1
|
Danov A, Pollin I, Moon E, Ho M, Wilson BA, Papathanos PA, Kaplan T, Levy A. Identification of novel toxins associated with the extracellular contractile injection system using machine learning. Mol Syst Biol 2024; 20:859-879. [PMID: 39069594 PMCID: PMC11297309 DOI: 10.1038/s44320-024-00053-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/06/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
Secretion systems play a crucial role in microbe-microbe or host-microbe interactions. Among these systems, the extracellular contractile injection system (eCIS) is a unique bacterial and archaeal extracellular secretion system that injects protein toxins into target organisms. However, the specific proteins that eCISs inject into target cells and their functions remain largely unknown. Here, we developed a machine learning classifier to identify eCIS-associated toxins (EATs). The classifier combines genetic and biochemical features to identify EATs. We also developed a score for the eCIS N-terminal signal peptide to predict EAT loading. Using the classifier we classified 2,194 genes from 950 genomes as putative EATs. We validated four new EATs, EAT14-17, showing toxicity in bacterial and eukaryotic cells, and identified residues of their respective active sites that are critical for toxicity. Finally, we show that EAT14 inhibits mitogenic signaling in human cells. Our study provides insights into the diversity and functions of EATs and demonstrates machine learning capability of identifying novel toxins. The toxins can be employed in various applications dependently or independently of eCIS.
Collapse
Affiliation(s)
- Aleks Danov
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Inbal Pollin
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Eric Moon
- Department of Microbiology, University of Illinois Urbana-Champaign, 601 South Goodwin Ave, Urbana, 61801, IL, USA
| | - Mengfei Ho
- Department of Microbiology, University of Illinois Urbana-Champaign, 601 South Goodwin Ave, Urbana, 61801, IL, USA
| | - Brenda A Wilson
- Department of Microbiology, University of Illinois Urbana-Champaign, 601 South Goodwin Ave, Urbana, 61801, IL, USA
| | - Philippos A Papathanos
- Department of Entomology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| |
Collapse
|
2
|
Lin L. The expanding universe of contractile injection systems in bacteria. Curr Opin Microbiol 2024; 79:102465. [PMID: 38520915 DOI: 10.1016/j.mib.2024.102465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
Contractile injection systems (CISs) are phage tail-like machineries found in a wide range of bacteria. They are often deployed by bacteria to translocate effectors into the extracellular space or into target cells. CISs are classified into intracellular type VI secretion systems (T6SSs) and extracellular CIS (eCISs). eCISs are assembled in cytoplasm and released into the extracellular milieu upon cell lysis, while T6SSs are the secretion systems widespread among Gram-negative bacteria and actively translocate effectors into the environment or into the adjacent cell, without lysis of T6SS-producing cells. Recently, several noncanonical CISs that exhibit distinct characteristics have been discovered. This review will provide an overview on these noncanonical CISs and their unique features, as well as new advances in reprogramming CISs for therapeutic protein delivery.
Collapse
Affiliation(s)
- Lin Lin
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| |
Collapse
|
3
|
Nagakubo T, Nishiyama T, Yamamoto T, Nomura N, Toyofuku M. Contractile injection systems facilitate sporogenic differentiation of Streptomyces davawensis through the action of a phage tapemeasure protein-related effector. Nat Commun 2024; 15:4442. [PMID: 38789435 PMCID: PMC11126660 DOI: 10.1038/s41467-024-48834-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Contractile injection systems (CISs) are prokaryotic phage tail-like nanostructures loading effector proteins that mediate various biological processes. Although CIS functions have been diversified through evolution and hold the great potential as protein delivery systems, the functional characterisation of CISs and their effectors is currently limited to a few CIS lineages. Here, we show that the CISs of Streptomyces davawensis belong to a unique group of bacterial CISs distributed across distant phyla and facilitate sporogenic differentiation of this bacterium. CIS loss results in decreases in extracellular DNA release, biomass accumulation, and spore formation in S. davawensis. CISs load an effector, which is a remote homolog of phage tapemeasure proteins, and its C-terminal domain has endonuclease activity responsible for the CIS-associated phenotypes. Our findings illustrate that CISs can contribute to the reproduction of bacteria through the action of the effector and suggest an evolutionary link between CIS effectors and viral cargos.
Collapse
Affiliation(s)
- Toshiki Nagakubo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan.
| | - Tatsuya Nishiyama
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Chiyoda, Japan
| | - Tatsuya Yamamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
- Life Science Center for Survival Dynamics, University of Tsukuba, Tsukuba, Japan
| | - Masanori Toyofuku
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan.
| |
Collapse
|
4
|
Kaur R, McGarry A, Shropshire JD, Leigh BA, Bordenstein SR. Prophage proteins alter long noncoding RNA and DNA of developing sperm to induce a paternal-effect lethality. Science 2024; 383:1111-1117. [PMID: 38452081 PMCID: PMC11187695 DOI: 10.1126/science.adk9469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
The extent to which prophage proteins interact with eukaryotic macromolecules is largely unknown. In this work, we show that cytoplasmic incompatibility factor A (CifA) and B (CifB) proteins, encoded by prophage WO of the endosymbiont Wolbachia, alter long noncoding RNA (lncRNA) and DNA during Drosophila sperm development to establish a paternal-effect embryonic lethality known as cytoplasmic incompatibility (CI). CifA is a ribonuclease (RNase) that depletes a spermatocyte lncRNA important for the histone-to-protamine transition of spermiogenesis. Both CifA and CifB are deoxyribonucleases (DNases) that elevate DNA damage in late spermiogenesis. lncRNA knockdown enhances CI, and mutagenesis links lncRNA depletion and subsequent sperm chromatin integrity changes to embryonic DNA damage and CI. Hence, prophage proteins interact with eukaryotic macromolecules during gametogenesis to create a symbiosis that is fundamental to insect evolution and vector control.
Collapse
Affiliation(s)
- Rupinder Kaur
- Pennsylvania State University, Departments of Biology and Entomology, University Park, PA 16802, USA
- One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
| | - Angelina McGarry
- Pennsylvania State University, Departments of Biology and Entomology, University Park, PA 16802, USA
- One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - J. Dylan Shropshire
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Brittany A. Leigh
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
| | - Seth R. Bordenstein
- Pennsylvania State University, Departments of Biology and Entomology, University Park, PA 16802, USA
- One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
| |
Collapse
|
5
|
Wang X, Leptihn S. Defense and anti-defense mechanisms of bacteria and bacteriophages. J Zhejiang Univ Sci B 2024; 25:181-196. [PMID: 38453634 PMCID: PMC10918411 DOI: 10.1631/jzus.b2300101] [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: 02/14/2023] [Accepted: 06/24/2023] [Indexed: 03/09/2024]
Abstract
In the post-antibiotic era, the overuse of antimicrobials has led to a massive increase in antimicrobial resistance, leaving medical doctors few or no treatment options to fight infections caused by superbugs. The use of bacteriophages is a promising alternative to treat infections, supplementing or possibly even replacing antibiotics. Using phages for therapy is possible, since these bacterial viruses can kill bacteria specifically, causing no harm to the normal flora. However, bacteria have developed a multitude of sophisticated and complex ways to resist infection by phages, including abortive infection and the clustered regularly interspersed short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system. Phages also can evolve and acquire new anti-defense strategies to continue predation. An in-depth exploration of both defense and anti-defense mechanisms would contribute to optimizing phage therapy, while we would also gain novel insights into the microbial world. In this paper, we summarize recent research on bacterial phage resistance and phage anti-defense mechanisms, as well as collaborative win-win systems involving both virus and host.
Collapse
Affiliation(s)
- Xiaoqing Wang
- School of Medicine, Lishui University, Lishui 323000, China.
| | - Sebastian Leptihn
- University of Edinburgh Medical School, Biomedical Sciences, College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh EH8 9JZ, UK.
- HMU Health and Medical University, Am Anger 64/73- 99084 Erfurt, Germany.
| |
Collapse
|
6
|
Sonani RR, Palmer LK, Esteves NC, Horton AA, Sebastian AL, Kelly RJ, Wang F, Kreutzberger MAB, Russell WK, Leiman PG, Scharf BE, Egelman EH. An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano. Nat Commun 2024; 15:756. [PMID: 38272938 PMCID: PMC10811340 DOI: 10.1038/s41467-024-44959-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, contraction of an external sheath powers the motion of an inner tube through the membrane. The structure, energetics, and mechanism of the machinery imply rigidity and straightness. The contractile tail of Agrobacterium tumefaciens bacteriophage Milano is flexible and bent to varying degrees, which sets it apart from other contractile tail-like systems. Here, we report structures of the Milano tail including the sheath-tube complex, baseplate, and putative receptor-binding proteins. The flexible-to-rigid transformation of the Milano tail upon contraction can be explained by unique electrostatic properties of the tail tube and sheath. All components of the Milano tail, including sheath subunits, are crosslinked by disulfides, some of which must be reduced for contraction to occur. The putative receptor-binding complex of Milano contains a tailspike, a tail fiber, and at least two small proteins that form a garland around the distal ends of the tailspikes and tail fibers. Despite being flagellotropic, Milano lacks thread-like tail filaments that can wrap around the flagellum, and is thus likely to employ a different binding mechanism.
Collapse
Affiliation(s)
- Ravi R Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - Lee K Palmer
- Mass Spectrometry Facility, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Nathaniel C Esteves
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Abigail A Horton
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Amanda L Sebastian
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Rebecca J Kelly
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
| | - William K Russell
- Mass Spectrometry Facility, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA.
| |
Collapse
|
7
|
Samson R, Dharne M, Khairnar K. Bacteriophages: Status quo and emerging trends toward one health approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168461. [PMID: 37967634 DOI: 10.1016/j.scitotenv.2023.168461] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.
Collapse
Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Krishna Khairnar
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Environmental Virology Cell (EVC), CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
| |
Collapse
|
8
|
Nesbit KT, Shikuma NJ. Future research directions of the model marine tubeworm Hydroides elegans and synthesis of developmental staging of the complete life cycle. Dev Dyn 2023; 252:1391-1400. [PMID: 37227089 PMCID: PMC10674040 DOI: 10.1002/dvdy.628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The biofouling marine tube worm, Hydroides elegans, is an indirect developing polychaete with significance as a model organism for questions in developmental biology and the evolution of host-microbe interactions. However, a complete description of the life cycle from fertilization through sexual maturity remains scattered in the literature, and lacks standardization. RESULTS AND DISCUSSION Here, we present a unified staging scheme synthesizing the major morphological changes that occur during the entire life cycle of the animal. These data represent a complete record of the life cycle, and serve as a foundation for connecting molecular changes with morphology. CONCLUSIONS The present synthesis and associated staging scheme are especially timely as this system gains traction within research communities. Characterizing the Hydroides life cycle is essential for investigating the molecular mechanisms that drive major developmental transitions, like metamorphosis, in response to bacteria.
Collapse
Affiliation(s)
- Katherine T. Nesbit
- Molecular Biology Division, San Diego State University, 5500 Campanile Drive, San Diego CA, 92182
| | - Nicholas J. Shikuma
- Molecular Biology Division, San Diego State University, 5500 Campanile Drive, San Diego CA, 92182
| |
Collapse
|
9
|
Heiman CM, Vacheron J, Keel C. Evolutionary and ecological role of extracellular contractile injection systems: from threat to weapon. Front Microbiol 2023; 14:1264877. [PMID: 37886057 PMCID: PMC10598620 DOI: 10.3389/fmicb.2023.1264877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Contractile injection systems (CISs) are phage tail-related structures that are encoded in many bacterial genomes. These devices encompass the cell-based type VI secretion systems (T6SSs) as well as extracellular CISs (eCISs). The eCISs comprise the R-tailocins produced by various bacterial species as well as related phage tail-like structures such as the antifeeding prophages (Afps) of Serratia entomophila, the Photorhabdus virulence cassettes (PVCs), and the metamorphosis-associated contractile structures (MACs) of Pseudoalteromonas luteoviolacea. These contractile structures are released into the extracellular environment upon suicidal lysis of the producer cell and play important roles in bacterial ecology and evolution. In this review, we specifically portray the eCISs with a focus on the R-tailocins, sketch the history of their discovery and provide insights into their evolution within the bacterial host, their structures and how they are assembled and released. We then highlight ecological and evolutionary roles of eCISs and conceptualize how they can influence and shape bacterial communities. Finally, we point to their potential for biotechnological applications in medicine and agriculture.
Collapse
Affiliation(s)
- Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | |
Collapse
|
10
|
Alker AT, Farrell MV, Aspiras AE, Dunbar TL, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine bacteria reveals functional insights during bacteria-stimulated metamorphosis. mBio 2023; 14:e0150223. [PMID: 37530556 PMCID: PMC10470607 DOI: 10.1128/mbio.01502-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 08/03/2023] Open
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea, which stimulates the metamorphosis of the model tubeworm, Hydroides elegans. Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for testing the genetic tractability of marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts resulted in the successful conjugation of 12 marine strains from the Alphaproteobacteria and Gammaproteobacteria classes. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with potential implications for environmental restoration and biotechnology. IMPORTANCE Marine Proteobacteria are attractive targets for genetic engineering due to their ability to produce a diversity of bioactive metabolites and their involvement in host-microbe symbioses. Modular cloning toolkits have become a standard for engineering model microbes, such as Escherichia coli, because they enable innumerable mix-and-match DNA assembly and engineering options. However, such modular tools have not yet been applied to most marine bacterial species. In this work, we adapt a modular plasmid toolkit for use in a set of 12 marine bacteria from the Gammaproteobacteria and Alphaproteobacteria classes. We demonstrate the utility of this genetic toolkit by engineering a marine Pseudoalteromonas bacterium to study their association with its host animal Hydroides elegans. This work provides a proof of concept that modular genetic tools can be applied to diverse marine bacteria to address basic science questions and for biotechnology innovations.
Collapse
Affiliation(s)
- Amanda T. Alker
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Morgan V. Farrell
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Alpher E. Aspiras
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Tiffany L. Dunbar
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Andriy Fedoriouk
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Jeffrey E. Jones
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Sama R. Mikhail
- Department of Biology, San Diego State University, San Diego, California, USA
| | | | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
| | - Nicholas J. Shikuma
- Department of Biology, San Diego State University, San Diego, California, USA
| |
Collapse
|
11
|
Lu S, Cai Y. Bacterial molecular syringe for drug delivery. Cell Host Microbe 2023; 31:917-919. [PMID: 37321174 DOI: 10.1016/j.chom.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 06/17/2023]
Abstract
Different protein-delivery tools are being actively developed for efficient drug delivery into host cells. A recent study by Kreitz et al. in Nature reported a syringe-like protein delivery vector engineered from natural endosymbiotic bacteria for potential human use.
Collapse
Affiliation(s)
- Sicong Lu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yujia Cai
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
12
|
Ohdera A, Attarwala K, Wu V, Henry R, Laird H, Hofmann DK, Fitt WK, Medina M. Comparative Genomic Insights into Bacterial Induction of Larval Settlement and Metamorphosis in the Upside-Down Jellyfish Cassiopea. mSphere 2023:e0031522. [PMID: 37154768 DOI: 10.1128/msphere.00315-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Bacteria are important mediators of the larval transition from pelagic to benthic environments for marine organisms. Bacteria can therefore dictate species distribution and success of an individual. Despite the importance of marine bacteria to animal ecology, the identity of inductive microbes for many invertebrates are unknown. Here, we report the first successful isolation of bacteria from natural substrates capable of inducing settlement and metamorphosis of the planula larvae stage of a true jellyfish, the upside-down jellyfish Cassiopea xamachana. Inductive bacteria belonged to multiple phyla, with various capacity to induce settlement and metamorphosis. The most inductive isolates belonged to the genus Pseudoalteromonas, a marine bacterium known to induce the pelago-benthic transition in other marine invertebrates. In sequencing the genome of the isolated Pseudoalteromonas and a semiinductive Vibrio, we found biosynthetic pathways previously implicated in larval settlement were absent in Cassiopea inducing taxa. We instead identified other candidate biosynthetic gene clusters involved in larval metamorphosis. These findings could provide hints to the ecological success of C. xamachana compared to sympatric congeneric species within mangrove environments and provide avenues to investigate the evolution of animal-microbe interactions. IMPORTANCE The pelagic to benthic transition for the larvae of many marine invertebrate species are thought to be triggered by microbial cues. The microbial species and exact cue that initiates this transition remains unknown for many animals. Here, we identify two bacterial species, a Pseudoalteromonas and a Vibrio, isolated from natural substrate that induce settlement and metamorphosis of the upside-down jellyfish Cassiopea xamachana. Genomic sequencing revealed both isolates lacked genes known to induce the life history transition in other marine invertebrates. Instead, we identified other gene clusters that may be important for jellyfish settlement and metamorphosis. This study is the first step to identifying the bacterial cue for C. xamachana, an ecologically important species to coastal ecosystems and an emerging model system. Understanding the bacterial cues provides insight into marine invertebrate ecology and evolution of animal-microbe interactions.
Collapse
Affiliation(s)
- Aki Ohdera
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
- National Museum of Natural History, Smithsonian Institute, Washington, DC, USA
| | - Khushboo Attarwala
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Victoria Wu
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Rubain Henry
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Henry Laird
- University of Wisconsin, Madison, Wisconsin, USA
| | | | - William K Fitt
- Odum School of Ecology, University of Georgia, Athens, Georgia, USA
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
- Smithsonian Tropical Research Institute, Smithsonian Institute, Washington, DC, USA
| |
Collapse
|
13
|
Kreitz J, Friedrich MJ, Guru A, Lash B, Saito M, Macrae RK, Zhang F. Programmable protein delivery with a bacterial contractile injection system. Nature 2023; 616:357-364. [PMID: 36991127 PMCID: PMC10097599 DOI: 10.1038/s41586-023-05870-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/21/2023] [Indexed: 03/31/2023]
Abstract
Endosymbiotic bacteria have evolved intricate delivery systems that enable these organisms to interface with host biology. One example, the extracellular contractile injection systems (eCISs), are syringe-like macromolecular complexes that inject protein payloads into eukaryotic cells by driving a spike through the cellular membrane. Recently, eCISs have been found to target mouse cells1-3, raising the possibility that these systems could be harnessed for therapeutic protein delivery. However, whether eCISs can function in human cells remains unknown, and the mechanism by which these systems recognize target cells is poorly understood. Here we show that target selection by the Photorhabdus virulence cassette (PVC)-an eCIS from the entomopathogenic bacterium Photorhabdus asymbiotica-is mediated by specific recognition of a target receptor by a distal binding element of the PVC tail fibre. Furthermore, using in silico structure-guided engineering of the tail fibre, we show that PVCs can be reprogrammed to target organisms not natively targeted by these systems-including human cells and mice-with efficiencies approaching 100%. Finally, we show that PVCs can load diverse protein payloads, including Cas9, base editors and toxins, and can functionally deliver them into human cells. Our results demonstrate that PVCs are programmable protein delivery devices with possible applications in gene therapy, cancer therapy and biocontrol.
Collapse
Affiliation(s)
- Joseph Kreitz
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mirco J Friedrich
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akash Guru
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Blake Lash
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Makoto Saito
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rhiannon K Macrae
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
14
|
Vladimirov M, Zhang RX, Mak S, Nodwell JR, Davidson AR. A contractile injection system is required for developmentally regulated cell death in Streptomyces coelicolor. Nat Commun 2023; 14:1469. [PMID: 36927736 PMCID: PMC10020575 DOI: 10.1038/s41467-023-37087-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
Diverse bacterial species produce extracellular contractile injection systems (eCISs). Although closely related to contractile phage tails, eCISs can inject toxic proteins into eukaryotic cells. Thus, these systems are commonly viewed as cytotoxic defense mechanisms that are not central to other aspects of bacterial biology. Here, we provide evidence that eCISs appear to participate in the complex developmental process of the bacterium Streptomyces coelicolor. In particular, we show that S. coelicolor produces eCIS particles during its normal growth cycle, and that strains lacking functional eCIS particles exhibit pronounced alterations in their developmental program. Furthermore, eCIS-deficient mutants display reduced levels of cell death and altered morphology during growth in liquid media. Our results suggest that the main role of eCISs in S. coelicolor is to modulate the developmental switch that leads to aerial hyphae formation and sporulation, rather than to attack other species.
Collapse
Affiliation(s)
- Maria Vladimirov
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ruo Xi Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Stefanie Mak
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Justin R Nodwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
15
|
Alker AT, Aspiras AE, Dunbar TL, Farrell MV, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526474. [PMID: 36778221 PMCID: PMC9915575 DOI: 10.1101/2023.01.31.526474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea , which stimulates the metamorphosis of the model tubeworm, Hydroides elegans . Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for rapidly creating and iteratively testing genetic tractability by modifying marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts enabled the successful transformation of twelve marine strains across two Proteobacteria classes, four orders and ten genera. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with broader implications for environmental restoration and biotechnology.
Collapse
|
16
|
Rischer M, Guo H, Beemelmanns C. Signalling molecules inducing metamorphosis in marine organisms. Nat Prod Rep 2022; 39:1833-1855. [PMID: 35822257 DOI: 10.1039/d1np00073j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: findings from early 1980s until early 2022Microbial-derived cues of marine biofilms induce settlement and metamorphosis of marine organisms, a process responsible for the emergence of diverse flora and fauna in marine habitats. Although this phenomenon is known for more than 80 years, the research field has only recently gained much momentum. Here, we summarize the currently existing biochemical and microbial knowledge about microbial signalling molecules, con-specific signals, and synthetic compounds that induce or prevent recruitment, settlement, and metamorphosis in invertebrate larvae. We discuss the possible modes of action and conclude with perspectives for future research directions in the field of marine chemical ecology.
Collapse
Affiliation(s)
- Maja Rischer
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany.
| | - Huijuan Guo
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany.
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraße 11a, Jena, 07745, Germany. .,Biochemistry of Microbial Metabolism, Institute of Biochemistry, Leipzig University, Johannisallee 21-23, Leipzig 04103, Germany
| |
Collapse
|
17
|
Bordenstein SR, Bordenstein SR. Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae. PLoS Genet 2022; 18:e1010227. [PMID: 35666732 PMCID: PMC9203015 DOI: 10.1371/journal.pgen.1010227] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 06/16/2022] [Accepted: 04/29/2022] [Indexed: 11/19/2022] Open
Abstract
Wolbachia are the most common obligate, intracellular bacteria in animals. They exist worldwide in arthropod and nematode hosts in which they commonly act as reproductive parasites or mutualists, respectively. Bacteriophage WO, the largest of Wolbachia’s mobile elements, includes reproductive parasitism genes, serves as a hotspot for genetic divergence and genomic rearrangement of the bacterial chromosome, and uniquely encodes a Eukaryotic Association Module with eukaryotic-like genes and an ensemble of putative host interaction genes. Despite WO’s relevance to genome evolution, selfish genetics, and symbiotic applications, relatively little is known about its origin, host range, diversification, and taxonomic classification. Here we analyze the most comprehensive set of 150 Wolbachia and phage WO assemblies to provide a framework for discretely organizing and naming integrated phage WO genomes. We demonstrate that WO is principally in arthropod Wolbachia with relatives in diverse endosymbionts and metagenomes, organized into four variants related by gene synteny, often oriented opposite the putative origin of replication in the Wolbachia chromosome, and the large serine recombinase is an ideal typing tool to distinguish the four variants. We identify a novel, putative lytic cassette and WO’s association with a conserved eleven gene island, termed Undecim Cluster, that is enriched with virulence-like genes. Finally, we evaluate WO-like Islands in the Wolbachia genome and discuss a new model in which Octomom, a notable WO-like Island, arose from a split with WO. Together, these findings establish the first comprehensive Linnaean taxonomic classification of endosymbiont phages, including non-Wolbachia phages from aquatic environments, that includes a new family and two new genera to capture the collective relatedness of these viruses.
Collapse
Affiliation(s)
- Sarah R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, United States of America
| |
Collapse
|
18
|
Diacylglycerol, PKC and MAPK signaling initiate tubeworm metamorphosis in response to bacteria. Dev Biol 2022; 487:99-109. [DOI: 10.1016/j.ydbio.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 11/21/2022]
|
19
|
Nagakubo T. Biological Functions and Applications of Virus-Related Bacterial Nanoparticles: A Review. Int J Mol Sci 2022; 23:ijms23052595. [PMID: 35269736 PMCID: PMC8910223 DOI: 10.3390/ijms23052595] [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: 12/22/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/25/2022] Open
Abstract
Accumulating evidence suggests that microorganisms produce various nanoparticles that exhibit a variety of biological functions. The structure of these bacterial nanoparticles ranges from membrane vesicles composed of membrane lipids to multicomponent proteinaceous machines. Of bacterial nanoparticles, bacterial phage tail-like nanoparticles, associated with virus-related genes, are found in bacteria from various environments and have diverse functions. Extracellular contractile injection systems (eCISs), a type of bacterial phage tail-like nanostructure, have diverse biological functions that mediate the interactions between the producer bacteria and target eukaryote. Known gram-negative bacterial eCISs can act as protein translocation systems and inject effector proteins that modulate eukaryotic cellular processes by attaching to the target cells. Further investigation of the functions of eCISs will facilitate the application of these nanomachines as nano-sized syringes in the field of nanomedicine and vaccine development. This review summarises the recent progress in elucidating the structures and biological functions of nanoparticles that resemble the tail components of phages that infect bacteria and discusses directions for future research to improve the clinical applicability of virus-related bacterial nanoparticles.
Collapse
Affiliation(s)
- Toshiki Nagakubo
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan;
- Microbiology Research Centre for Sustainability (MiCS), University of Tsukuba, Tsukuba 305-8577, Japan
| |
Collapse
|
20
|
Xu J, Ericson CF, Lien YW, Rutaganira FUN, Eisenstein F, Feldmüller M, King N, Pilhofer M. Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis. Nat Microbiol 2022; 7:397-410. [PMID: 35165385 PMCID: PMC8894135 DOI: 10.1038/s41564-022-01059-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/05/2022] [Indexed: 12/11/2022]
Abstract
Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell–cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a ‘cap adaptor’ located at the distal end, a ‘plug’ exposed to the tube lumen, and a ‘cage’ formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re−engineering CISs. The characterization of an extracellular contractile injection system (eCIS) from the marine bacterium Algoriphagus machipongonensis (AlgoCIS) reveals structural features linked to the assembly and function of this nanomachine.
Collapse
|
21
|
Shikuma NJ. Bacteria-Stimulated Metamorphosis: an Ocean of Insights from Investigating a Transient Host-Microbe Interaction. mSystems 2021; 6:e0075421. [PMID: 34463566 DOI: 10.1128/msystems.00754-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent research on host-microbe interactions has focused on intimate symbioses. Yet transient interactions, such as the stimulation of animal metamorphosis by bacteria, can have significant impacts on each partner. During these short-lived interactions, swimming animal larvae identify a desirable location on the seafloor and undergo metamorphosis into a juvenile based on the presence of specific bottom-dwelling bacteria. While this phenomenon is critical for seeding new animals to establish or maintain benthic ecosystems, there is an ocean of fundamental questions that remain unanswered. Here, I propose an updated model of how bacteria stimulate animal metamorphosis based on evidence that bacteria inject a stimulatory protein that prompts tubeworm metamorphosis. I consider what we hope to learn about stimulatory bacterial products, how animals recognize these products, and the consequences for both partners. Finally, I provide examples of how studying an enigmatic host-microbe interaction can serve as an engine for scientific discovery.
Collapse
Affiliation(s)
- Nicholas J Shikuma
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, California, USA
| |
Collapse
|
22
|
Investigating the process of sheath maturation in Anti-feeding prophage- a phage tail-like protein translocation structure. J Bacteriol 2021; 203:e0010421. [PMID: 34370558 DOI: 10.1128/jb.00104-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Anti-feeding prophage (Afp) produced by the bacterium Serratia entomophila is the archetype, external contractile injection system (eCIS). Afp and its orthologues are characterized by three sheath proteins while contractile bacteriophages and pyocins encode only one. Using targeted mutagenesis, transmission electron microscopy (TEM) and pull-down studies, we interrogated the roles of the three sheath proteins (Afp2, Afp3 and Afp4) in Afp assembly, in particular, the interaction between the two sequence-related helical-sheath forming proteins Afp2 and Afp3 and their cross-talks with the tail termination sheath capping protein (Trp) Afp16 in the sheath maturation process. The expressed assemblies for afp2- mutant were mostly a mixture of isolated tail fibres, detached baseplates without tail fibres and sheath-less, inner tube baseplate complexes (TBC) of length similar to that in mature Afp, which were surrounded in many cases by fibrillar polymerized material. In the afp3- mutant, variable length TBC with similar but shorter length fibrillar polymerized material, largely bereft of tail-fibres, were observed; while, only detached baseplate assemblies were seen for the afp4- mutant. Further, we found that a) only trans complementation of afp2 with its mutated counterpart restored mature Afp particles with full biological activity, b) purified Afp3 pulled down Afp2 by forming a SDS-resistant complex but not vice versa, c) Afp16 had a greater affinity for binding Afp2 or Afp3 than Afp4 and d) Afp4 is required for the association of the polymerized sheath on the baseplate via Afp2. A proposed model for sheath maturation and assembly in Afp is presented. Importance Members of the contractile bacteriophage related but evolutionarily divergent, eCIS contain not one but three sheath proteins - two of which, namely Afp2 and Afp3 in the Afp, arranged as alternate hexameric stacks constitute the helical sheath. We revealed that Afp2 and Afp3 even though they are highly similar, possess markedly distinct, crucial roles in Afp assembly. We find that Afp3, by virtue of its interaction with the tail terminating protein Afp16, regulates tube and sheath length while Afp2 is critical to proper sheath polymerisation and assembly of the baseplate. The resulting model for the Afp assembly will further guide in the manipulation of Afp and its related eCISs as nano delivery vehicles for pest control and phage therapy.
Collapse
|
23
|
Cavalcanti GS, Alker AT, Delherbe N, Malter KE, Shikuma NJ. The Influence of Bacteria on Animal Metamorphosis. Annu Rev Microbiol 2021; 74:137-158. [PMID: 32905754 DOI: 10.1146/annurev-micro-011320-012753] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The swimming larvae of many marine animals identify a location on the seafloor to settle and undergo metamorphosis based on the presence of specific surface-bound bacteria. While bacteria-stimulated metamorphosis underpins processes such as the fouling of ship hulls, animal development in aquaculture, and the recruitment of new animals to coral reef ecosystems, little is known about the mechanisms governing this microbe-animal interaction. Here we review what is known and what we hope to learn about how bacteria and the factors they produce stimulate animal metamorphosis. With a few emerging model systems, including the tubeworm Hydroides elegans, corals, and the hydrozoan Hydractinia, we have begun to identify bacterial cues that stimulate animal metamorphosis and test hypotheses addressing their mechanisms of action. By understanding the mechanisms by which bacteria promote animal metamorphosis, we begin to illustrate how, and explore why, the developmental decision of metamorphosis relies on cues from environmental bacteria.
Collapse
Affiliation(s)
- Giselle S Cavalcanti
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, California 92182, USA; , , , ,
| | - Amanda T Alker
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, California 92182, USA; , , , ,
| | - Nathalie Delherbe
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, California 92182, USA; , , , ,
| | - Kyle E Malter
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, California 92182, USA; , , , ,
| | - Nicholas J Shikuma
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, California 92182, USA; , , , ,
| |
Collapse
|
24
|
Wang X, Cheng J, Shen J, Liu L, Li N, Gao N, Jiang F, Jin Q. Characterization of Photorhabdus Virulence Cassette as a causative agent in the emerging pathogen Photorhabdus asymbiotica. SCIENCE CHINA-LIFE SCIENCES 2021; 65:618-630. [PMID: 34185241 DOI: 10.1007/s11427-021-1955-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
The extracellular contractile injection systems (eCISs) are encoded in the genomes of a large number of bacteria and archaea. We have previously characterized the overall structure of Photorhabdus Virulence Cassette (PVC), a typical member of the eCIS family. PVC resembles the contractile tail of bacteriophages and exerts its action by the contraction of outer sheath and injection of inner tube plus central spike. Nevertheless, the biological function of PVC effectors and the mechanism of effector translocation are still lacking. By combining cryo-electron microscopy and functional experiments, here we show that the PVC effectors Pdp1 (a new family of widespread dNTP pyrophosphatase effector in eCIS) and Pnf (a deamidase effector) are loaded inside the inner tube lumen in a "Peas in the Pod" mode. Moreover, we observe that Pdp1 and Pnf can be directly injected into J774A.1 murine macrophage and kill the target cells by disrupting the dNTP pools and actin cytoskeleton formation, respectively. Our results provide direct evidence of how PVC cargoes are loaded and delivered directly into mammalian macrophages.
Collapse
Affiliation(s)
- Xia Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Jiaxuan Cheng
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jiawei Shen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Liguo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Feng Jiang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| |
Collapse
|
25
|
Geller AM, Pollin I, Zlotkin D, Danov A, Nachmias N, Andreopoulos WB, Shemesh K, Levy A. The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins. Nat Commun 2021; 12:3743. [PMID: 34145238 PMCID: PMC8213781 DOI: 10.1038/s41467-021-23777-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/14/2021] [Indexed: 12/26/2022] Open
Abstract
The extracellular Contractile Injection System (eCIS) is a toxin-delivery particle that evolved from a bacteriophage tail. Four eCISs have previously been shown to mediate interactions between bacteria and their invertebrate hosts. Here, we identify eCIS loci in 1,249 bacterial and archaeal genomes and reveal an enrichment of these loci in environmental microbes and their apparent absence from mammalian pathogens. We show that 13 eCIS-associated toxin genes from diverse microbes can inhibit the growth of bacteria and/or yeast. We identify immunity genes that protect bacteria from self-intoxication, further supporting an antibacterial role for some eCISs. We also identify previously undescribed eCIS core genes, including a conserved eCIS transcriptional regulator. Finally, we present our data through an extensive eCIS repository, termed eCIStem. Our findings support eCIS as a toxin-delivery system that is widespread among environmental prokaryotes and likely mediates antagonistic interactions with eukaryotes and other prokaryotes.
Collapse
Affiliation(s)
- Alexander Martin Geller
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Inbal Pollin
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - David Zlotkin
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Aleks Danov
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Nimrod Nachmias
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Keren Shemesh
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel.
| |
Collapse
|
26
|
Computational prediction of secreted proteins in gram-negative bacteria. Comput Struct Biotechnol J 2021; 19:1806-1828. [PMID: 33897982 PMCID: PMC8047123 DOI: 10.1016/j.csbj.2021.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/29/2022] Open
Abstract
Gram-negative bacteria harness multiple protein secretion systems and secrete a large proportion of the proteome. Proteins can be exported to periplasmic space, integrated into membrane, transported into extracellular milieu, or translocated into cytoplasm of contacting cells. It is important for accurate, genome-wide annotation of the secreted proteins and their secretion pathways. In this review, we systematically classified the secreted proteins according to the types of secretion systems in Gram-negative bacteria, summarized the known features of these proteins, and reviewed the algorithms and tools for their prediction.
Collapse
|
27
|
Song N, Chen L, Zhou Z, Ren X, Liu B, Zhou S, Wang C, Wu Y, Waterfield NR, Yang J, Yang G. Genome-wide dissection reveals diverse pathogenic roles of bacterial Tc toxins. PLoS Pathog 2021; 17:e1009102. [PMID: 33540421 PMCID: PMC7861908 DOI: 10.1371/journal.ppat.1009102] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/26/2020] [Indexed: 12/21/2022] Open
Abstract
Tc toxins were originally identified in entomopathogenic bacteria, which are important as biological pest control agents. Tc toxins are heteromeric exotoxins composed of three subunit types, TcA, TcB, and TcC. The C-terminal portion of the TcC protein encodes the actual toxic domain, which is translocated into host cells by an injectosome nanomachine comprising the other subunits. Currently the pathogenic roles and distribution of Tc toxins among different bacterial genera remain unclear. Here we have performed a comprehensive genome-wide analysis, and established a database that includes 1,608 identified Tc loci containing 2,528 TcC proteins in 1,421 Gram-negative and positive bacterial genomes. Our findings indicate that TcCs conform to the architecture of typical polymorphic toxins, with C-terminal hypervariable regions (HVR) encoding more than 100 different classes of putative toxic domains, most of which have not been previously recognized. Based on further analysis of Tc loci in the genomes of all Salmonella and Yersinia strains in EnteroBase, a “two-level” evolutionary dynamics scenario is proposed for TcC homologues. This scenario implies that the conserved TcC RHS core domain plays a critical role in the taxonomical specific distribution of TcC HVRs. This study provides an extensive resource for the future development of Tc toxins as valuable agrochemical tools. It furthermore implies that Tc proteins, which are encoded by a wide range of pathogens, represent an important versatile toxin superfamily with diverse pathogenic mechanisms. Entomopathogenic bacteria deploy a range of toxins to combat their insect hosts. The Tc toxins were first identified in Photorhabdus as having potent oral toxicity to insects, with a mode of action distinct from the well-studied Bacillus thuringiensis Cry toxins. As such the Tc toxins have been considered as potential candidates for novel crop protection strategies. This could mitigate against the potential risks of pest insects developing resistance to the traditionally used Cry toxin-based systems. To date, the generality of diverse Tc toxins and their related pathogenic roles has remained mainly obscure. Our analysis has showed Tc toxins are widely distributed among Gram-negative and positive bacterial genomes. A database was constructed including thousands of Tc loci with hundreds of different putative TcC toxic domains, any one of which might represent candidates for the development of future pest control systems. Moreover, the findings of this study are of wider significance because Tc toxin homologues have been shown to be encoded by a range of human pathogens. These include Salmonella and Yersinia, suggesting their potential roles in human infectious diseases. Together, this study describes the characteristics and distribution of Tc toxins among diverse bacterial genera, and provides a new insight into their roles in different pathogenesis mechanisms. This study also describes findings of potential importance to their development as tools for biotechnological applications.
Collapse
Affiliation(s)
- Nan Song
- Beijing Institute of Tropical Medicine, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhemin Zhou
- Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Xingmei Ren
- Beijing Institute of Tropical Medicine, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Siyu Zhou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Caihong Wang
- Beijing Institute of Tropical Medicine, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yun Wu
- Beijing Institute of Tropical Medicine, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | | | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail: (JY); (GY)
| | - Guowei Yang
- Beijing Institute of Tropical Medicine, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- * E-mail: (JY); (GY)
| |
Collapse
|
28
|
Alker AT, Delherbe N, Purdy TN, Moore BS, Shikuma NJ. Genetic examination of the marine bacterium Pseudoalteromonas luteoviolacea and effects of its metamorphosis-inducing factors. Environ Microbiol 2020; 22:4689-4701. [PMID: 32840026 PMCID: PMC8214333 DOI: 10.1111/1462-2920.15211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/13/2022]
Abstract
Pseudoalteromonas luteoviolacea is a globally distributed marine bacterium that stimulates the metamorphosis of marine animal larvae, an important bacteria-animal interaction that can promote the recruitment of animals to benthic ecosystems. Recently, different P. luteoviolacea isolates have been shown to produce two stimulatory factors that can induce tubeworm and coral metamorphosis; Metamorphosis-Associated Contractile structures (MACs) and tetrabromopyrrole (TBP) respectively. However, it remains unclear what proportion of P. luteoviolacea isolates possess the genes encoding MACs, and what phenotypic effect MACs and TBP have on other larval species. Here, we show that 9 of 19 sequenced P. luteoviolacea genomes genetically encode both MACs and TBP. While P. luteoviolacea biofilms producing MACs stimulate the metamorphosis of the tubeworm Hydroides elegans, TBP biosynthesis genes had no effect under the conditions tested. Although MACs are lethal to larvae of the cnidarian Hydractinia symbiologicarpus, P. luteoviolacea mutants unable to produce MACs are capable of stimulating metamorphosis. Our findings reveal a hidden complexity of interactions between a single bacterial species, the factors it produces and two species of larvae belonging to different phyla.
Collapse
Affiliation(s)
- Amanda T. Alker
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, 92182
| | - Nathalie Delherbe
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, 92182
| | - Trevor N. Purdy
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093
| | - Nicholas J. Shikuma
- Department of Biology and Viral Information Institute, San Diego State University, San Diego, CA, 92182
| |
Collapse
|
29
|
Chen L, Song N, Liu B, Zhang N, Alikhan NF, Zhou Z, Zhou Y, Zhou S, Zheng D, Chen M, Hapeshi A, Healey J, Waterfield NR, Yang J, Yang G. Genome-wide Identification and Characterization of a Superfamily of Bacterial Extracellular Contractile Injection Systems. Cell Rep 2020; 29:511-521.e2. [PMID: 31597107 PMCID: PMC6899500 DOI: 10.1016/j.celrep.2019.08.096] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/11/2019] [Accepted: 08/28/2019] [Indexed: 11/30/2022] Open
Abstract
Several phage-tail-like nanomachines were shown to play an important role in the interactions between bacteria and their eukaryotic hosts. These apparatuses appear to represent a new injection paradigm. Here, with three verified extracellular contractile injection systems (eCISs), a protein profile and genomic context-based iterative approach was applied to identify 631 eCIS-like loci from the 11,699 publicly available complete bacterial genomes. The eCIS superfamily, which is phylogenetically diverse and sub-divided into six families, is distributed among Gram-negative and -positive bacteria in addition to archaea. Our results show that very few bacteria are seen to possess intact operons of both eCIS and type VI secretion systems (T6SSs). An open access online database of all detected eCIS-like loci is presented to facilitate future studies. The presence of this bacterial injection machine in a multitude of organisms suggests that it may play an important ecological role in the life cycles of many bacteria. eCIS loci are widely distributed among bacteria genomes eCIS loci encode phage-tail-like proteinaceous machines eCIS superfamily is grouped into six families with distinct genetic features
Collapse
Affiliation(s)
- Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Nan Song
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China; Beijing Institute of Tropical Medicine, Beijing 100050, China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Nan Zhang
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China; Beijing Institute of Tropical Medicine, Beijing 100050, China
| | - Nabil-Fareed Alikhan
- Warwick Medical School, Warwick University, Coventry CV4 7AL, UK; Microbes in the Food Chain, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UG, UK
| | - Zhemin Zhou
- Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
| | - Yanyan Zhou
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Siyu Zhou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Dandan Zheng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Mingxing Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Alexia Hapeshi
- Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
| | - Joseph Healey
- Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
| | | | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China.
| | - Guowei Yang
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China; Beijing Institute of Tropical Medicine, Beijing 100050, China.
| |
Collapse
|
30
|
Rojas MI, Cavalcanti GS, McNair K, Benler S, Alker AT, Cobián-Güemes AG, Giluso M, Levi K, Rohwer F, Bailey BA, Beyhan S, Edwards RA, Shikuma NJ. A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes. mSystems 2020; 5:e00648-20. [PMID: 32723799 PMCID: PMC7394362 DOI: 10.1128/msystems.00648-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022] Open
Abstract
Many commensal bacteria antagonize each other or their host by producing syringe-like secretion systems called contractile injection systems (CIS). Members of the Bacteroidales family have been shown to produce only one type of CIS-a contact-dependent type 6 secretion system that mediates bacterium-bacterium interactions. Here, we show that a second distinct cluster of genes from Bacteroidales bacteria from the human microbiome may encode yet-uncharacterized injection systems that we term Bacteroidales injection systems (BIS). We found that BIS genes are present in the gut microbiomes of 99% of individuals from the United States and Europe and that BIS genes are more prevalent in the gut microbiomes of healthy individuals than in those individuals suffering from inflammatory bowel disease. Gene clusters similar to that of the BIS mediate interactions between bacteria and diverse eukaryotes, like amoeba, insects, and tubeworms. Our findings highlight the ubiquity of the BIS gene cluster in the human gut and emphasize the relevance of the gut microbiome to the human host. These results warrant investigations into the structure and function of the BIS and how they might mediate interactions between Bacteroidales bacteria and the human host or microbiome.IMPORTANCE To engage with host cells, diverse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture membranes, often delivering effectors to target cells. Although CIS are key for pathogens to cause disease, paradoxically, similar injection systems have been identified within healthy human microbiome bacteria. Here, we show that gene clusters encoding a predicted CIS, which we term Bacteroidales injection systems (BIS), are present in the microbiomes of nearly all adult humans tested from Western countries. BIS genes are enriched within human gut microbiomes and are expressed both in vitro and in vivo Further, a greater abundance of BIS genes is present within healthy gut microbiomes than in those humans with with inflammatory bowel disease (IBD). Our discovery provides a potentially distinct means by which our microbiome interacts with the human host or its microbiome.
Collapse
Affiliation(s)
- Maria I Rojas
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Giselle S Cavalcanti
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Katelyn McNair
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Sean Benler
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Amanda T Alker
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Ana G Cobián-Güemes
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Melissa Giluso
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Kyle Levi
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Forest Rohwer
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Barbara A Bailey
- Department of Mathematics and Statistics, San Diego State University, San Diego, California, USA
| | - Sinem Beyhan
- Department of Biology, San Diego State University, San Diego, California, USA
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, California, USA
| | - Robert A Edwards
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Nicholas J Shikuma
- Viral Information Institute, San Diego State University, San Diego, California, USA
- Department of Biology, San Diego State University, San Diego, California, USA
- Computational Science Research Center, San Diego State University, San Diego, California, USA
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, California, USA
| |
Collapse
|
31
|
Abstract
Different model systems have, over the years, contributed to our current understanding of the molecular mechanisms underpinning the various types of interaction between bacteria and their animal hosts. The genus
Photorhabdus
comprises Gram-negative insect pathogenic bacteria that are normally found as symbionts that colonize the gut of the infective juvenile stage of soil-dwelling nematodes from the family Heterorhabditis. The nematodes infect susceptible insects and release the bacteria into the insect haemolymph where the bacteria grow, resulting in the death of the insect. At this stage the nematodes feed on the bacterial biomass and, following several rounds of reproduction, the nematodes develop into infective juveniles that leave the insect cadaver in search of new hosts. Therefore
Photorhabdus
has three distinct and obligate roles to play during this life-cycle: (1)
Photorhabdus
must kill the insect host; (2)
Photorhabdus
must be capable of supporting nematode growth and development; and (3)
Photorhabdus
must be able to colonize the gut of the next generation of infective juveniles before they leave the insect cadaver. In this review I will discuss how genetic analysis has identified key genes involved in mediating, and regulating, the interaction between
Photorhabdus
and each of its invertebrate hosts. These studies have resulted in the characterization of several new families of toxins and a novel inter-kingdom signalling molecule and have also uncovered an important role for phase variation in the regulation of these different roles.
Collapse
Affiliation(s)
- David J Clarke
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| |
Collapse
|
32
|
Ericson CF, Eisenstein F, Medeiros JM, Malter KE, Cavalcanti GS, Zeller RW, Newman DK, Pilhofer M, Shikuma NJ. A contractile injection system stimulates tubeworm metamorphosis by translocating a proteinaceous effector. eLife 2019; 8:46845. [PMID: 31526475 PMCID: PMC6748791 DOI: 10.7554/elife.46845] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/05/2019] [Indexed: 12/25/2022] Open
Abstract
The swimming larvae of many marine animals identify a location on the sea floor to undergo metamorphosis based on the presence of specific bacteria. Although this microbe–animal interaction is critical for the life cycles of diverse marine animals, what types of biochemical cues from bacteria that induce metamorphosis has been a mystery. Metamorphosis of larvae of the tubeworm Hydroides elegans is induced by arrays of phage tail-like contractile injection systems, which are released by the bacterium Pseudoalteromonas luteoviolacea. Here we identify the novel effector protein Mif1. By cryo-electron tomography imaging and functional assays, we observe Mif1 as cargo inside the tube lumen of the contractile injection system and show that the mif1 gene is required for inducing metamorphosis. Purified Mif1 is sufficient for triggering metamorphosis when electroporated into tubeworm larvae. Our results indicate that the delivery of protein effectors by contractile injection systems may orchestrate microbe–animal interactions in diverse contexts. Many marine animals, including corals and tubeworms, begin life as larvae swimming in open water before transforming into adults that anchor themselves to the seabed. These transformations, known as metamorphoses, are often triggered by certain types of bacteria that form friendly relationships (or “symbioses”) with the animals. One such symbiosis forms between a bacterium called Pseudoalteromonas luteoviolacea and a tubeworm known as Hydroides elegans. Previous studies have shown that P. luteoviolacea produces syringe-like structures known as Metamorphosis Associated Contractile structures (or MACs for short) that are responsible for stimulating metamorphosis in the tubeworm larvae. Some viruses that infect bacteria use similar structures to inject molecules into their host cells. However, it was not clear whether MACs were also able to inject molecules into cells. Here, Ericson, Eisenstein et al. used a technique called cryo-electron tomography combined with genetic and biochemical approaches to study how the MACs of P. luteoviolacea trigger metamorphosis in tubeworms. The experiments identified a protein in the bacteria named Mif1 that was required for the tubeworms to transform. The bacteria loaded Mif1 into the tube of the MAC structure and then injected it into the tubeworms. Further experiments showed that inserting Mif1 alone into tubeworms was sufficient to activate metamorphosis. Mif1 is the first protein from bacteria to be shown to activate metamorphosis, but it is likely that many more remain to be discovered. Since other marine animals also form symbioses with bacteria, understanding how Mif1 and other similar proteins work may inform efforts to restore coral reefs and other fragile ecosystems, and increase the production of oysters and other shellfish. Furthermore, MACs and related structures may have the potential to be developed into biotechnology tools that deliver drugs and other molecules directly into animal cells.
Collapse
Affiliation(s)
- Charles F Ericson
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States.,Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Fabian Eisenstein
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - João M Medeiros
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Kyle E Malter
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Giselle S Cavalcanti
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Robert W Zeller
- Department of Biology, San Diego State University, San Diego, United States
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, United States
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Nicholas J Shikuma
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| |
Collapse
|
33
|
Abstract
The proteins injected by bacteria into eukaryotic organisms can lead to fates as diverse as death and metamorphosis.
Collapse
Affiliation(s)
- Sophie A Howard
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonUnited Kingdom
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life SciencesImperial College LondonLondonUnited Kingdom
| |
Collapse
|
34
|
An effector with nuclease activity. Nat Rev Microbiol 2019; 17:529. [DOI: 10.1038/s41579-019-0246-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|