203-021-02689-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 11/28/2022]
Abstract
Colicins are agents of allelopathic interactions produced by certain enterobacteria which give them a competitive advantage in the environment. These protein molecules are mostly encoded by plasmids. The colicin operon consists of the activity, immunity and the lysis genes. The activity protein is responsible for the killing activity, the immunity protein protects the producer cell from the lethal action of colicin and the lysis protein facilitates its release. Colicins are primarily composed of three domains, namely the receptor-binding domain, the translocation domain and the cytotoxic domain. The protein molecule binds to its cognate receptor on the target cell via the receptor-binding domain and undergoes translocation into the cell either via the Tol system or the Ton system. After gaining entry into the target cell, there are various mechanisms by which colicins exert their lethality. These comprise DNase activity, RNase activity and pore formation in the target cell membrane or peptidoglycan synthesis inhibition. This review gives a detailed insight into the structural and functional aspect of colicins and their mode of action. This knowledge is of immense significance because colicins are being considered as very useful alternatives to conventional antibiotics in the treatment of multidrug-resistant infections. Besides, they also have a negligible harmful impact on the commensals. Thus, before tapping their therapeutic potential, it is imperative to know their structure and mechanism of action in detail.
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Affiliation(s)
- Fatema Calcuttawala
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India.
| | - Ankita Pal
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India
| | - Papri Nath
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India
| | - Riya Kar
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India
| | - Debraj Hazra
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India
| | - Rajat Pal
- Department of Microbiology, Sister Nivedita University, Kolkata, 700156, India
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12
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Bin Hafeez A, Jiang X, Bergen PJ, Zhu Y. Antimicrobial Peptides: An Update on Classifications and Databases. Int J Mol Sci 2021; 22:11691. [PMID: 34769122 PMCID: PMC8583803 DOI: 10.3390/ijms222111691] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.
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Affiliation(s)
- Ahmer Bin Hafeez
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan;
| | - Xukai Jiang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Phillip J. Bergen
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
| | - Yan Zhu
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
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13
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Abstract
Colicins are protein antibiotics deployed by Escherichia coli to eliminate competing strains. Colicins frequently exploit outer membrane (OM) nutrient transporters to penetrate the selectively permeable bacterial cell envelope. Here, by applying live-cell fluorescence imaging, we were able to monitor the entry of the pore-forming toxin colicin B (ColB) into E. coli and localize it within the periplasm. We further demonstrate that single-stranded DNA coupled to ColB can also be transported to the periplasm, emphasizing that the import routes of colicins can be exploited to carry large cargo molecules into bacteria. Moreover, we characterize the molecular mechanism of ColB association with its OM receptor FepA by applying a combination of photoactivated cross-linking, mass spectrometry, and structural modeling. We demonstrate that complex formation is coincident with large-scale conformational changes in the colicin. Thereafter, active transport of ColB through FepA involves the colicin taking the place of the N-terminal half of the plug domain that normally occludes this iron transporter. IMPORTANCE Decades of excessive use of readily available antibiotics has generated a global problem of antibiotic resistance and, hence, an urgent need for novel antibiotic solutions. Bacteriocins are protein-based antibiotics produced by bacteria to eliminate closely related competing bacterial strains. Bacteriocin toxins have evolved to bypass the complex cell envelope in order to kill bacterial cells. Here, we uncover the cellular penetration mechanism of a well-known but poorly understood bacteriocin called colicin B that is active against Escherichia coli. Moreover, we demonstrate that the colicin B-import pathway can be exploited to deliver conjugated DNA cargo into bacterial cells. Our work leads to a better understanding of the way bacteriocins, as potential alternative antibiotics, execute their mode of action as well as highlighting how they might even be exploited in the genomic manipulation of Gram-negative bacteria.
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14
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Shushan A, Kosloff M. Structural design principles for specific ultra-high affinity interactions between colicins/pyocins and immunity proteins. Sci Rep 2021; 11:3789. [PMID: 33589691 PMCID: PMC7884437 DOI: 10.1038/s41598-021-83265-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/28/2021] [Indexed: 12/13/2022] Open
Abstract
The interactions of the antibiotic proteins colicins/pyocins with immunity proteins is a seminal model system for studying protein–protein interactions and specificity. Yet, a precise and quantitative determination of which structural elements and residues determine their binding affinity and specificity is still lacking. Here, we used comparative structure-based energy calculations to map residues that substantially contribute to interactions across native and engineered complexes of colicins/pyocins and immunity proteins. We show that the immunity protein α1–α2 motif is a unique structurally-dissimilar element that restricts interaction specificity towards all colicins/pyocins, in both engineered and native complexes. This motif combines with a diverse and extensive array of electrostatic/polar interactions that enable the exquisite specificity that characterizes these interactions while achieving ultra-high affinity. Surprisingly, the divergence of these contributing colicin residues is reciprocal to residue conservation in immunity proteins. The structurally-dissimilar immunity protein α1–α2 motif is recognized by divergent colicins similarly, while the conserved immunity protein α3 helix interacts with diverse colicin residues. Electrostatics thus plays a key role in setting interaction specificity across all colicins and immunity proteins. Our analysis and resulting residue-level maps illuminate the molecular basis for these protein–protein interactions, with implications for drug development and rational engineering of these interfaces.
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Affiliation(s)
- Avital Shushan
- The Department of Human Biology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838, Haifa, Israel
| | - Mickey Kosloff
- The Department of Human Biology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838, Haifa, Israel.
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15
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Chen LY. Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions. FRONTIERS IN PHYSICS 2020; 8:202. [PMID: 32542181 PMCID: PMC7295167 DOI: 10.3389/fphy.2020.00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Thermodynamic integration (TI), a powerful formalism for computing Gibbs free energy, has been implemented for many biophysical processes with alchemical schemes that require delicate human efforts to choose/design biasing potentials for sampling the desired biophysical events and to remove their artifactitious consequences afterwards. Theoretically, an alchemical scheme is exact but practically, an unsophisticated implementation of this exact formula can cause error amplifications. Small relative errors in the input parameters can be amplified many times in their propagation into the computed free energy [due to subtraction of similar numbers such as (105 ± 5)‒(100 ± 5) = 5 ± 7]. In this paper, we present an unsophisticated implementation of TI in 3n dimensions (3nD) (n=1,2,3…) for the potential of mean force along a 3nD path connecting one state in the bound state ensemble to one state in the unbound state ensemble. Fluctuations in these 3nD are integrated in the bound and unbound state ensembles but not along the 3nD path. Using TI3nD, we computed the standard binding free energies of three protein complexes: trometamol in Salmonella effector SpvD (n=1), biotin-avidin (n=2), and Colicin E9 endonuclease with cognate immunity protein Im9 (n=3). We employed three different protocols in three independent computations of E9-Im9 to show TI3nD's robustness. We also computed the hydration energies of ten biologically relevant compounds (n=1 for water, acetamide, urea, glycerol, trometamol, ammonium and n=2 for erythritol, 1,3-propanediol, xylitol, biotin). Each of the 15 computations is accomplishable within one (for hydration) to ten (for E9-Im9) days on an inexpensive GPU workstation. The computed results all agree with the available experimental data.
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Affiliation(s)
- Liao Y Chen
- Department of Physics, University of Texas at San Antonio, San Antonio, Texas 78249 U.S.A
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16
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Simons A, Alhanout K, Duval RE. Bacteriocins, Antimicrobial Peptides from Bacterial Origin: Overview of Their Biology and Their Impact against Multidrug-Resistant Bacteria. Microorganisms 2020; 8:E639. [PMID: 32349409 PMCID: PMC7285073 DOI: 10.3390/microorganisms8050639] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 12/18/2022] Open
Abstract
Currently, the emergence and ongoing dissemination of antimicrobial resistance among bacteria are critical health and economic issue, leading to increased rates of morbidity and mortality related to bacterial infections. Research and development for new antimicrobial agents is currently needed to overcome this problem. Among the different approaches studied, bacteriocins seem to be a promising possibility. These molecules are peptides naturally synthesized by ribosomes, produced by both Gram-positive bacteria (GPB) and Gram-negative bacteria (GNB), which will allow these bacteriocin producers to survive in highly competitive polymicrobial environment. Bacteriocins exhibit antimicrobial activity with variable spectrum depending on the peptide, which may target several bacteria. Already used in some areas such as agro-food, bacteriocins may be considered as interesting candidates for further development as antimicrobial agents used in health contexts, particularly considering the issue of antimicrobial resistance. The aim of this review is to present an updated global report on the biology of bacteriocins produced by GPB and GNB, as well as their antibacterial activity against relevant bacterial pathogens, and especially against multidrug-resistant bacteria.
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Affiliation(s)
- Alexis Simons
- Université de Lorraine, CNRS, L2CM, F-54000 Nancy, France
- Institut Micalis, équipe Bactéries Pathogènes et Santé, Faculté de Pharmacie, Université Paris-Saclay—INRAE—AgroParisTech, 92296 Châtenay-Malabry, France
| | - Kamel Alhanout
- Université de Lorraine, CNRS, L2CM, F-54000 Nancy, France
| | - Raphaël E. Duval
- Université de Lorraine, CNRS, L2CM, F-54000 Nancy, France
- ABC Platform, Faculté de Pharmacie, F-54505 Vandœuvre-lès-Nancy, France
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17
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Behrens HM, Lowe ED, Gault J, Housden NG, Kaminska R, Weber TM, Thompson CMA, Mislin GLA, Schalk IJ, Walker D, Robinson CV, Kleanthous C. Pyocin S5 Import into Pseudomonas aeruginosa Reveals a Generic Mode of Bacteriocin Transport. mBio 2020; 11:e03230-19. [PMID: 32156826 PMCID: PMC7064778 DOI: 10.1128/mbio.03230-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/28/2020] [Indexed: 11/20/2022] Open
Abstract
Pyocin S5 (PyoS5) is a potent protein bacteriocin that eradicates the human pathogen Pseudomonas aeruginosa in animal infection models, but its import mechanism is poorly understood. Here, using crystallography, biophysical and biochemical analyses, and live-cell imaging, we define the entry process of PyoS5 and reveal links to the transport mechanisms of other bacteriocins. In addition to its C-terminal pore-forming domain, elongated PyoS5 comprises two novel tandemly repeated kinked 3-helix bundle domains that structure-based alignments identify as key import domains in other pyocins. The central domain binds the lipid-bound common polysaccharide antigen, allowing the pyocin to accumulate on the cell surface. The N-terminal domain binds the ferric pyochelin transporter FptA while its associated disordered region binds the inner membrane protein TonB1, which together drive import of the bacteriocin across the outer membrane. Finally, we identify the minimal requirements for sensitizing Escherichia coli toward PyoS5, as well as other pyocins, and suggest that a generic pathway likely underpins the import of all TonB-dependent bacteriocins across the outer membrane of Gram-negative bacteria.IMPORTANCE Bacteriocins are toxic polypeptides made by bacteria to kill their competitors, making them interesting as potential antibiotics. Here, we reveal unsuspected commonalities in bacteriocin uptake pathways, through molecular and cellular dissection of the import pathway for the pore-forming bacteriocin pyocin S5 (PyoS5), which targets Pseudomonas aeruginosa In addition to its C-terminal pore-forming domain, PyoS5 is composed of two tandemly repeated helical domains that we also identify in other pyocins. Functional analyses demonstrate that they have distinct roles in the import process. One recognizes conserved sugars projected from the surface, while the other recognizes a specific outer membrane siderophore transporter, FptA, in the case of PyoS5. Through engineering of Escherichia coli cells, we show that pyocins can be readily repurposed to kill other species. This suggests basic ground rules for the outer membrane translocation step that likely apply to many bacteriocins targeting Gram-negative bacteria.
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Affiliation(s)
- Hannah M Behrens
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Edward D Lowe
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Joseph Gault
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Nicholas G Housden
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - T Moritz Weber
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Catriona M A Thompson
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gaëtan L A Mislin
- UMR 7242, Biotechnologie et Signalisation Cellulaire, ESBS, Illkirch, France
| | - Isabelle J Schalk
- UMR 7242, Biotechnologie et Signalisation Cellulaire, ESBS, Illkirch, France
| | - Daniel Walker
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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18
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Xie M, Yu L, Bruschweiler-Li L, Xiang X, Hansen AL, Brüschweiler R. Functional protein dynamics on uncharted time scales detected by nanoparticle-assisted NMR spin relaxation. SCIENCE ADVANCES 2019; 5:eaax5560. [PMID: 31453342 PMCID: PMC6693908 DOI: 10.1126/sciadv.aax5560] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/09/2019] [Indexed: 05/03/2023]
Abstract
Protein function depends critically on intrinsic internal dynamics, which is manifested in distinct ways, such as loop motions that regulate protein recognition and catalysis. Under physiological conditions, dynamic processes occur on a wide range of time scales from subpicoseconds to seconds. Commonly used NMR spin relaxation in solution provides valuable information on very fast and slow motions but is insensitive to the intermediate nanosecond to microsecond range that exceeds the protein tumbling correlation time. Presently, very little is known about the nature and functional role of these motions. It is demonstrated here how transverse spin relaxation becomes exquisitely sensitive to these motions at atomic resolution when studying proteins in the presence of nanoparticles. Application of this novel cross-disciplinary approach reveals large-scale dynamics of loops involved in functionally critical protein-protein interactions and protein-calcium ion recognition that were previously unobservable.
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Affiliation(s)
- Mouzhe Xie
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Lei Yu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210, USA
| | - Xinyao Xiang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Alexandar L. Hansen
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210, USA
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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19
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Ghequire MGK, De Mot R. LlpB represents a second subclass of lectin-like bacteriocins. Microb Biotechnol 2019; 12:567-573. [PMID: 30702207 PMCID: PMC6465234 DOI: 10.1111/1751-7915.13373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/11/2022] Open
Abstract
Bacteriocins are secreted bacterial proteins that selectively kill related strains. Lectin-like bacteriocins are atypical bacteriocins not requiring a cognate immunity factor and have been primarily studied in Pseudomonas. These so-called LlpAs are composed of a tandem of B-lectin domains. One domain interacts with d-rhamnose residues in the common polysaccharide antigen of Pseudomonas lipopolysaccharide (LPS). The other lectin domain is crucial for interference with the outer membrane protein assembly machinery by interacting with surface-exposed loops of its central component BamA. Via genome mining, we identified a second subclass of Pseudomonas lectin-like proteins, termed LlpB, consisting of a single B-lectin domain. We show that these proteins also display bactericidal activity. Among LlpB-resistant transposon mutants of an LlpB-susceptible Pseudomonas strain, a major subset was hit in an acyltransferase gene, predicted to be involved in LPS core modification, hereby suggesting that LlpBs equally attach to LPS for surface anchoring. This indicates that LPS binding and target strain specificity are condensed in a single B-lectin domain. The identification of this second subclass of lectin-like bacteriocins further expands the toolbox of antibacterial warfare deployed by bacteria and holds potential for their integration in biotechnological applications.
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Affiliation(s)
- Maarten G. K. Ghequire
- Centre of Microbial and Plant GeneticsKU LeuvenKasteelpark Arenberg 20 bus 24603001HeverleeBelgium
| | - René De Mot
- Centre of Microbial and Plant GeneticsKU LeuvenKasteelpark Arenberg 20 bus 24603001HeverleeBelgium
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20
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Atanaskovic I, Kleanthous C. Tools and Approaches for Dissecting Protein Bacteriocin Import in Gram-Negative Bacteria. Front Microbiol 2019; 10:646. [PMID: 31001227 PMCID: PMC6455109 DOI: 10.3389/fmicb.2019.00646] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022] Open
Abstract
Bacteriocins of Gram-negative bacteria are typically multi-domain proteins that target and kill bacteria of the same or closely related species. There is increasing interest in protein bacteriocin import; from a fundamental perspective to understand how folded proteins are imported into bacteria and from an applications perspective as species-specific antibiotics to combat multidrug resistant bacteria. In order to translocate across the cell envelope and cause cell death, protein bacteriocins hijack nutrient uptake pathways. Their import is energized by parasitizing intermembrane protein complexes coupled to the proton motive force, which delivers a toxic domain into the cell. A plethora of genetic, structural, biochemical, and biophysical methods have been applied to find cell envelope components involved in bacteriocin import since their discovery almost a century ago. Here, we review the various approaches that now exist for investigating how protein bacteriocins translocate into Gram-negative bacteria and highlight areas of research that will need methodological innovations to fully understand this process. We also highlight recent studies demonstrating how bacteriocins can be used to probe organization and architecture of the Gram-negative cell envelope itself.
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Affiliation(s)
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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21
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Netzer R, Listov D, Lipsh R, Dym O, Albeck S, Knop O, Kleanthous C, Fleishman SJ. Ultrahigh specificity in a network of computationally designed protein-interaction pairs. Nat Commun 2018; 9:5286. [PMID: 30538236 PMCID: PMC6290019 DOI: 10.1038/s41467-018-07722-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/21/2018] [Indexed: 01/21/2023] Open
Abstract
Protein networks in all organisms comprise homologous interacting pairs. In these networks, some proteins are specific, interacting with one or a few binding partners, whereas others are multispecific and bind a range of targets. We describe an algorithm that starts from an interacting pair and designs dozens of new pairs with diverse backbone conformations at the binding site as well as new binding orientations and sequences. Applied to a high-affinity bacterial pair, the algorithm results in 18 new ones, with cognate affinities from pico- to micromolar. Three pairs exhibit 3-5 orders of magnitude switch in specificity relative to the wild type, whereas others are multispecific, collectively forming a protein-interaction network. Crystallographic analysis confirms design accuracy, including in new backbones and polar interactions. Preorganized polar interaction networks are responsible for high specificity, thus defining design principles that can be applied to program synthetic cellular interaction networks of desired affinity and specificity. The molecular basis of ultrahigh specificity in protein-protein interactions remains obscure. The authors present a computational method to design atomically accurate new pairs exhibiting >100,000-fold specificity switches, generating a large and complex interaction network.
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Affiliation(s)
- Ravit Netzer
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Rosalie Lipsh
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Orly Dym
- Structural Proteomics Unit, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Shira Albeck
- Structural Proteomics Unit, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Orli Knop
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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22
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Chang JW, Sato Y, Ogawa T, Arakawa T, Fukai S, Fushinobu S, Masaki H. Crystal structure of the central and the C-terminal RNase domains of colicin D implicated its translocation pathway through inner membrane of target cell. J Biochem 2018; 164:329-339. [PMID: 29905832 DOI: 10.1093/jb/mvy056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 06/10/2018] [Indexed: 12/18/2022] Open
Abstract
Colicins are protein toxins produced by and toxic to Escherichia coli strains. Colicin D consists of an N-terminal domain (NTD), central domain (CD) and C-terminal RNase domain (CRD). The cognate immunity protein, ImmD, is co-synthesized in producer cells to block the toxic tRNase activity of the CRD. Previous studies have reported the crystal structure of CRD/ImmD complex. Colicin D hijacks the surface receptor FepA and the energy transducer TonB system using the NTD for translocation across the outer membrane of the target cells. The CD is required for endoproteolytic processing and the translocation of CRD across the inner membrane, and the membrane-associated protease FtsH and the signal peptidase LepB are exploited in this process. Although several regions of the CD have been identified in interactions with the hijacked inner membrane system or immunity protein, the structural basis of the CD is unknown. In this study, we determined the crystal structure of colicin D, containing both the CD and CRD. The full-length colicin D/ImmD heterodimer structure was built by superimposing the CD-CRD structure with the previously determined partial structures. The overall translocation process of colicin D, including the interaction between CD and LepB, is discussed.
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Affiliation(s)
- Jung-Wei Chang
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Yusuke Sato
- Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.,Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan
| | - Tetsuhiro Ogawa
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Shuya Fukai
- Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.,Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Haruhiko Masaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan
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23
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Ghequire MGK, Öztürk B. A Colicin M-Type Bacteriocin from Pseudomonas aeruginosa Targeting the HxuC Heme Receptor Requires a Novel Immunity Partner. Appl Environ Microbiol 2018; 84:e00716-18. [PMID: 29980560 PMCID: PMC6121995 DOI: 10.1128/aem.00716-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/28/2018] [Indexed: 12/16/2022] Open
Abstract
Pyocins are bacteriocins secreted by Pseudomonas aeruginosa, and they assist in the colonization of different niches. A major subset of these antibacterial proteins adopt a modular organization characteristic of polymorphic toxins. They include a receptor-binding domain, a segment enabling membrane passage, and a toxin module at the carboxy terminus, which eventually kills the target cells. To protect themselves from their own products, bacteriocin-producing strains express an immunity gene concomitantly with the bacteriocin. We show here that a pyocin equipped with a phylogenetically distinct ColM toxin domain, PaeM4, mediates antagonism against a large set of P. aeruginosa isolates. Immunity to PaeM4 is provided by the inner membrane protein PmiC, which is equipped with a transmembrane topology not previously described for the ColM family. Given that strains lacking a pmiC gene are killed by PaeM4, the presence of such an immunity partner likely is a key criterion for escaping cellular death mediated by PaeM4. The presence of a TonB box in PaeM4 and enhanced bacteriocin activity under iron-poor conditions strongly suggested the targeting of a TonB-dependent receptor. Evaluation of PaeM4 activities against TonB-dependent receptor knockout mutants in P. aeruginosa PAO1 revealed that the heme receptor HxuC (PA1302) serves as a PaeM4 target at the cellular surface. Because other ColM-type pyocins may target the ferrichrome receptor FiuA, our results illustrate the versatility in target recognition conferred by the polymorphic nature of ColM-type bacteriocins.IMPORTANCE The antimicrobial armamentarium of a bacterium is a major asset for colonizing competitive environments. Bacteriocins comprise a subset of these compounds. Pyocins are an example of such antibacterial proteins produced by Pseudomonas aeruginosa, killing other P. aeruginosa strains. A large group of these molecules show a modular protein architecture that includes a receptor-binding domain for initial target cell attachment and a killer domain. In this study, we have shown that a novel modular pyocin (PaeM4) that kills target bacteria via interference with peptidoglycan assembly takes advantage of the HxuC heme receptor. Cells can protect themselves from killing by the presence of a dedicated immunity partner, an integral inner membrane protein that adopts a transmembrane topology distinct from that of proteins currently known to provide immunity against such toxin activity. Understanding the receptors with which pyocins interact and how immunity to pyocins is achieved is a pivotal step toward the rational design of bacteriocin cocktails for the treatment of P. aeruginosa infections.
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Affiliation(s)
| | - Başak Öztürk
- Leibniz Institut DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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24
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Rassam P, Long KR, Kaminska R, Williams DJ, Papadakos G, Baumann CG, Kleanthous C. Intermembrane crosstalk drives inner-membrane protein organization in Escherichia coli. Nat Commun 2018. [PMID: 29540681 PMCID: PMC5852019 DOI: 10.1038/s41467-018-03521-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Gram-negative bacteria depend on energised protein complexes that connect the two membranes of the cell envelope. However, β-barrel outer-membrane proteins (OMPs) and α-helical inner-membrane proteins (IMPs) display quite different organisation. OMPs cluster into islands that restrict their lateral mobility, while IMPs generally diffuse throughout the cell. Here, using live cell imaging of Escherichia coli, we demonstrate that when transient, energy-dependent transmembrane connections are formed, IMPs become subjugated by the inherent organisation of OMPs and that such connections impact IMP function. We show that while establishing a translocon for import, the colicin ColE9 sequesters the IMPs of the proton motive force (PMF)-linked Tol-Pal complex into islands mirroring those of colicin-bound OMPs. Through this imposed organisation, the bacteriocin subverts the outer-membrane stabilising role of Tol-Pal, blocking its recruitment to cell division sites and slowing membrane constriction. The ordering of IMPs by OMPs via an energised inter-membrane bridge represents an emerging functional paradigm in cell envelope biology.
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Affiliation(s)
- Patrice Rassam
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,Laboratoire de Bioimagerie et Pathologie, UMR 7021, CNRS, Université de Strasbourg, Faculté de pharmacie, 74 Route du Rhin, 67401, Illkirch, France
| | - Kathleen R Long
- Department of Biology, University of York, York, YO10 5DD, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - David J Williams
- Department of Biology, University of York, York, YO10 5DD, UK.,Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Grigorios Papadakos
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,Division of Neurobiology, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | | | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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25
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Abstract
Bacteria host an arsenal of antagonism-mediating molecules to combat for ecologic space. Bacteriocins represent a pivotal group of secreted antibacterial peptides and proteins assisting in this fight, mainly eliminating relatives. Colicin M, a model for peptidoglycan-interfering bacteriocins in Gram-negative bacteria, appears to be part of a set of polymorphic toxins equipped with such a catalytic domain (ColM) targeting lipid II. Diversifying recombination has enabled parasitism of different receptors and has also given rise to hybrid bacteriocins in which ColM is associated with another toxin module. Remarkably, ColM toxins have recruited a diverse array of immunity partners, comprising cytoplasmic membrane-associated proteins with different topologies. Together, these findings suggest that different immunity mechanisms have evolved for ColM, in contrast to bacteriocins with nuclease activities.
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26
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Mills A, Duong F. Lipopolysaccharides promote binding and unfolding of the antibacterial colicin E3 rRNAse domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2454-2460. [PMID: 28888366 DOI: 10.1016/j.bbamem.2017.08.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 11/17/2022]
Abstract
Nuclease colicins are antibacterial proteins produced by certain strains of E. coli to reduce competition from rival strains. These colicins are generally organized with an N-terminal transport (T)-domain, a central receptor binding (R)-domain, and a C-terminal cytotoxic nuclease domain. These colicins are always produced in complex with an inhibitory immunity protein, which dissociates prior entrance of the cytotoxic domain in the target cell. How exactly colicins traverse the cell envelope is not understood, yet this knowledge is important for the design of new antibacterial therapies. In this report, we find that the cytotoxic rRNAse domain of colicin E3, lacking both T- and R-domains, is sufficient to inhibit cell growth provided the immunity protein Im3 has been removed. Thus, while the T-domain is needed for dissociation of Im3, the rRNAse alone can associate to the cell surface without R-domain. Accordingly, we find a high affinity interaction (Kd ~1-2μM) between the rRNAse domain and lipopolysaccharides (LPS). Furthermore, we show that binding of ColE3 to LPS destabilizes the secondary structure of the toxin, which is expectedly crucial for transport through the narrow pore of the porin OmpF. The effect of LPS on binding and unfolding of ColE3 may be indicative of a broader role of LPS for transport of colicins in general.
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Affiliation(s)
- Allan Mills
- Department of Biochemistry & Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Franck Duong
- Department of Biochemistry & Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
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27
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Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models. PLoS Comput Biol 2017; 13:e1005652. [PMID: 28715501 PMCID: PMC5536347 DOI: 10.1371/journal.pcbi.1005652] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 07/31/2017] [Accepted: 06/21/2017] [Indexed: 11/28/2022] Open
Abstract
Bacteria exploit an arsenal of antimicrobial peptides and proteins to compete with each other. Three main competition systems have been described: type six secretion systems (T6SS); contact dependent inhibition (CDI); and bacteriocins. Unlike T6SS and CDI systems, bacteriocins do not require contact between bacteria but are diffusible toxins released into the environment. Identified almost a century ago, our understanding of bacteriocin distribution and prevalence in bacterial populations remains poor. In the case of protein bacteriocins, this is because of high levels of sequence diversity and difficulties in distinguishing their killing domains from those of other competition systems. Here, we develop a robust bioinformatics pipeline exploiting Hidden Markov Models for the identification of nuclease bacteriocins (NBs) in bacteria of which, to-date, only a handful are known. NBs are large (>60 kDa) toxins that target nucleic acids (DNA, tRNA or rRNA) in the cytoplasm of susceptible bacteria, usually closely related to the producing organism. We identified >3000 NB genes located on plasmids or on the chromosome from 53 bacterial species distributed across different ecological niches, including human, animals, plants, and the environment. A newly identified NB predicted to be specific for Pseudomonas aeruginosa (pyocin Sn) was produced and shown to kill P. aeruginosa thereby validating our pipeline. Intriguingly, while the genes encoding the machinery needed for NB translocation across the cell envelope are widespread in Gram-negative bacteria, NBs are found exclusively in γ-proteobacteria. Similarity network analysis demonstrated that NBs fall into eight groups each with a distinct arrangement of protein domains involved in import. The only structural feature conserved across all groups was a sequence motif critical for cell-killing that is generally not found in bacteriocins targeting the periplasm, implying a specific role in translocating the nuclease to the cytoplasm. Finally, we demonstrate a significant association between nuclease colicins, NBs specific for Escherichia coli, and virulence factors, suggesting NBs play a role in infection processes, most likely by enabling pathogens to outcompete commensal bacteria. Bacteria deploy a variety of antimicrobials to kill competing bacteria. Nuclease bacteriocins are a miscellaneous group of protein toxins that target closely related species, cleaving nucleic acids in the cytoplasm. It has proved difficult to establish how widespread bacteriocins are in bacterial populations due to the high diversity of bacteriocin-encoding genes. Here, we describe an in silico approach to identify nuclease bacteriocin genes in bacterial genomes and to distinguish them from other competition toxins. Bacteria that contain nuclease bacteriocin genes are found in many different types of environment but are prevalent in niches where interbacterial competition is likely to be high. Nuclease bacteriocins are found exclusively in γ-proteobacteria and are particularly abundant in the Enterobacteriaceae and Pseudomonadaceae families. Although the sequences we identify are indeed diverse (<20% sequence identity between protein families) we show that all nuclease bacteriocins contain an invariant motif, usually within a common structural scaffold, that is implicated in translocating the cytotoxic nuclease to the cytoplasm. Finally, we show that nuclease bacteriocins in pathogenic E. coli are strongly associated with virulence factors suggesting they play a role in pathogenicity mechanisms.
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28
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Calcuttawala F, Hariharan C, Pazhani GP, Saha DR, Ramamurthy T. Characterization of E-type colicinogenic plasmids from Shigella sonnei. FEMS Microbiol Lett 2017; 364:3071828. [DOI: 10.1093/femsle/fnx060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 03/14/2017] [Indexed: 12/14/2022] Open
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29
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Zakharov SD, Wang XS, Cramer WA. The Colicin E1 TolC-Binding Conformer: Pillar or Pore Function of TolC in Colicin Import? Biochemistry 2016; 55:5084-94. [PMID: 27536862 DOI: 10.1021/acs.biochem.6b00621] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The mechanism by which the drug export protein TolC is utilized for import of the cytotoxin colicin E1 across the outer membrane and periplasmic space is addressed. Studies of the initial binding of colicin E1 with TolC, occlusion of membrane-incorporated TolC ion channels, and the structure underlying the colicin-TolC complex were based on the interactions with TolC of individual colicin translocation domain (T-domain) peptides from a set of 19 that span different segments of the T-domain. These studies led to identification of a short 20-residue segment 101-120, a "TolC box", located near the center of the colicin T-domain, which is necessary for binding of colicin to TolC. Omission of this segment eliminated the ability of the T-domain to occlude TolC channels and to co-elute with TolC on a size-exclusion column. Far-ultraviolet circular dichroism spectral and thermal stability analysis of the structure of T-domain peptides implies (i) a helical hairpin conformation of the T-domain, (ii) the overlap of the TolC-binding site with a hinge of the helical hairpin, and (iii) a TolC-dependent stage of colicin import in which a central segment of the T-domain in a helical hairpin conformation binds to the TolC entry port following initial binding to the BtuB receptor. These studies provide the first structure-based information about the interaction of colicin E1 with the unique TolC protein. The model inferred for binding of the T-domain to TolC implies reservations about the traditional model for colicin import in which TolC functions to provide a channel for translocation of the colicin in an unfolded state across the bacterial outer membrane and a large part of the periplasmic space.
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Affiliation(s)
- Stanislav D Zakharov
- Department of Biological Sciences, Purdue University , Hockmeyer Building of Structural Biology, West Lafayette, Indiana 47907, United States
| | - Xin S Wang
- Department of Biological Sciences, Purdue University , Hockmeyer Building of Structural Biology, West Lafayette, Indiana 47907, United States
| | - William A Cramer
- Department of Biological Sciences, Purdue University , Hockmeyer Building of Structural Biology, West Lafayette, Indiana 47907, United States
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30
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Németh E, Balogh RK, Borsos K, Czene A, Thulstrup PW, Gyurcsik B. Intrinsic protein disorder could be overlooked in cocrystallization conditions: An SRCD case study. Protein Sci 2016; 25:1977-1988. [PMID: 27508941 DOI: 10.1002/pro.3010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/08/2016] [Indexed: 12/21/2022]
Abstract
X-ray diffractometry dominates protein studies, as it can provide 3D structures of these diverse macromolecules or their molecular complexes with interacting partners: substrates, inhibitors, and/or cofactors. Here, we show that under cocrystallization conditions the results could reflect induced protein folds instead of the (partially) disordered original structures. The analysis of synchrotron radiation circular dichroism spectra revealed that the Im7 immunity protein stabilizes the native-like solution structure of unfolded NColE7 nuclease mutants via complex formation. This is consistent with the fact that among the several available crystal structures with its inhibitor or substrate, all NColE7 structures are virtually the same. Our results draw attention to the possible structural consequence of protein modifications, which is often hidden by compensational effects of intermolecular interactions. The growing evidence on the importance of protein intrinsic disorder thus, demands more extensive complementary experiments in solution phase with the unligated form of the protein of interest.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary.,MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary
| | - Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary
| | - Katalin Borsos
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary
| | - Anikó Czene
- MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Szeged, 6720, Hungary. .,MTA-SZTE, Bioinorganic Chemistry Research Group, Hungarian Academy of Sciences, Szeged, 6720, Hungary.
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31
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Abstract
Contact-dependent growth inhibition (CDI) is a widespread mechanism of bacterial competition. CDI(+) bacteria deliver the toxic C-terminal region of contact-dependent inhibition A proteins (CdiA-CT) into neighboring target bacteria and produce CDI immunity proteins (CdiI) to protect against self-inhibition. The CdiA-CT(EC536) deployed by uropathogenic Escherichia coli 536 (EC536) is a bacterial toxin 28 (Ntox28) domain that only exhibits ribonuclease activity when bound to the cysteine biosynthetic enzyme O-acetylserine sulfhydrylase A (CysK). Here, we present crystal structures of the CysK/CdiA-CT(EC536) binary complex and the neutralized ternary complex of CysK/CdiA-CT/CdiI(EC536) CdiA-CT(EC536) inserts its C-terminal Gly-Tyr-Gly-Ile peptide tail into the active-site cleft of CysK to anchor the interaction. Remarkably, E. coli serine O-acetyltransferase uses a similar Gly-Asp-Gly-Ile motif to form the "cysteine synthase" complex with CysK. The cysteine synthase complex is found throughout bacteria, protozoa, and plants, indicating that CdiA-CT(EC536) exploits a highly conserved protein-protein interaction to promote its toxicity. CysK significantly increases CdiA-CT(EC536) thermostability and is required for toxin interaction with tRNA substrates. These observations suggest that CysK stabilizes the toxin fold, thereby organizing the nuclease active site for substrate recognition and catalysis. By contrast, Ntox28 domains from Gram-positive bacteria lack C-terminal Gly-Tyr-Gly-Ile motifs, suggesting that they do not interact with CysK. We show that the Ntox28 domain from Ruminococcus lactaris is significantly more thermostable than CdiA-CT(EC536), and its intrinsic tRNA-binding properties support CysK-independent nuclease activity. The striking differences between related Ntox28 domains suggest that CDI toxins may be under evolutionary pressure to maintain low global stability.
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32
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Structural and biophysical analysis of nuclease protein antibiotics. Biochem J 2016; 473:2799-812. [PMID: 27402794 PMCID: PMC5264503 DOI: 10.1042/bcj20160544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/07/2016] [Indexed: 01/28/2023]
Abstract
Protein antibiotics (bacteriocins) are a large and diverse family of multidomain toxins that kill specific Gram-negative bacteria during intraspecies competition for resources. Our understanding of the mechanism of import of such potent toxins has increased significantly in recent years, especially with the reporting of several structures of bacteriocin domains. Less well understood is the structural biochemistry of intact bacteriocins and how these compare across bacterial species. Here, we focus on endonuclease (DNase) bacteriocins that target the genomes of Escherichia coli and Pseudomonas aeruginosa, known as E-type colicins and S-type pyocins, respectively, bound to their specific immunity (Im) proteins. First, we report the 3.2 Å structure of the DNase colicin ColE9 in complex with its ultra-high affinity Im protein, Im9. In contrast with Im3, which when bound to the ribonuclease domain of the homologous colicin ColE3 makes contact with the translocation (T) domain of the toxin, we find that Im9 makes no such contact and only interactions with the ColE9 cytotoxic domain are observed. Second, we report small-angle X-ray scattering data for two S-type DNase pyocins, S2 and AP41, into which are fitted recently determined X-ray structures for isolated domains. We find that DNase pyocins and colicins are both highly elongated molecules, even though the order of their constituent domains differs. We discuss the implications of these architectural similarities and differences in the context of the translocation mechanism of protein antibiotics through the cell envelope of Gram-negative bacteria.
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33
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Preorganization of the catalytic Zn2+-binding site in the HNH nuclease motif—A solution study. J Inorg Biochem 2015; 151:143-9. [DOI: 10.1016/j.jinorgbio.2015.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/31/2015] [Accepted: 03/31/2015] [Indexed: 11/18/2022]
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34
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Joshi A, Grinter R, Josts I, Chen S, Wojdyla JA, Lowe ED, Kaminska R, Sharp C, McCaughey L, Roszak AW, Cogdell RJ, Byron O, Walker D, Kleanthous C. Structures of the Ultra-High-Affinity Protein-Protein Complexes of Pyocins S2 and AP41 and Their Cognate Immunity Proteins from Pseudomonas aeruginosa. J Mol Biol 2015; 427:2852-66. [PMID: 26215615 PMCID: PMC4548480 DOI: 10.1016/j.jmb.2015.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/16/2015] [Accepted: 07/20/2015] [Indexed: 11/25/2022]
Abstract
How ultra-high-affinity protein-protein interactions retain high specificity is still poorly understood. The interaction between colicin DNase domains and their inhibitory immunity (Im) proteins is an ultra-high-affinity interaction that is essential for the neutralisation of endogenous DNase catalytic activity and for protection against exogenous DNase bacteriocins. The colicin DNase-Im interaction is a model system for the study of high-affinity protein-protein interactions. However, despite the fact that closely related colicin-like bacteriocins are widely produced by Gram-negative bacteria, this interaction has only been studied using colicins from Escherichia coli. In this work, we present the first crystal structures of two pyocin DNase-Im complexes from Pseudomonas aeruginosa, pyocin S2 DNase-ImS2 and pyocin AP41 DNase-ImAP41. These structures represent divergent DNase-Im subfamilies and are important in extending our understanding of protein-protein interactions for this important class of high-affinity protein complex. A key finding of this work is that mutations within the immunity protein binding energy hotspot, helix III, are tolerated by complementary substitutions at the DNase-Immunity protein binding interface. Im helix III is strictly conserved in colicins where an Asp forms polar interactions with the DNase backbone. ImAP41 contains an Asp-to-Gly substitution in helix III and our structures show the role of a co-evolved substitution where Pro in DNase loop 4 occupies the volume vacated and removes the unfulfilled hydrogen bond. We observe the co-evolved mutations in other DNase-Immunity pairs that appear to underpin the split of this family into two distinct groups.
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Affiliation(s)
- Amar Joshi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Rhys Grinter
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Inokentijs Josts
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sabrina Chen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Justyna A Wojdyla
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Edward D Lowe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Connor Sharp
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Laura McCaughey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Aleksander W Roszak
- WestCHEM, School of Chemistry, College of Science and Engineering, University of Glasgow, Glasgow G12 8QQ, UK; Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Richard J Cogdell
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Olwyn Byron
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Daniel Walker
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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35
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Abstract
ABSTRACT
The scientific and technical ambition of contemporary synthetic biology is the engineering of biological objects with a degree of predictability comparable to those made through electric and industrial manufacturing. To this end, biological parts with given specifications are sequence-edited, standardized, and combined into devices, which are assembled into complete systems. This goal, however, faces the customary context dependency of biological ingredients and their amenability to mutation. Biological orthogonality (i.e., the ability to run a function in a fashion minimally influenced by the host) is thus a desirable trait in any deeply engineered construct. Promiscuous conjugative plasmids found in environmental bacteria have evolved precisely to autonomously deploy their encoded activities in a variety of hosts, and thus they become excellent sources of basic building blocks for genetic and metabolic circuits. In this article we review a number of such reusable functions that originated in environmental plasmids and keep their properties and functional parameters in a variety of hosts. The properties encoded in the corresponding sequences include
inter alia
origins of replication, DNA transfer machineries, toxin-antitoxin systems, antibiotic selection markers, site-specific recombinases, effector-dependent transcriptional regulators (with their cognate promoters), and metabolic genes and operons. Several of these sequences have been standardized as BioBricks and/or as components of the SEVA (Standard European Vector Architecture) collection. Such formatting facilitates their physical composability, which is aimed at designing and deploying complex genetic constructs with new-to-nature properties.
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36
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Farrance OE, Paci E, Radford SE, Brockwell DJ. Extraction of accurate biomolecular parameters from single-molecule force spectroscopy experiments. ACS NANO 2015; 9:1315-1324. [PMID: 25646767 DOI: 10.1021/nn505135d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The atomic force microscope (AFM) is able to manipulate biomolecules and their complexes with exquisite force sensitivity and distance resolution. This capability, complemented by theoretical models, has greatly improved our understanding of the determinants of mechanical strength in proteins and revealed the diverse effects of directional forces on the energy landscape of biomolecules. In unbinding experiments, the interacting partners are usually immobilized on their respective substrates via extensible linkers. These linkers affect both the force and contour length (Lc) of the complex at rupture. Surprisingly, while the former effect is well understood, the latter is largely neglected, leading to incorrect estimations of Lc, a parameter that is often used as evidence for the detection of specific interactions and remodeling events and for the inference of interaction regions. To address this problem, a model that predicts contour length measurements from single-molecule forced-dissociation experiments is presented that considers attachment position on the AFM tip, geometric effects, and polymer dynamics of the linkers. Modeled data are compared with measured contour length distributions from several different experimental systems, revealing that current methods underestimate contour lengths. The model enables nonspecific interactions to be identified unequivocally, allows accurate determination of Lc, and, by comparing experimental and modeled distributions, enables partial unfolding events before rupture to be identified unequivocally.
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Affiliation(s)
- Oliver E Farrance
- Astbury Centre for Structural and Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds, West Yorkshire, LS2 9JT, U.K
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Warszawski S, Netzer R, Tawfik DS, Fleishman SJ. A "fuzzy"-logic language for encoding multiple physical traits in biomolecules. J Mol Biol 2014; 426:4125-4138. [PMID: 25311857 PMCID: PMC4270444 DOI: 10.1016/j.jmb.2014.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/21/2014] [Accepted: 10/02/2014] [Indexed: 12/16/2022]
Abstract
To carry out their activities, biological macromolecules balance different physical traits, such as stability, interaction affinity, and selectivity. How such often opposing traits are encoded in a macromolecular system is critical to our understanding of evolutionary processes and ability to design new molecules with desired functions. We present a framework for constraining design simulations to balance different physical characteristics. Each trait is represented by the equilibrium fractional occupancy of the desired state relative to its alternatives, ranging from none to full occupancy, and the different traits are combined using Boolean operators to effect a "fuzzy"-logic language for encoding any combination of traits. In another paper, we presented a new combinatorial backbone design algorithm AbDesign where the fuzzy-logic framework was used to optimize protein backbones and sequences for both stability and binding affinity in antibody-design simulation. We now extend this framework and find that fuzzy-logic design simulations reproduce sequence and structure design principles seen in nature to underlie exquisite specificity on the one hand and multispecificity on the other hand. The fuzzy-logic language is broadly applicable and could help define the space of tolerated and beneficial mutations in natural biomolecular systems and design artificial molecules that encode complex characteristics.
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Affiliation(s)
- Shira Warszawski
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ravit Netzer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sarel J Fleishman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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Ghequire MGK, De Mot R. Ribosomally encoded antibacterial proteins and peptides from Pseudomonas. FEMS Microbiol Rev 2014; 38:523-68. [PMID: 24923764 DOI: 10.1111/1574-6976.12079] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/05/2014] [Accepted: 05/16/2014] [Indexed: 12/26/2022] Open
Abstract
Members of the Pseudomonas genus produce diverse secondary metabolites affecting other bacteria, fungi or predating nematodes and protozoa but are also equipped with the capacity to secrete different types of ribosomally encoded toxic peptides and proteins, ranging from small microcins to large tailocins. Studies with the human pathogen Pseudomonas aeruginosa have revealed that effector proteins of type VI secretion systems are part of the antibacterial armamentarium deployed by pseudomonads. A novel class of antibacterial proteins with structural similarity to plant lectins was discovered by studying antagonism among plant-associated Pseudomonas strains. A genomic perspective on pseudomonad bacteriocinogeny shows that the modular architecture of S pyocins of P. aeruginosa is retained in a large diversified group of bacteriocins, most of which target DNA or RNA. Similar modularity is present in as yet poorly characterized Rhs (recombination hot spot) proteins and CDI (contact-dependent inhibition) proteins. Well-delimited domains for receptor recognition or cytotoxicity enable the design of chimeric toxins with novel functionalities, which has been applied successfully for S and R pyocins. Little is known regarding how these antibacterials are released and ultimately reach their targets. Other remaining issues concern the identification of environmental triggers activating these systems and assessment of their ecological impact in niches populated by pseudomonads.
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Németh E, Körtvélyesi T, Thulstrup PW, Christensen HEM, Kožíšek M, Nagata K, Czene A, Gyurcsik B. Fine tuning of the catalytic activity of colicin E7 nuclease domain by systematic N-terminal mutations. Protein Sci 2014; 23:1113-22. [PMID: 24895333 DOI: 10.1002/pro.2497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/20/2014] [Accepted: 05/29/2014] [Indexed: 11/11/2022]
Abstract
The nuclease domain of colicin E7 (NColE7) promotes the nonspecific cleavage of nucleic acids at its C-terminal HNH motif. Interestingly, the deletion of four N-terminal residues (446-449 NColE7 = KRNK) resulted in complete loss of the enzyme activity. R447A mutation was reported to decrease the nuclease activity, but a detailed analysis of the role of the highly positive and flexible N-terminus is still missing. Here, we present the study of four mutants, with a decreased activity in the following order: NColE7 >> KGNK > KGNG ∼ GGNK > GGNG. At the same time, the folding, the metal-ion, and the DNA-binding affinity were unaffected by the mutations as revealed by linear and circular dichroism spectroscopy, isothermal calorimetric titrations, and gel mobility shift experiments. Semiempirical quantum chemical calculations and molecular dynamics simulations revealed that K446, K449, and/or the N-terminal amino group are able to approach the active centre in the absence of the other positively charged residues. The results suggested a complex role of the N-terminus in the catalytic process that could be exploited in the design of a controlled nuclease.
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Affiliation(s)
- Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, 6720, Szeged, Hungary; Department of Physical Chemistry and Material Sciences, University of Szeged, 6720, Szeged, Hungary
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40
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Mora L, de Zamaroczy M. In vivo processing of DNase colicins E2 and E7 is required for their import into the cytoplasm of target cells. PLoS One 2014; 9:e96549. [PMID: 24840776 PMCID: PMC4026351 DOI: 10.1371/journal.pone.0096549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/08/2014] [Indexed: 11/19/2022] Open
Abstract
DNase colicins E2 and E7, both of which appropriate the BtuB/Tol translocation machinery to cross the outer membrane, undergo a processing step as they enter the cytoplasm. This endoproteolytic cleavage is essential for their killing action. A processed form of the same size, 18.5 kDa, which corresponds to the C-terminal catalytic domain, was detected in the cytoplasm of bacteria treated with either of the two DNase colicins. The inner-membrane protease FtsH is necessary for the processing that allows the translocation of the colicin DNase domain into the cytoplasm. The processing occurs near residue D420, at the same position as the FtsH-dependent cleavage in RNase colicins E3 and D. The cleavage site is located 30 amino acids upstream of the DNase domain. In contrast, the previously reported periplasm-dependent colicin cleavage, located at R452 in colicin E2, was shown to be generated by the outer-membrane protease OmpT and we show that this cleavage is not physiologically relevant for colicin import. Residue R452, whose mutated derivatives led to toxicity defect, was shown to have no role in colicin processing and translocation, but it plays a key role in the catalytic activity, as previously reported for other DNase colicins. Membrane associated forms of colicins E2 and E7 were detected on target cells as proteinase K resistant peptides, which include both the receptor-binding and DNase domains. A similar, but much less proteinase K-resistant form was also detected with RNase colicin E3. These colicin forms are not relevant for colicin import, but their detection on the cell surface indicates that whole nuclease-colicin molecules are found in a stable association with the outer-membrane receptor BtuB of the target cells.
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Affiliation(s)
- Liliana Mora
- Institut de Biologie Physico-Chimique, CNRS, UPR 9073, Paris, France
| | - Miklos de Zamaroczy
- Institut de Biologie Physico-Chimique, CNRS, UPR 9073, Paris, France
- * E-mail:
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41
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Hansen AL, Kay LE. Measurement of histidine pKa values and tautomer populations in invisible protein states. Proc Natl Acad Sci U S A 2014; 111:E1705-12. [PMID: 24733918 PMCID: PMC4035968 DOI: 10.1073/pnas.1400577111] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The histidine imidazole side chain plays a critical role in protein function and stability. Its importance for catalysis is underscored by the fact that histidines are localized to active sites in ∼ 50% of all enzymes. NMR spectroscopy has become an important tool for studies of histidine side chains through the measurement of site-specific pK(a)s and tautomer populations. To date, such studies have been confined to observable protein ground states; however, a complete understanding of the role of histidine electrostatics in protein function and stability requires that similar investigations be extended to rare, transiently formed conformers that populate the energy landscape, yet are often "invisible" in standard NMR spectra. Here we present NMR experiments and a simple strategy for studies of such conformationally excited states based on measurement of histidine (13)Cγ, (13)Cδ2 chemical shifts and (1)Hε-(13)Cε one-bond scalar couplings. The methodology is first validated and then used to obtain pKa values and tautomer distributions for histidine residues of an invisible on-pathway folding intermediate of the colicin E7 immunity protein. Our results imply that the side chains of H40 and H47 are exposed in the intermediate state and undergo significant conformational rearrangements during folding to the native structure. Further, the pKa values explain the pH-dependent stability differences between native and intermediate states over the pH range 5.5-6.5 and they suggest that imidazole deprotonation is not a barrier to the folding of this protein.
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Affiliation(s)
- Alexandar L. Hansen
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
| | - Lewis E. Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8; and
- Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
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42
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Kim YC, Tarr AW, Penfold CN. Colicin import into E. coli cells: a model system for insights into the import mechanisms of bacteriocins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1717-31. [PMID: 24746518 DOI: 10.1016/j.bbamcr.2014.04.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/04/2014] [Accepted: 04/06/2014] [Indexed: 01/03/2023]
Abstract
Bacteriocins are a diverse group of ribosomally synthesized protein antibiotics produced by most bacteria. They range from small lanthipeptides produced by lactic acid bacteria to much larger multi domain proteins of Gram negative bacteria such as the colicins from Escherichia coli. For activity bacteriocins must be released from the producing cell and then bind to the surface of a sensitive cell to instigate the import process leading to cell death. For over 50years, colicins have provided a working platform for elucidating the structure/function studies of bacteriocin import and modes of action. An understanding of the processes that contribute to the delivery of a colicin molecule across two lipid membranes of the cell envelope has advanced our knowledge of protein-protein interactions (PPI), protein-lipid interactions and the role of order-disorder transitions of protein domains pertinent to protein transport. In this review, we provide an overview of the arrangement of genes that controls the synthesis and release of the mature protein. We examine the uptake processes of colicins from initial binding and sequestration of binding partners to crossing of the outer membrane, and then discuss the translocation of colicins through the cell periplasm and across the inner membrane to their cytotoxic site of action. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Young Chan Kim
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK
| | - Alexander W Tarr
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK
| | - Christopher N Penfold
- School of Life Sciences, University of Nottingham, Queens Medical Centre, Nottingham, NG7 2UH, UK.
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43
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Mapping of the binding landscape for a picomolar protein-protein complex through computation and experiment. Structure 2014; 22:636-45. [PMID: 24613488 DOI: 10.1016/j.str.2014.01.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 01/17/2014] [Accepted: 01/21/2014] [Indexed: 11/22/2022]
Abstract
Our understanding of protein evolution would greatly benefit from mapping of binding landscapes, i.e., changes in protein-protein binding affinity due to all single mutations. However, experimental generation of such landscapes is a tedious task due to a large number of possible mutations. Here, we use a simple computational protocol to map the binding landscape for two homologous high-affinity complexes, involving a snake toxin fasciculin and acetylcholinesterase from two different species. To verify our computational predictions, we experimentally measure binding between 25 Fas mutants and the 2 enzymes. Both computational and experimental results demonstrate that the Fas sequence is close to the optimum when interacting with its targets, yet a few mutations could further improve Kd, kon, and koff. Our computational predictions agree well with experimental results and generate distributions similar to those observed in other high-affinity PPIs, demonstrating the potential of simple computational protocols in capturing realistic binding landscapes.
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44
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Ghazaryan L, Soares MIM, Gillor O. Auto-regulation of DNA degrading bacteriocins: molecular and ecological aspects. Antonie van Leeuwenhoek 2014; 105:823-34. [PMID: 24558115 DOI: 10.1007/s10482-014-0136-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/04/2014] [Indexed: 11/29/2022]
Abstract
Colicins, proteinaceous antibiotics produced by Escherichia coli, specifically target competing strains killing them through one of a variety of mechanisms, including pore formation and nucleic acid degradation. The genes encoding colicins display a unique form of expression, which is tightly regulated, involving the DNA damage response regulatory system (the SOS response system), confined to stressful conditions and released by degradation of the producing cell. Given their lethal nature, colicin production has evolved a sophisticated system for repression and expression. While exploring the expression of 13 colicins we identified a novel means of induction unique to strains that kill by DNA degradation: these colicinogenic strains mildly poison themselves inflicting DNA damage that induces their DNA repair system (the SOS system), and their own expression. We established that among the four known DNase colicins (E2, E7, E8 and E9), three act to induce their own production. Using different stresses we show that this form of self-regulation entails high cost when growth conditions are not optimal, and is not carried out by individual cells but is a population-mediated trait. We discuss this novel form of colicins' regulation and expression, and its possible molecular mechanism and evolutionary implications.
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Affiliation(s)
- Lusine Ghazaryan
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben Gurion, 84990, Beer-Sheva, Israel
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45
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Crnigoj M, Podlesek Z, Budič M, Zgur-Bertok D. The Escherichia coli uropathogenic-specific-protein-associated immunity protein 3 (Imu3) has nucleic acid -binding activity. BMC Microbiol 2014; 14:16. [PMID: 24472116 PMCID: PMC3917654 DOI: 10.1186/1471-2180-14-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/20/2014] [Indexed: 11/19/2022] Open
Abstract
Background The Escherichia coli uropathogenic-specific protein (Usp) is a bacteriocin-like genotoxin, active against mammalian cells and associated with E. coli strains that provoke pyelonephritis, prostatitis and bacteraemia. Usp is encoded by a small pathogenicity island with three downstream small open reading frames (Imu1-3) that are believed to provide immunity to the producer. To prevent host suicide, colicins, bacteriocins of E. coli, form tight complexes with their cognate immunity proteins. Colicin – immunity protein complexes are among the strongest protein complexes known. Here, the Usp associated immunity protein 3 (Imu3) was partially characterized to gain insight into its role and mechanism of activity. Results Isolation and partial characterisation of the Usp-associated immunity protein-3 (Imu3) revealed that, while Usp and Imu3 do not form a high affinity complex, Imu3 exhibits DNA and RNA binding activity. Imu3 was also shown to protect DNA against degradation by colicin E7. Conclusions Our data infer that nonspecific DNA binding of the Imu3 immunity protein, prevents suicide of E. coli producing the genotoxin Usp.
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Affiliation(s)
| | | | | | - Darja Zgur-Bertok
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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46
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Hammami R, Fernandez B, Lacroix C, Fliss I. Anti-infective properties of bacteriocins: an update. Cell Mol Life Sci 2013; 70:2947-67. [PMID: 23109101 PMCID: PMC11113238 DOI: 10.1007/s00018-012-1202-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/05/2012] [Accepted: 10/18/2012] [Indexed: 02/01/2023]
Abstract
Bacteriocin production is a widespread phenomenon among bacteria. Bacteriocins hold great promise for the treatment of diseases caused by pathogenic bacteria and could be used in the future as alternatives to existing antibiotics. The anti-infective potential of bacteriocins for inhibiting pathogens has been shown in various food matrices including cheese, meat, and vegetables. However, their inhibition of pathogens in vivo remains unclear and needs more investigation, due mainly to difficulties associated with demonstrating their health benefits. Many bacteriocins produced by established or potential probiotic organisms have been evaluated as potential therapeutic agents and interesting findings have been documented in vitro as well as in a few in vivo studies. Some recent in vivo studies point to the efficacy of bacteriocin-based treatments of human and animal infections. While further investigation remains necessary before the possibilities for bacteriocins in clinical practice can be described more fully, this review provides an overview of their potential applications to human and veterinary health.
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Affiliation(s)
- Riadh Hammami
- STELA Dairy Research Centre, Nutraceuticals and Functional Foods Institute, Université Laval, Quebec, QC, Canada.
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47
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Braun V, Patzer SI. Intercellular communication by related bacterial protein toxins: colicins, contact-dependent inhibitors, and proteins exported by the type VI secretion system. FEMS Microbiol Lett 2013; 345:13-21. [PMID: 23701660 DOI: 10.1111/1574-6968.12180] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 05/15/2013] [Accepted: 05/16/2013] [Indexed: 12/15/2022] Open
Abstract
Bacteria are in constant conflict with competing bacterial and eukaryotic cells. To cope with the various challenges, bacteria developed distinct strategies, such as toxins that inhibit the growth or kill rivals of the same ecological niche. In recent years, two toxin systems have been discovered - the type VI secretion system and the contact-dependent growth inhibition (CDI) system. These systems have structural and functional similarities and share features with the long-known gram-negative bacteriocins, such as small immunity proteins that bind to and inactivate the toxins, and target sites on DNA, tRNA, rRNA, murein (peptidoglycan), or the cytoplasmic membrane. Colicins, CdiA proteins, and certain type VI toxins have a modular design with the transport functions localized in the N-terminal region and the activity functions localized in the C-terminal region. Despite these common properties, the sequences of toxins and immunity proteins of colicins, CDI systems, and type VI systems show little similarity.
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Affiliation(s)
- Volkmar Braun
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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48
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Rodriguez-Larrea D, Bayley H. Multistep protein unfolding during nanopore translocation. NATURE NANOTECHNOLOGY 2013; 8:288-95. [PMID: 23474543 PMCID: PMC4830145 DOI: 10.1038/nnano.2013.22] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 01/25/2013] [Indexed: 05/18/2023]
Abstract
Cells are divided into compartments and separated from the environment by lipid bilayer membranes. Essential molecules are transported back and forth across the membranes. We have investigated how folded proteins use narrow transmembrane pores to move between compartments. During this process, the proteins must unfold. To examine co-translocational unfolding of individual molecules, we tagged protein substrates with oligonucleotides to enable potential-driven unidirectional movement through a model protein nanopore, a process that differs fundamentally from extension during force spectroscopy measurements. Our findings support a four-step translocation mechanism for model thioredoxin substrates. First, the DNA tag is captured by the pore. Second, the oligonucleotide is pulled through the pore, causing local unfolding of the C terminus of the thioredoxin adjacent to the pore entrance. Third, the remainder of the protein unfolds spontaneously. Finally, the unfolded polypeptide diffuses through the pore into the recipient compartment. The unfolding pathway elucidated here differs from those revealed by denaturation experiments in solution, for which two-state mechanisms have been proposed.
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Affiliation(s)
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
- Correspondence should be addressed to H. Bayley ()
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49
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Hansen AL, Bouvignies G, Kay LE. Probing slowly exchanging protein systems via ¹³Cα-CEST: monitoring folding of the Im7 protein. JOURNAL OF BIOMOLECULAR NMR 2013; 55:279-289. [PMID: 23386228 DOI: 10.1007/s10858-013-9711-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/20/2013] [Indexed: 06/01/2023]
Abstract
A¹³C(α) chemical exchange saturation transfer based experiment is presented for the study of protein systems undergoing slow interconversion between an 'observable' ground state and one or more 'invisible' excited states. Here a labeling strategy whereby [2-(13)C]-glucose is the sole carbon source is exploited, producing proteins with ¹³C at the C(α) position, while the majority of residues remain unlabeled at CO or C(β). The new experiment is demonstrated with an application to the folding reaction of the Im7 protein that involves an on-pathway excited state. The obtained excited state (13)C(α) chemical shifts are cross validated by comparison to values extracted from analysis of CPMG relaxation dispersion profiles, establishing the utility of the methodology.
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Affiliation(s)
- Alexandar L Hansen
- Department of Molecular Genetics, The University of Toronto, Toronto, ON, M5S 1A8, Canada
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50
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Farrance OE, Hann E, Kaminska R, Housden NG, Derrington SR, Kleanthous C, Radford SE, Brockwell DJ. A force-activated trip switch triggers rapid dissociation of a colicin from its immunity protein. PLoS Biol 2013; 11:e1001489. [PMID: 23431269 PMCID: PMC3576412 DOI: 10.1371/journal.pbio.1001489] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 01/09/2013] [Indexed: 01/24/2023] Open
Abstract
A single-molecule force study shows that rapid dissociation of a high-affinity protein interaction can be triggered by site-specific remodelling of one protein partner, and that prevention of remodelling maintains avidity. Colicins are protein antibiotics synthesised by Escherichia coli strains to target and kill related bacteria. To prevent host suicide, colicins are inactivated by binding to immunity proteins. Despite their high avidity (Kd≈fM, lifetime ≈4 days), immunity protein release is a pre-requisite of colicin intoxication, which occurs on a timescale of minutes. Here, by measuring the dynamic force spectrum of the dissociation of the DNase domain of colicin E9 (E9) and immunity protein 9 (Im9) complex using an atomic force microscope we show that application of low forces (<20 pN) increases the rate of complex dissociation 106-fold, to a timescale (lifetime ≈10 ms) compatible with intoxication. We term this catastrophic force-triggered increase in off-rate a trip bond. Using mutational analysis, we elucidate the mechanism of this switch in affinity. We show that the N-terminal region of E9, which has sparse contacts with the hydrophobic core, is linked to an allosteric activator region in E9 (residues 21–30) whose remodelling triggers immunity protein release. Diversion of the force transduction pathway by the introduction of appropriately positioned disulfide bridges yields a force resistant complex with a lifetime identical to that measured by ensemble techniques. A trip switch within E9 is ideal for its function as it allows bipartite complex affinity, whereby the stable colicin:immunity protein complex required for host protection can be readily converted to a kinetically unstable complex whose dissociation is necessary for cellular invasion and competitor death. More generally, the observation of two force phenotypes for the E9:Im9 complex demonstrates that force can re-sculpt the underlying energy landscape, providing new opportunities to modulate biological reactions in vivo; this rationalises the commonly observed discrepancy between off-rates measured by dynamic force spectroscopy and ensemble methods. Many proteins interact with other proteins as part of their function. One method of modulating the activity of protein complexes is to break them apart. Some complexes, however, are extremely kinetically stable and it is unclear how these can dissociate on a biologically relevant timescale. In this study we address this question using protein complexes between colicin E9 (a bacterial toxin) and its immunity protein Im9. These highly avid complexes (with a lifetime of days) must be broken apart for colicin to be activated. By using single-molecule force methods we show that pulling on one end of colicin E9 drastically destabilises the complex so that it dissociates a million-fold faster than its intrinsic rate. We then show that preventing this destabilisation (by the insertion of cross-links that pin the N-terminus of E9 in place) yields a kinetically stable complex. It has previously been postulated that force can destabilise a protein complex by partially unfolding one or more binding partners. Our work provides new experimental evidence that shows this is the case and provides a mechanism for this phenomenon, which we term a trip bond. For the E9:Im9 complex, trip bond behaviour allows a stable complex to be rapidly dissociated by application of a surprisingly small force.
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Affiliation(s)
- Oliver E. Farrance
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - Eleanore Hann
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Sasha R. Derrington
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sheena E. Radford
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
| | - David J. Brockwell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, United Kingdom
- * E-mail:
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