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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.
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Affiliation(s)
- Lin Lin
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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2
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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.
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Affiliation(s)
- Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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3
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Ericson CF, Pilhofer M. Mix-and-match tools for protein injection into cells. Nature 2023; 616:254-255. [PMID: 36991045 DOI: 10.1038/d41586-023-00847-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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4
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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.
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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.
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5
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Cytoplasmic contractile injection systems mediate cell death in Streptomyces. Nat Microbiol 2023; 8:711-726. [PMID: 36894633 PMCID: PMC10066040 DOI: 10.1038/s41564-023-01341-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023]
Abstract
Contractile injection systems (CIS) are bacteriophage tail-like structures that mediate bacterial cell-cell interactions. While CIS are highly abundant across diverse bacterial phyla, representative gene clusters in Gram-positive organisms remain poorly studied. Here we characterize a CIS in the Gram-positive multicellular model organism Streptomyces coelicolor and show that, in contrast to most other CIS, S. coelicolor CIS (CISSc) mediate cell death in response to stress and impact cellular development. CISSc are expressed in the cytoplasm of vegetative hyphae and are not released into the medium. Our cryo-electron microscopy structure enabled the engineering of non-contractile and fluorescently tagged CISSc assemblies. Cryo-electron tomography showed that CISSc contraction is linked to reduced cellular integrity. Fluorescence light microscopy furthermore revealed that functional CISSc mediate cell death upon encountering different types of stress. The absence of functional CISSc had an impact on hyphal differentiation and secondary metabolite production. Finally, we identified three putative effector proteins, which when absent, phenocopied other CISSc mutants. Our results provide new functional insights into CIS in Gram-positive organisms and a framework for studying novel intracellular roles, including regulated cell death and life-cycle progression in multicellular bacteria.
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Studying Plant-Insect Interactions through the Analyses of the Diversity, Composition, and Functional Inference of Their Bacteriomes. Microorganisms 2022; 11:microorganisms11010040. [PMID: 36677331 PMCID: PMC9863603 DOI: 10.3390/microorganisms11010040] [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: 11/04/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
As with many other trophic interactions, the interchange of microorganisms between plants and their herbivorous insects is unavoidable. To test the hypothesis that the composition and diversity of the insect bacteriome are driven by the bacteriome of the plant, the bacteriomes of both the plant Datura inoxia and its specialist insect Lema daturaphila were characterised using 16S sRNA gene amplicon sequencing. Specifically, the bacteriomes associated with seeds, leaves, eggs, guts, and frass were described and compared. Then, the functions of the most abundant bacterial lineages found in the samples were inferred. Finally, the patterns of co-abundance among both bacteriomes were determined following a multilayer network approach. In accordance with our hypothesis, most genera were shared between plants and insects, but their abundances differed significantly within the samples collected. In the insect tissues, the most abundant genera were Pseudomonas (24.64%) in the eggs, Serratia (88.46%) in the gut, and Pseudomonas (36.27%) in the frass. In contrast, the most abundant ones in the plant were Serratia (40%) in seeds, Serratia (67%) in foliar endophytes, and Hymenobacter (12.85%) in foliar epiphytes. Indeed, PERMANOVA analysis showed that the composition of the bacteriomes was clustered by sample type (F = 9.36, p < 0.001). Functional inferences relevant to the interaction showed that in the plant samples, the category of Biosynthesis of secondary metabolites was significantly abundant (1.4%). In turn, the category of Xenobiotics degradation and metabolism was significantly present (2.5%) in the insect samples. Finally, the phyla Proteobacteria and Actinobacteriota showed a pattern of co-abundance in the insect but not in the plant, suggesting that the co-abundance and not the presence−absence patterns might be more important when studying ecological interactions.
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Artsimovitch I, Ramírez-Sarmiento CA. Metamorphic proteins under a computational microscope: Lessons from a fold-switching RfaH protein. Comput Struct Biotechnol J 2022; 20:5824-5837. [PMID: 36382197 PMCID: PMC9630627 DOI: 10.1016/j.csbj.2022.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/28/2022] Open
Abstract
Metamorphic proteins constitute unexpected paradigms of the protein folding problem, as their sequences encode two alternative folds, which reversibly interconvert within biologically relevant timescales to trigger different cellular responses. Once considered a rare aberration, metamorphism may be common among proteins that must respond to rapidly changing environments, exemplified by NusG-like proteins, the only transcription factors present in every domain of life. RfaH, a specialized paralog of bacterial NusG, undergoes an all-α to all-β domain switch to activate expression of virulence and conjugation genes in many animal and plant pathogens and is the quintessential example of a metamorphic protein. The dramatic nature of RfaH structural transformation and the richness of its evolutionary history makes for an excellent model for studying how metamorphic proteins switch folds. Here, we summarize the structural and functional evidence that sparked the discovery of RfaH as a metamorphic protein, the experimental and computational approaches that enabled the description of the molecular mechanism and refolding pathways of its structural interconversion, and the ongoing efforts to find signatures and general properties to ultimately describe the protein metamorphome.
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Affiliation(s)
- Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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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.
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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
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9
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Structure of a thylakoid-anchored contractile injection system in multicellular cyanobacteria. Nat Microbiol 2022; 7:386-396. [PMID: 35165386 PMCID: PMC8894136 DOI: 10.1038/s41564-021-01055-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/20/2021] [Indexed: 01/10/2023]
Abstract
Contractile injection systems (CISs) mediate cell–cell interactions by phage tail-like structures, using two distinct modes of action: extracellular CISs are released into the medium, while type 6 secretion systems (T6SSs) are attached to the cytoplasmic membrane and function upon cell–cell contact. Here, we characterized a CIS in the multicellular cyanobacterium Anabaena, with features distinct from extracellular CISs and T6SSs. Cryo-electron tomography of focused ion beam-milled cells revealed that CISs were anchored in thylakoid membrane stacks, facing the cell periphery. Single particle cryo-electron microscopy showed that this unique in situ localization was mediated by extensions of tail fibre and baseplate components. On stress, cyanobacteria induced the formation of ghost cells, presenting thylakoid-anchored CISs to the environment. Functional assays suggest that these CISs may mediate ghost cell formation and/or interactions of ghost cells with other organisms. Collectively, these data provide a framework for understanding the evolutionary re-engineering of CISs and potential roles of these CISs in cyanobacterial programmed cell death. The characterization of a contractile injection system anchored in the thylakoid membrane of Anabaena reveals structural features linked to the unique localization and function of this cyanobacterial nanomachine.
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Identification of Diverse Toxin Complex Clusters and an eCIS Variant in Serratia proteamaculans Pathovars of the New Zealand Grass Grub ( Costelytra Giveni) and Manuka Beetle ( Pyronota Spp.) Larvae. Microbiol Spectr 2021; 9:e0112321. [PMID: 34668742 PMCID: PMC8528098 DOI: 10.1128/spectrum.01123-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The grass grub endemic to New Zealand, Costelytra giveni (Coleoptera: Scarabaeidae), and the manuka beetle, Pyronota festiva and P. setosa (Coleoptera: Scarabaeidae), are prevalent pest species. Through assessment of bacterial strains isolated from diseased cadavers of these insect species, 19 insect-active Serratia proteamaculans variants and a single Serratia entomophila strain were isolated. When independently bioassayed, these isolates differed in host range, the rate of disease progression, and 12-day mortality rates, which ranged from 60 to 100% of the challenged larvae. A Pyronota spp.-derived S. proteamaculans isolate caused a transient disease phenotype in challenged C. giveni larvae, whereby larvae appeared diseased before recovering to a healthy state. Genome sequence analysis revealed that all but two of the sequenced isolates contained a variant of the S. entomophila amber-disease-associated plasmid, pADAP. Each isolate also encoded one of seven distinct members of the toxin complex (Tc) family of insect-active toxins, five of which are newly described, or a member of the extracellular contractile injection (eCIS) machine family, with a new AfpX variant designated SpF. Targeted mutagenesis of each of the predicted Tc- or eCIS-encoding regions abolished or attenuated pathogenicity. Host-range testing showed that several of the S. proteamaculans Tc-encoding isolates affected both Pyronota and C. giveni species, with other isolates specific for either Pyronota spp. or C. giveni. The isolation of several distinct host-specific pathotypes of Serratia spp. may reflect pathogen-host speciation. IMPORTANCE New pathotypes of the insect pathogen Serratia, each with differing virulence attributes and host specificity toward larvae of the New Zealand manuka beetle and grass grub, have been identified. All of the Serratia proteamaculans isolates contained one of seven different insect-active toxin clusters or one of three eCIS variants. The diversity of these Serratia-encoded virulence clusters, resulting in differences in larval disease progression and host specificity in endemic scarab larvae, suggests speciation of these pathogens with their insect hosts. The differing virulence properties of these Serratia species may affect their potential infectivity and distribution among the insect populations. Based on their differing geographic isolation and pathotypes, several of these Serratia isolates, including the manuka beetle-active isolates, are likely to be more effective biopesticides in specific environments or could be used in combination for greater effect.
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11
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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.
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12
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Bacillus pumilus 15.1, a Strain Active against Ceratitis capitata, Contains a Novel Phage and a Phage-Related Particle with Bacteriocin Activity. Int J Mol Sci 2021; 22:ijms22158164. [PMID: 34360927 PMCID: PMC8347963 DOI: 10.3390/ijms22158164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
A 98.1 Kb genomic region from B. pumilus 15.1, a strain isolated as an entomopathogen toward C. capitata, the Mediterranean fruit fly, has been characterised in search of potential virulence factors. The 98.1 Kb region shows a high number of phage-related protein-coding ORFs. Two regions with different phylogenetic origins, one with 28.7 Kb in size, highly conserved in Bacillus strains, and one with 60.2 Kb in size, scarcely found in Bacillus genomes are differentiated. The content of each region is thoroughly characterised using comparative studies. This study demonstrates that these two regions are responsible for the production, after mitomycin induction, of a phage-like particle that packages DNA from the host bacterium and a novel phage for B. pumilus, respectively. Both the phage-like particles and the novel phage are observed and characterised by TEM, and some of their structural proteins are identified by protein fingerprinting. In addition, it is found that the phage-like particle shows bacteriocin activity toward other B. pumilus strains. The effect of the phage-like particles and the phage in the toxicity of the strain toward C. capitata is also evaluated.
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13
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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.
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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.
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14
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Rocchi I, Ericson CF, Malter KE, Zargar S, Eisenstein F, Pilhofer M, Beyhan S, Shikuma NJ. A Bacterial Phage Tail-like Structure Kills Eukaryotic Cells by Injecting a Nuclease Effector. Cell Rep 2020; 28:295-301.e4. [PMID: 31291567 DOI: 10.1016/j.celrep.2019.06.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/09/2019] [Accepted: 06/05/2019] [Indexed: 11/28/2022] Open
Abstract
Many bacteria interact with target organisms using syringe-like structures called contractile injection systems (CISs). CISs structurally resemble headless bacteriophages and share evolutionarily related proteins such as the tail tube, sheath, and baseplate complex. In many cases, CISs mediate trans-kingdom interactions between bacteria and eukaryotes by delivering effectors to target cells. However, the specific effectors and their modes of action are often unknown. Here, we establish an ex vivo model to study an extracellular CIS (eCIS) called metamorphosis-associated contractile structures (MACs) that target eukaryotic cells. MACs kill two eukaryotic cell lines, fall armyworm Sf9 cells and J774A.1 murine macrophage cells, by translocating an effector termed Pne1. Before the identification of Pne1, no CIS effector exhibiting nuclease activity against eukaryotic cells had been described. Our results define a new mechanism of CIS-mediated bacteria-eukaryote interaction and are a step toward developing CISs as novel delivery systems for eukaryotic hosts.
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Affiliation(s)
- Iara Rocchi
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Charles F Ericson
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Kyle E Malter
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Sahar Zargar
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Fabian Eisenstein
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Sinem Beyhan
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA.
| | - Nicholas J Shikuma
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA.
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15
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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
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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.
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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.
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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
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17
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Vlisidou I, Hapeshi A, Healey JR, Smart K, Yang G, Waterfield NR. The Photorhabdus asymbiotica virulence cassettes deliver protein effectors directly into target eukaryotic cells. eLife 2019; 8:46259. [PMID: 31526474 PMCID: PMC6748792 DOI: 10.7554/elife.46259] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/12/2019] [Indexed: 01/19/2023] Open
Abstract
Photorhabdus is a highly effective insect pathogen and symbiont of insecticidal nematodes. To exert its potent insecticidal effects, it elaborates a myriad of toxins and small molecule effectors. Among these, the Photorhabdus Virulence Cassettes (PVCs) represent an elegant self-contained delivery mechanism for diverse protein toxins. Importantly, these self-contained nanosyringes overcome host cell membrane barriers, and act independently, at a distance from the bacteria itself. In this study, we demonstrate that Pnf, a PVC needle complex associated toxin, is a Rho-GTPase, which acts via deamidation and transglutamination to disrupt the cytoskeleton. TEM and Western blots have shown a physical association between Pnf and its cognate PVC delivery mechanism. We demonstrate that for Pnf to exert its effect, translocation across the cell membrane is absolutely essential.
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Affiliation(s)
- Isabella Vlisidou
- All Wales Genetics Laboratory, Institute of Medical Genetics, University Hospital of Wales, Cardiff, United Kingdom
| | - Alexia Hapeshi
- Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Joseph Rj Healey
- Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Katie Smart
- Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Guowei Yang
- Beijing Friendship Hospital, Capital Medical University, Beijing, China
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18
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Wrobel A, Leo JC, Linke D. Overcoming Fish Defences: The Virulence Factors of Yersinia ruckeri. Genes (Basel) 2019; 10:genes10090700. [PMID: 31514317 PMCID: PMC6770984 DOI: 10.3390/genes10090700] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/02/2019] [Accepted: 09/05/2019] [Indexed: 12/24/2022] Open
Abstract
Yersinia ruckeri is the causative agent of enteric redmouth disease, a bacterial infection of marine and freshwater fish. The disease mainly affects salmonids, and outbreaks have significant economic impact on fish farms all over the world. Vaccination routines are in place against the major serotypes of Y. ruckeri but are not effective in all cases. Despite the economic importance of enteric redmouth disease, a detailed molecular understanding of the disease is lacking. A considerable number of mostly omics-based studies have been performed in recent years to identify genes related to Y. ruckeri virulence. This review summarizes the knowledge on Y. ruckeri virulence factors. Understanding the molecular pathogenicity of Y. ruckeri will aid in developing more efficient vaccines and antimicrobial compounds directed against enteric redmouth disease.
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Affiliation(s)
- Agnieszka Wrobel
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| | - Jack C Leo
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK.
| | - Dirk Linke
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
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Abstract
In every cell from bacteria to mammals, NusG-like proteins bind transcribing RNA polymerase to modulate the rate of nascent RNA synthesis and to coordinate it with numerous cotranscriptional processes that ultimately determine the transcript fate. Housekeeping NusG factors regulate expression of the bulk of the genome, whereas their highly specialized paralogs control just a few targets. In every cell from bacteria to mammals, NusG-like proteins bind transcribing RNA polymerase to modulate the rate of nascent RNA synthesis and to coordinate it with numerous cotranscriptional processes that ultimately determine the transcript fate. Housekeeping NusG factors regulate expression of the bulk of the genome, whereas their highly specialized paralogs control just a few targets. In Escherichia coli, NusG stimulates silencing of horizontally acquired genes, while its paralog RfaH counters NusG action by activating a subset of these genes. Acting alone or as part of regulatory complexes, NusG factors can promote uninterrupted RNA synthesis, bring about transcription pausing or premature termination, modulate RNA processing, and facilitate translation. Recent structural and mechanistic studies of NusG homologs from all domains of life reveal molecular details of multifaceted interactions that underpin their unexpectedly diverse regulatory roles. NusG proteins share conserved binding sites on RNA polymerase and many effects on the transcription elongation complex but differ in their mechanisms of recruitment, interactions with nucleic acids and secondary partners, and regulatory outcomes. Strikingly, some can alternate between autoinhibited and activated states that possess dramatically different secondary structures to achieve exquisite target specificity.
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20
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Siozios S, Pilgrim J, Darby AC, Baylis M, Hurst GDD. The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont. PeerJ 2019; 7:e6448. [PMID: 30809447 PMCID: PMC6387759 DOI: 10.7717/peerj.6448] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/15/2019] [Indexed: 01/02/2023] Open
Abstract
Background It is estimated that 13% of arthropod species carry the heritable symbiont Cardinium hertigii. 16S rRNA and gyrB sequence divides this species into at least four groups (A–D), with the A group infecting a range of arthropods, the B group infecting nematode worms, the C group infecting Culicoides biting midges, and the D group associated with the marine copepod Nitocra spinipes. To date, genome sequence has only been available for strains from groups A and B, impeding general understanding of the evolutionary history of the radiation. We present a draft genome sequence for a C group Cardinium, motivated both by the paucity of genomic information outside of the A and B group, and the importance of Culicoides biting midge hosts as arbovirus vectors. Methods We reconstructed the genome of cCpun, a Cardinium strain from group C that naturally infects Culicoides punctatus, through Illumina sequencing of infected host specimens. Results The draft genome presented has high completeness, with BUSCO scores comparable to closed group A Cardinium genomes. Phylogenomic analysis based on concatenated single copy core proteins do not support Cardinium from arthropod hosts as a monophyletic group, with nematode Cardinium strains nested within the two groups infecting arthropod hosts. Analysis of the genome of cCpun revealed expansion of a variety of gene families classically considered important in symbiosis (e.g., ankyrin domain containing genes), and one set—characterized by DUF1703 domains—not previously associated with symbiotic lifestyle. This protein group encodes putative secreted nucleases, and the cCpun genome carried at least 25 widely divergent paralogs, 24 of which shared a common ancestor in the C group. The genome revealed no evidence in support of B vitamin provisioning to its haematophagous host, and indeed suggests Cardinium may be a net importer of biotin. Discussion These data indicate strains of Cardinium within nematodes cluster within Cardinium strains found in insects. The draft genome of cCpun further produces new hypotheses as to the interaction of the symbiont with the midge host, in particular the biological role of DUF1703 nuclease proteins that are predicted as being secreted by cCpun. In contrast, the coding content of this genome provides no support for a role for the symbiont in provisioning the host with B vitamins.
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Affiliation(s)
- Stefanos Siozios
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Jack Pilgrim
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alistair C Darby
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Matthew Baylis
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections (HPRU-EZI), University of Liverpool, Liverpool, UK
| | - Gregory D D Hurst
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
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21
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22
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Serratia proteamaculans Strain AGR96X Encodes an Antifeeding Prophage (Tailocin) with Activity against Grass Grub (Costelytra giveni) and Manuka Beetle (Pyronota Species) Larvae. Appl Environ Microbiol 2018; 84:AEM.02739-17. [PMID: 29549100 DOI: 10.1128/aem.02739-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/08/2018] [Indexed: 11/20/2022] Open
Abstract
A highly virulent Serratia proteamaculans strain, AGR96X, exhibiting specific pathogenicity against larvae of the New Zealand grass grub (Costelytra giveni; Coleoptera: Scarabaeidae) and the New Zealand manuka beetle (Pyronota festiva and P. setosa; Coleoptera: Scarabaeidae), was isolated from a diseased grass grub larva. A 12-day median lethal dose of 4.89 × 103 ± 0.92 × 103 cells per grass grub larva was defined for AGR96X, and death occurred within 5 to 12 days following the ingestion of a high bacterial dose. During the infection period, the bacterium rapidly multiplied within the insect host and invaded the hemocoel, leading to a mean bacterial load of 8.2 × 109 cells per larva at 6 days postingestion. Genome sequencing of strain AGR96X revealed the presence of a variant of the Serratia entomophila antifeeding prophage (Afp), a tailocin designated AfpX. Unlike Afp, AfpX contains two Afp16 tail-length termination protein orthologs and two putative toxin components. A 37-kb DNA fragment encoding the AfpX-associated region was cloned, transformed into Escherichia coli, and fed to C. giveni and Pyronota larvae, causing mortality. In addition, the deletion of the afpX15 putative chaperone component abolished the virulence of AGR96X. Unlike S. entomophila Afp, the AfpX tailocin could be induced by mitomycin C. Transmission electron microscopy analysis revealed the presence of Afp-like particles of various lengths, and when the purified AfpX tailocin was fed to grass grub or manuka beetle larvae, they underwent phenotypic changes similar to those of larvae fed AGR96X.IMPORTANCESerratia proteamaculans strain AGR96X shows dual activity against larvae of endemic New Zealand pasture pests, the grass grub (Costelytra giveni) and the manuka beetle (Pyronota spp.). Unlike Serratia entomophila, the causal agent of amber disease, which takes 3 to 4 months to kill grass grub larvae, AGR96X causes mortality within 5 to 12 days of ingestion and invades the insect hemocoel. AGR96X produces a unique variant of the S. entomophila antifeeding prophage (Afp), a cell-free phage-like entity that is proposed to deliver protein toxins to the grass grub target site, causing a cessation of feeding activity. Unlike other Afp variants, AGR96X Afp, named AfpX, contains two tail-length termination proteins, resulting in greater variability in the AfpX length. AfpX shows dual activity against both grass grub and manuka beetle larvae. AGR96X is a viable alternative to S. entomophila for pest control in New Zealand pasture systems.
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Taylor NMI, van Raaij MJ, Leiman PG. Contractile injection systems of bacteriophages and related systems. Mol Microbiol 2018; 108:6-15. [PMID: 29405518 DOI: 10.1111/mmi.13921] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2018] [Indexed: 12/31/2022]
Abstract
Contractile tail bacteriophages, or myobacteriophages, use a sophisticated biomolecular structure to inject their genome into the bacterial host cell. This structure consists of a contractile sheath enveloping a rigid tube that is sharpened by a spike-shaped protein complex at its tip. The spike complex forms the centerpiece of a baseplate complex that terminates the sheath and the tube. The baseplate anchors the tail to the target cell membrane with the help of fibrous proteins emanating from it and triggers contraction of the sheath. The contracting sheath drives the tube with its spiky tip through the target cell membrane. Subsequently, the bacteriophage genome is injected through the tube. The structural transformation of the bacteriophage T4 baseplate upon binding to the host cell has been recently described in near-atomic detail. In this review we discuss structural elements and features of this mechanism that are likely to be conserved in all contractile injection systems (systems evolutionary and structurally related to contractile bacteriophage tails). These include the type VI secretion system (T6SS), which is used by bacteria to transfer effectors into other bacteria and into eukaryotic cells, and tailocins, a large family of contractile bacteriophage tail-like compounds that includes the P. aeruginosa R-type pyocins.
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Affiliation(s)
- Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Mark J van Raaij
- Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CSIC), Calle Darwin 3, E-28049 Madrid, Spain
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, 301 University Blvd, University of Texas Medical Branch, Galveston, TX 77555-0647, USA
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24
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Inaba H, Ueno T. Artificial bio-nanomachines based on protein needles derived from bacteriophage T4. Biophys Rev 2017; 10:641-658. [PMID: 29147941 DOI: 10.1007/s12551-017-0336-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/07/2017] [Indexed: 12/17/2022] Open
Abstract
Bacteriophage T4 is a natural bio-nanomachine which achieves efficient infection of host cells via cooperative motion of specific three-dimensional protein architectures. The relationships between the protein structures and their dynamic functions have recently been clarified. In this review we summarize the design principles for fabrication of nanomachines using the component proteins of bacteriophage T4 based on these recent advances. We focus on the protein needle known as gp5, which is located at the center of the baseplate at the end of the contractile tail of bacteriophage T4. This protein needle plays a critical role in directly puncturing host cells, and analysis has revealed that it contains a common motif used for cell puncture in other known injection systems, such as T6SS. Our artificial needle based on the β-helical domain of gp5 retains the ability to penetrate cells and can be engineered to deliver various cargos into living cells. Thus, the unique components of bacteriophage T4 and other natural nanomachines have great potential for use as molecular scaffolds in efforts to fabricate new bio-nanomachines.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
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25
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Labreuche Y, Chenivesse S, Jeudy A, Le Panse S, Boulo V, Ansquer D, Pagès S, Givaudan A, Czjzek M, Le Roux F. Nigritoxin is a bacterial toxin for crustaceans and insects. Nat Commun 2017; 8:1248. [PMID: 29093459 PMCID: PMC5665878 DOI: 10.1038/s41467-017-01445-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 09/14/2017] [Indexed: 11/29/2022] Open
Abstract
The Tetraconata (Pancrustacea) concept proposes that insects are more closely related to aquatic crustaceans than to terrestrial centipedes or millipedes. The question therefore arises whether insects have kept crustacean-specific genetic traits that could be targeted by specific toxins. Here we show that a toxin (nigritoxin), originally identified in a bacterial pathogen of shrimp, is lethal for organisms within the Tetraconata and non-toxic to other animals. X-ray crystallography reveals that nigritoxin possesses a new protein fold of the α/β type. The nigritoxin N-terminal domain is essential for cellular translocation and likely encodes specificity for Tetraconata. Once internalized by eukaryotic cells, nigritoxin induces apoptotic cell death through structural features that are localized in the C-terminal domain of the protein. We propose that nigritoxin will be an effective means to identify a Tetraconata evolutionarily conserved pathway and speculate that nigritoxin holds promise as an insecticidal protein. The Tetraconata concept suggests that insects and crustaceans may share evolutionarily conserved pathways. Here, the authors describe the animal tropism and structure-function relationship of nigritoxin, showing that this protein is lethal for insects and crustaceans but harmless to other animals.
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Affiliation(s)
- Yannick Labreuche
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France.,Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Sabine Chenivesse
- Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Alexandra Jeudy
- Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Sophie Le Panse
- CNRS, FR 2424, Plateforme Merimage, Station Biologique de Roscoff, Place Georges Teissier, CS 90074, F-29688, Roscoff cedex, France
| | - Viviane Boulo
- Département Lagons, Ecosystèmes et Aquaculture Durables en Nouvelle-Calédonie, IFREMER, BP 2059, 98846, Nouméa cedex, New Caledonia
| | - Dominique Ansquer
- Département Lagons, Ecosystèmes et Aquaculture Durables en Nouvelle-Calédonie, IFREMER, BP 2059, 98846, Nouméa cedex, New Caledonia
| | - Sylvie Pagès
- UMR 1333 "Diversité, Génomes & Interactions Microorganismes - Insectes" Université Montpellier 2 - Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Alain Givaudan
- UMR 1333 "Diversité, Génomes & Interactions Microorganismes - Insectes" Université Montpellier 2 - Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Frédérique Le Roux
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France. .,Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France.
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26
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Shi D, Svetlov D, Abagyan R, Artsimovitch I. Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor. Nucleic Acids Res 2017; 45:8835-8843. [PMID: 28605514 PMCID: PMC5587751 DOI: 10.1093/nar/gkx523] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/05/2017] [Indexed: 01/20/2023] Open
Abstract
Transcription factors from the NusG family bind to the elongating RNA polymerase to enable synthesis of long RNAs in all domains of life. In bacteria, NusG frequently co-exists with specialized paralogs that regulate expression of a small set of targets, many of which encode virulence factors. Escherichia coli RfaH is the exemplar of this regulatory mechanism. In contrast to NusG, which freely binds to RNA polymerase, RfaH exists in a structurally distinct autoinhibitory state in which the RNA polymerase-binding site is buried at the interface between two RfaH domains. Binding to an ops DNA sequence triggers structural transformation wherein the domains dissociate and RfaH refolds into a NusG-like structure. Formation of the autoinhibitory state, and thus sequence-specific recruitment, represents the decisive step in the evolutionary history of the RfaH subfamily. We used computational and experimental approaches to identify the residues that confer the unique regulatory properties of RfaH. Our analysis highlighted highly conserved Ile and Phe residues at the RfaH interdomain interface. Replacement of these residues with equally conserved Glu and Val counterpart residues in NusG destabilized interactions between the RfaH domains and allowed sequence-independent recruitment to RNA polymerase, suggesting a plausible pathway for diversification of NusG paralogs.
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Affiliation(s)
- Da Shi
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego, CA 92093, USA
| | - Dmitri Svetlov
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA.,The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego, CA 92093, USA
| | - Irina Artsimovitch
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
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Chattopadhyay P, Banerjee G, Mukherjee S. Recent trends of modern bacterial insecticides for pest control practice in integrated crop management system. 3 Biotech 2017; 7:60. [PMID: 28444605 DOI: 10.1007/s13205-017-0717-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/31/2017] [Indexed: 10/19/2022] Open
Abstract
Food security and safety are the major concern in ever expanding human population on the planet earth. Each and every year insect pests cause a serious damage in agricultural field that cost billions of dollars annually to farmers. The loss in term of productivity and high cost of chemical pesticides enhance the production cost. Irrespective use of chemical pesticides (such as Benzene hexachloride, Endosulfan, Aldicarb, and Fenobucarb) in agricultural field raised several types of environmental issues. Furthermore, continuous use of chemical pesticides creates a selective pressure which helps in emerging of resistance pest. These excess chemical pesticide residues also contaminate the environment including the soil and water. Therefore, the biological control of insect pest in the agricultural field gains more importance due to food safety and environment friendly nature. In this regard, bacterial insecticides offer better alternative to chemical pesticides. It not only helps to establish food security through fighting against insect pests but also ensure the food safety. In this review, we have categorized insect pests and the corresponding bacterial insecticides, and critically analyzed the importance and mode of action of bacterial pesticides. We also have summarized the use of biopesticides in integrated pest management system. We have tried to focus the future research area in this field for the upcoming scientists.
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Dr. Alois Huger - Laying the foundations for an integrated insect pathology. J Invertebr Pathol 2016; 143:83-89. [PMID: 27871814 DOI: 10.1016/j.jip.2016.11.010] [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: 08/10/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/21/2022]
Abstract
Dr. Rer. Nat. Alois M. Huger had a long and distinguished career at the Institut für biologische Schädlingsbekämpfung (Institute for Biological Pest Control) Darmstadt, Germany, where he became one of the world's leading insect pathologists. He applied his experience and understanding of insect tissues and specialist skills in microscopy to diagnosis and elucidation of the pathology of insect diseases. During his career he discovered the Oryctes nudivirus and Bacillus thuringiensis subsp. tenebrionis, and was a member of teams unravelling amber disease in scarab beetles and the role of bacteria in parthenogenesis of parasitoids. He researched and described the life cycles of microsporidian and rickettsial pathogens of insects and was the first to describe the ultrastructure of a microsporidian spore. Dr. Huger carried out diagnosis of diseased insects over a period of 55years and has left us with many publications and a database containing thousands of records for ongoing investigation. Working with multiple pathogens in different systems, Dr. Huger obtained an overview second to none in the complexities of insect/pathogen relationships and has been at the forefront of making these discoveries benefit humanity. He is a worthy recipient of the Founders' Lecture Honoree Award, the highest honour of the Society for Invertebrate Pathology.
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Sugar and Spice Make Bacteria Not Nice: Protein Glycosylation and Its Influence in Pathogenesis. J Mol Biol 2016; 428:3206-3220. [DOI: 10.1016/j.jmb.2016.04.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/04/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023]
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Hurst MRH, Beattie A, Altermann E, Moraga RM, Harper LA, Calder J, Laugraud A. The Draft Genome Sequence of the Yersinia entomophaga Entomopathogenic Type Strain MH96T. Toxins (Basel) 2016; 8:toxins8050143. [PMID: 27187466 PMCID: PMC4885058 DOI: 10.3390/toxins8050143] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 01/28/2023] Open
Abstract
Here we report the draft genome of Yersinia entomophaga type strain MH96T. The genome shows 93.8% nucleotide sequence identity to that of Yersinia nurmii type strain APN3a-cT, and comprises a single chromosome of approximately 4,275,531 bp. In silico analysis identified that, in addition to the previously documented Y. entomophaga Yen-TC gene cluster, the genome encodes a diverse array of toxins, including two type III secretion systems, and five rhs-associated gene clusters. As well as these multicomponent systems, several orthologs of known insect toxins, such as VIP2 toxin and the binary toxin PirAB, and distant orthologs of some mammalian toxins, including repeats-in-toxin, a cytolethal distending toxin, hemolysin-like genes and an adenylate cyclase were identified. The genome also contains a large number of hypothetical proteins and orthologs of known effector proteins, such as LopT, as well as genes encoding a wide range of proteolytic determinants, including metalloproteases and pathogen fitness determinants, such as genes involved in iron metabolism. The bioinformatic data derived from the current in silico analysis, along with previous information on the pathobiology of Y. entomophaga against its insect hosts, suggests that a number of these virulence systems are required for survival in the hemocoel and incapacitation of the insect host.
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Affiliation(s)
- Mark R H Hurst
- AgResearch, Farm Systems & Environment, Lincoln Research Centre, Christchurch 8140, New Zealand.
| | - Amy Beattie
- AgResearch, Farm Systems & Environment, Lincoln Research Centre, Christchurch 8140, New Zealand.
| | - Eric Altermann
- AgResearch Limited, Rumen Microbiology, Palmerston North 4474, New Zealand.
- Riddet Institute, Massey University, Palmerston North 4474, New Zealand.
| | - Roger M Moraga
- AgResearch Limited, Bioinformatics & Statistics, Hamilton 3214, New Zealand.
| | - Lincoln A Harper
- AgResearch, Farm Systems & Environment, Lincoln Research Centre, Christchurch 8140, New Zealand.
| | - Joanne Calder
- AgResearch, Farm Systems & Environment, Lincoln Research Centre, Christchurch 8140, New Zealand.
| | - Aurelie Laugraud
- AgResearch Limited, Bioinformatics & Statistics, Lincoln Research Centre, Christchurch 8140, New Zealand.
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Tyrosine glycosylation of Rho by Yersinia toxin impairs blastomere cell behaviour in zebrafish embryos. Nat Commun 2015; 6:7807. [PMID: 26190758 PMCID: PMC4518317 DOI: 10.1038/ncomms8807] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 06/15/2015] [Indexed: 12/20/2022] Open
Abstract
Yersinia species cause zoonotic infections, including enterocolitis and plague. Here we studied Yersinia ruckeri antifeeding prophage 18 (Afp18), the toxin component of the phage tail-derived protein translocation system Afp, which causes enteric redmouth disease in salmonid fish species. Here we show that microinjection of the glycosyltransferase domain Afp18G into zebrafish embryos blocks cytokinesis, actin-dependent motility and cell blebbing, eventually abrogating gastrulation. In zebrafish ZF4 cells, Afp18G depolymerizes actin stress fibres by mono-O-GlcNAcylation of RhoA at tyrosine-34; thereby Afp18G inhibits RhoA activation by guanine nucleotide exchange factors, and blocks RhoA, but not Rac and Cdc42 downstream signalling. The crystal structure of tyrosine-GlcNAcylated RhoA reveals an open conformation of the effector loop distinct from recently described structures of GDP- or GTP-bound RhoA. Unravelling of the molecular mechanism of the toxin component Afp18 as glycosyltransferase opens new perspectives in studies of phage tail-derived protein translocation systems, which are preserved from archaea to human pathogenic prokaryotes. Yersinia ruckeri is the source of redmouth disease in fish. Here the authors analysed the Yersinia toxin Afp18 and show that it acts to inhibit RhoA activation by glycosylating a distinct tyrosine residue inducing a signalling incompetent structural conformation.
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Rybakova D, Schramm P, Mitra AK, Hurst MRH. Afp14 is involved in regulating the length of Anti-feeding prophage (Afp). Mol Microbiol 2015; 96:815-26. [DOI: 10.1111/mmi.12974] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Daria Rybakova
- Innovative Farm Systems; AgResearch; Lincoln Research Centre; Private Bag 4749 Christchurch 8140 New Zealand
| | - Peter Schramm
- Academy of Life Science, Engineering, and Design; Saxion University of Applied Science; Enschede M.H. Tromplaan 28 7513 AB Enschede The Netherlands
| | - Alok K. Mitra
- School of Biological Sciences; University of Auckland; Thomas Building 3A Symonds Street Auckland New Zealand
| | - Mark R. H. Hurst
- Innovative Farm Systems; AgResearch; Lincoln Research Centre; Private Bag 4749 Christchurch 8140 New Zealand
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NandyMazumdar M, Artsimovitch I. Ubiquitous transcription factors display structural plasticity and diverse functions: NusG proteins - Shifting shapes and paradigms. Bioessays 2015; 37:324-34. [PMID: 25640595 DOI: 10.1002/bies.201400177] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Numerous accessory factors modulate RNA polymerase response to regulatory signals and cellular cues and establish communications with co-transcriptional RNA processing. Transcription regulators are astonishingly diverse, with similar mechanisms arising via convergent evolution. NusG/Spt5 elongation factors comprise the only universally conserved and ancient family of regulators. They bind to the conserved clamp helices domain of RNA polymerase, which also interacts with non-homologous initiation factors in all domains of life, and reach across the DNA channel to form processivity clamps that enable uninterrupted RNA chain synthesis. In addition to this ubiquitous function, NusG homologs exert diverse, and sometimes opposite, effects on gene expression by competing with each other and other regulators for binding to the clamp helices and by recruiting auxiliary factors that facilitate termination, antitermination, splicing, translation, etc. This surprisingly diverse range of activities and the underlying unprecedented structural changes make studies of these "transformer" proteins both challenging and rewarding.
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Affiliation(s)
- Monali NandyMazumdar
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
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Sarris PF, Ladoukakis ED, Panopoulos NJ, Scoulica EV. A phage tail-derived element with wide distribution among both prokaryotic domains: a comparative genomic and phylogenetic study. Genome Biol Evol 2014; 6:1739-47. [PMID: 25015235 PMCID: PMC4122934 DOI: 10.1093/gbe/evu136] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Prophage sequences became an integral part of bacterial genomes as a consequence of coevolution, encoding fitness or virulence factors. Such roles have been attributed to phage-derived elements identified in several Gram-negative species: The type VI secretion system (T6SS), the R- and F-type pyocins, and the newly discovered Serratia entomophila antifeeding prophage (Afp), and the Photorhabdus luminescens virulence cassette (PVC). In this study, we provide evidence that remarkably conserved gene clusters, homologous to Afp/PVC, are not restricted to Gram-negative bacteria but are widespread throughout all prokaryotes including the Archaea. Even though they are phylogenetically closer to pyocins, they share key characteristics in common with the T6SS, such as the use of a chaperon-type AAA+ ATPase and the lack of a host cell lysis mechanism. We thus suggest that Afp/PVC-like elements could be classified as phage-like-protein-translocation structures (PLTSs) rather than as pyocins. The reconstruction of phylogeny and the conserved gene content suggest that the diversification of prophage sequences to PLTS occurred in bacteria early in evolution and only once, but PLTS clusters have been horizontally transferred to some of the bacterial lineages and to the Archaea. The adaptation of this element in such a wide host range is suggestive of its versatile use in prokaryotes.
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Affiliation(s)
- Panagiotis F Sarris
- Laboratory of Clinical Bacteriology and Molecular Microbiology, Faculty of Medicine, University of Crete, Heraklion, GreecePresent address: The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.
| | | | - Nickolas J Panopoulos
- Department of Biology, University of Crete, Heraklion, GreeceDepartment of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside
| | - Effie V Scoulica
- Laboratory of Clinical Bacteriology and Molecular Microbiology, Faculty of Medicine, University of Crete, Heraklion, Greece
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36
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Castagnola A, Stock SP. Common Virulence Factors and Tissue Targets of Entomopathogenic Bacteria for Biological Control of Lepidopteran Pests. INSECTS 2014; 5:139-66. [PMID: 24634779 PMCID: PMC3952272 DOI: 10.3390/insects5010139] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 12/13/2013] [Accepted: 12/17/2013] [Indexed: 01/13/2023]
Abstract
This review focuses on common insecticidal virulence factors from entomopathogenic bacteria with special emphasis on two insect pathogenic bacteria Photorhabdus (Proteobacteria: Enterobacteriaceae) and Bacillus (Firmicutes: Bacillaceae). Insect pathogenic bacteria of diverse taxonomic groups and phylogenetic origin have been shown to have striking similarities in the virulence factors they produce. It has been suggested that the detection of phage elements surrounding toxin genes, horizontal and lateral gene transfer events, and plasmid shuffling occurrences may be some of the reasons that virulence factor genes have so many analogs throughout the bacterial kingdom. Comparison of virulence factors of Photorhabdus, and Bacillus, two bacteria with dissimilar life styles opens the possibility of re-examining newly discovered toxins for novel tissue targets. For example, nematodes residing in the hemolymph may release bacteria with virulence factors targeting neurons or neuromuscular junctions. The first section of this review focuses on toxins and their context in agriculture. The second describes the mode of action of toxins from common entomopathogens and the third draws comparisons between Gram positive and Gram negative bacteria. The fourth section reviews the implications of the nervous system in biocontrol.
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Affiliation(s)
- Anaïs Castagnola
- Center for Insect Science, University of Arizona, 1007 E. Lowell Street, Tucson, AZ 85721, USA; E-Mail:
| | - S. Patricia Stock
- Department of Entomology, University of Arizona, 1140 E. South Campus Dr., Tucson, AZ 85721, USA
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Tomar SK, Artsimovitch I. NusG-Spt5 proteins-Universal tools for transcription modification and communication. Chem Rev 2013; 113:8604-19. [PMID: 23638618 PMCID: PMC4259564 DOI: 10.1021/cr400064k] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sushil Kumar Tomar
- Department of Microbiology and The Center for RNA Biology, The Ohio State University , Columbus, Ohio 43210, United States
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Petersen LM, Tisa LS. Friend or foe? A review of the mechanisms that driveSerratiatowards diverse lifestyles. Can J Microbiol 2013; 59:627-40. [DOI: 10.1139/cjm-2013-0343] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Found widespread around the globe, Serratia are Gram-negative bacteria capable of thriving in a diverse number of environments that include water, soil, and the digestive tracts of various animals. Known for their ability to produce a myriad of extracellular enzymes, these bacteria also produce various secondary metabolites that directly contribute to their survival. While the effects Serratia species have on other organisms range from parasitic to symbiotic, what these bacteria have in common is their ability to resist attack, respond appropriately to environmental conditions, and outcompete other microorganisms when colonizing their respective niche. This review highlights the mechanisms utilized by Serratia species that drive their ubiquitous nature, with emphasis on the latest findings. Also discussed is how secreted compounds drive these bacteria towards pathogenic, mutualistic, and antagonistic associations.
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Affiliation(s)
- Lauren M. Petersen
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
| | - Louis S. Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
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39
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Heymann JB, Bartho JD, Rybakova D, Venugopal HP, Winkler DC, Sen A, Hurst MRH, Mitra AK. Three-dimensional structure of the toxin-delivery particle antifeeding prophage of Serratia entomophila. J Biol Chem 2013; 288:25276-25284. [PMID: 23857636 DOI: 10.1074/jbc.m113.456145] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Serratia entomophila antifeeding prophage (Afp) is a bullet-shaped toxin-delivery apparatus similar to the R-pyocins of Pseudomonas aeruginosa. Morphologically it resembles the sheathed tail of bacteriophages such as T4, including a baseplate at one end. It also shares features with the type VI secretion systems. Cryo-electron micrographs of tilted Afp specimens (up to 60 degrees) were analyzed to determine the correct cyclic symmetry to overcome the limitation imposed by exclusively side views in nominally untilted specimens. An asymmetric reconstruction shows clear 6-fold cyclic symmetry contrary to a previous conclusion of 4-fold symmetry based on analysis of only the preferred side views (Sen, A., Rybakova, D., Hurst, M. R., and Mitra, A. K. (2010) J. Bacteriol. 192, 4522-4525). Electron tomography of negatively stained Afp revealed right-handed helical striations in many of the particles, establishing the correct hand. Higher quality micrographs of untilted specimens were processed to produce a reconstruction at 2.0-nm resolution with imposed 6-fold symmetry. The helical parameters of the sheath were determined to be 8.14 nm for the subunit rise along and 40.5° for the rotation angle around the helix. The sheath is similar to that of the T4 phage tail but with a different arrangement of the subdomain of the polymerizing sheath protein(s). The central tube is similar to the diameter and axial width of the Hcp1 hexamer of P. aeruginosa type VI secretion system. The tube extends through the baseplate into a needle resembling the "puncture device" of the T4 tail. The tube contains density that may be the toxin and/or a length-determining protein.
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Affiliation(s)
- J Bernard Heymann
- From the NIAMS, National Institutes of Health, Bethesda, Maryland 20892
| | - Joseph D Bartho
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand, and
| | - Daria Rybakova
- Innovative Farm Systems, Agresearch, Lincoln, Christchurch 8140, New Zealand
| | - Hari P Venugopal
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand, and
| | - Dennis C Winkler
- From the NIAMS, National Institutes of Health, Bethesda, Maryland 20892
| | - Anindito Sen
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand, and
| | - Mark R H Hurst
- Innovative Farm Systems, Agresearch, Lincoln, Christchurch 8140, New Zealand
| | - Alok K Mitra
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand, and.
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Rybakova D, Radjainia M, Turner A, Sen A, Mitra AK, Hurst MRH. Role of antifeeding prophage (Afp) protein Afp16 in terminating the length of the Afp tailocin and stabilizing its sheath. Mol Microbiol 2013; 89:702-14. [DOI: 10.1111/mmi.12305] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2013] [Indexed: 11/30/2022]
Affiliation(s)
| | - Mazdak Radjainia
- School of Biological Sciences; University of Auckland; Thomas Building, 3A Symonds Street; Auckland; New Zealand
| | - Adrian Turner
- School of Biological Sciences; University of Auckland; Thomas Building, 3A Symonds Street; Auckland; New Zealand
| | | | - Alok K. Mitra
- School of Biological Sciences; University of Auckland; Thomas Building, 3A Symonds Street; Auckland; New Zealand
| | - Mark R. H. Hurst
- Innovative Farm Systems; AgResearch; Lincoln Research Centre; Private Bag 4749; Christchurch; 8140; New Zealand
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Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits. ISME JOURNAL 2013; 7:1985-96. [PMID: 23739050 DOI: 10.1038/ismej.2013.90] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/29/2013] [Accepted: 05/06/2013] [Indexed: 11/08/2022]
Abstract
Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.
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Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii. PLoS Genet 2012; 8:e1003012. [PMID: 23133394 PMCID: PMC3486910 DOI: 10.1371/journal.pgen.1003012] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/22/2012] [Indexed: 11/28/2022] Open
Abstract
Terrestrial arthropods are commonly infected with maternally inherited bacterial symbionts that cause cytoplasmic incompatibility (CI). In CI, the outcome of crosses between symbiont-infected males and uninfected females is reproductive failure, increasing the relative fitness of infected females and leading to spread of the symbiont in the host population. CI symbionts have profound impacts on host genetic structure and ecology and may lead to speciation and the rapid evolution of sex determination systems. Cardinium hertigii, a member of the Bacteroidetes and symbiont of the parasitic wasp Encarsia pergandiella, is the only known bacterium other than the Alphaproteobacteria Wolbachia to cause CI. Here we report the genome sequence of Cardinium hertigii cEper1. Comparison with the genomes of CI–inducing Wolbachia pipientis strains wMel, wRi, and wPip provides a unique opportunity to pinpoint shared proteins mediating host cell interaction, including some candidate proteins for CI that have not previously been investigated. The genome of Cardinium lacks all major biosynthetic pathways but harbors a complete biotin biosynthesis pathway, suggesting a potential role for Cardinium in host nutrition. Cardinium lacks known protein secretion systems but encodes a putative phage-derived secretion system distantly related to the antifeeding prophage of the entomopathogen Serratia entomophila. Lastly, while Cardinium and Wolbachia genomes show only a functional overlap of proteins, they show no evidence of laterally transferred elements that would suggest common ancestry of CI in both lineages. Instead, comparative genomics suggests an independent evolution of CI in Cardinium and Wolbachia and provides a novel context for understanding the mechanistic basis of CI. Many arthropods are infected with bacterial symbionts that are maternally transmitted and have a great impact on their hosts' biology, ecology, and evolution. One of the most common phenotypes of facultative symbionts appears to be cytoplasmic incompatibility (CI), a type of reproductive failure in which bacteria in males modify sperm in a way that reduces the reproductive success of uninfected female mates. In spite of considerable interest, the genetic basis for CI is largely unknown. Cardinium hertigii, a symbiont of tiny parasitic wasps, is the only bacterial group other than the well-studied Wolbachia that is known to cause CI. Analysis of the Cardinium genome indicates that CI evolved independently in Wolbachia and Cardinium. However, a suite of shared proteins was likely involved in mediating host cell interactions, and CI shows functional overlap in both lineages. Our analysis suggests the presence of an unusual phage-derived, putative secretion system and reveals that Cardinium encodes biosynthetic pathways that suggest a potential role in host nutrition. Our findings provide a novel comparative context for understanding the mechanistic basis of CI and substantially increase our knowledge on reproductive manipulator symbionts that do not only severely affect population genetic structure of arthropods but may also serve as powerful tools in pest management.
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Rodríguez-Segura Z, Chen J, Villalobos FJ, Gill S, Nuñez-Valdez ME. The lipopolysaccharide biosynthesis core of the Mexican pathogenic strain Serratia entomophila is associated with toxicity to larvae of Phyllophaga blanchardi. J Invertebr Pathol 2012; 110:24-32. [DOI: 10.1016/j.jip.2012.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 12/03/2011] [Accepted: 01/21/2012] [Indexed: 11/29/2022]
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Leiman PG, Shneider MM. Contractile tail machines of bacteriophages. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:93-114. [PMID: 22297511 DOI: 10.1007/978-1-4614-0980-9_5] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Bacteriophages with contractile tails epitomize the concepts of "virus" and "phage" for many because the tails of these phages undergo a large conformational change - resembling the action of a syringe - upon the attachment to the host cell. The contractile tails belong to the recently recognized class of "contractile systems," which includes phage tails, their close relatives R-type pyocins, the bacterial type VI secretion system, and the virulence cassette of Photorhabdus. Their function is to deliver large proteins and/or DNA into the cytoplasm of a bacterial or eukaryotic cell. The structure of the core components of all contractile tail-like systems is conserved, but the corresponding genes have diverged to such a degree that the common ancestry can no longer be easily detected at the level of amino acid sequence. At present, it is unclear, whether the contractile systems originated in bacteria or in phages. This chapter describes the structure and function of phage contractile tails and compares them with other phage tails and with other known contractile systems.
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Affiliation(s)
- Petr G Leiman
- Institut de physique des systèmes biologiques, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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45
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Shanchez-Contreras M, Vlisidou I. The diversity of insect-bacteria interactions and its applications for disease control. Biotechnol Genet Eng Rev 2011; 25:203-43. [PMID: 21412357 DOI: 10.5661/bger-25-203] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Prokaryotic microorganisms are widespread in all environments on Earth, establishing diverse interactions with many eukaryotic taxa, including insects. These associations may be symbiotic, pathogenic and vectoring. Independently of the type of interaction, each association starts with the adhesion of the microorganism to the host, entry and "invasion" of the host, then progresses to establishment and dissemination within the host, by avoiding host immune responses, and concludes with transmission back to the environment or to a new host. Advances in genomics and genetics have allowed the dissection of these processes and provided important information on the elements driving the shaping of the members of each association. Furthermore, many mechanisms involved in the establishment of the associations have been scrutinised, along with the development of new methods for the management of insect populations.
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Hurst MRH, Becher SA, O'Callaghan M. Nucleotide sequence of the Serratia entomophila plasmid pADAP and the Serratia proteamaculans pU143 plasmid virulence associated region. Plasmid 2010; 65:32-41. [PMID: 20950642 DOI: 10.1016/j.plasmid.2010.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 10/05/2010] [Accepted: 10/06/2010] [Indexed: 10/19/2022]
Abstract
Some strains of Serratia entomophila and S. proteamaculans cause amber disease of the New Zealand grass grub Costelytra zealandica (Coleoptera: Scarabaeidae), an important pasture pest in New Zealand. The disease determinants of S. entomophila, are encoded on a 153,404-bp plasmid, termed pADAP for amber disease associated plasmid. The S. proteamaculans strain 143 (Sp143) exhibits an unusual pathotype, where only 60-70% of C. zealandica larvae infected with the bacterium succumb to disease. DNA sequence analysis of the Sp143 pU143 virulence associated region identified high DNA similarity to the pADAP sep virulence associated region, with DNA sequence variation in the sepA gene and the variable region of the sepC component. No pADAP anti-feeding prophage orthologue was detected in the Sp143 genome. The region of pADAP replication was cloned and found to replicate in S. entomophila but not in Escherichia coli. DNA sequence analysis of the plasmid pSG348 repA gene from the French isolate of Serratia grimesii, identified 93% DNA identity to the pADAP repA gene. A comparison of the pU143 virulence associated region with the completed pADAP nucleotide sequence is given.
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Affiliation(s)
- Mark R H Hurst
- Biocontrol and Biosecurity, AgResearch, Lincoln Research Centre, Private Bag 4749, Christchurch 8140, New Zealand.
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Structural study of the Serratia entomophila antifeeding prophage: three-dimensional structure of the helical sheath. J Bacteriol 2010; 192:4522-5. [PMID: 20601477 DOI: 10.1128/jb.00224-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sheath of the Serratia entomophila antifeeding prophage, which is pathogenic to the New Zealand grass grub Costelytra zealandica, is a 3-fold helix formed by a 4-fold symmetric repeating motif disposed around a helical inner tube. This structure, determined by electron microscopy and image processing, is distinct from that of the other known morphologically similar bacteriophage sheaths.
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Gatehouse H, Tan B, Christeller J, Hurst M, Marshall S, Jackson T. Phenotypic changes and the fate of digestive enzymes during induction of amber disease in larvae of the New Zealand grass grub (Costelytra zealandica). J Invertebr Pathol 2009; 101:215-21. [DOI: 10.1016/j.jip.2009.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 04/27/2009] [Accepted: 05/17/2009] [Indexed: 10/20/2022]
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Jubelin G, Chavez CV, Taieb F, Banfield MJ, Samba-Louaka A, Nobe R, Nougayrède JP, Zumbihl R, Givaudan A, Escoubas JM, Oswald E. Cycle inhibiting factors (CIFs) are a growing family of functional cyclomodulins present in invertebrate and mammal bacterial pathogens. PLoS One 2009; 4:e4855. [PMID: 19308257 PMCID: PMC2654923 DOI: 10.1371/journal.pone.0004855] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 02/16/2009] [Indexed: 01/04/2023] Open
Abstract
The cycle inhibiting factor (Cif) produced by enteropathogenic and enterohemorrhagic Escherichia coli was the first cyclomodulin to be identified that is injected into host cells via the type III secretion machinery. Cif provokes cytopathic effects characterized by G1 and G2 cell cycle arrests, accumulation of the cyclin-dependent kinase inhibitors (CKIs) p21waf1/cip1 and p27kip1 and formation of actin stress fibres. The X-ray crystal structure of Cif revealed it to be a divergent member of a superfamily of enzymes including cysteine proteases and acetyltransferases that share a conserved catalytic triad. Here we report the discovery and characterization of four Cif homologs encoded by different pathogenic or symbiotic bacteria isolated from vertebrates or invertebrates. Cif homologs from the enterobacteria Yersinia pseudotuberculosis, Photorhabdus luminescens, Photorhabdus asymbiotica and the β-proteobacterium Burkholderia pseudomallei all induce cytopathic effects identical to those observed with Cif from pathogenic E. coli. Although these Cif homologs are remarkably divergent in primary sequence, the catalytic triad is strictly conserved and was shown to be crucial for cell cycle arrest, cytoskeleton reorganization and CKIs accumulation. These results reveal that Cif proteins form a growing family of cyclomodulins in bacteria that interact with very distinct hosts including insects, nematodes and humans.
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Affiliation(s)
- Grégory Jubelin
- INRA, UMR1225, Toulouse, France
- Université de Toulouse, ENVT, UMR 1225, Toulouse, France
| | - Carolina Varela Chavez
- INRA, UMR 1133 Laboratoire EMIP, Montpellier, France
- Université Montpellier 2, UMR 1133 Laboratoire EMIP, Montpellier, France
| | - Frédéric Taieb
- INRA, UMR1225, Toulouse, France
- Université de Toulouse, ENVT, UMR 1225, Toulouse, France
| | - Mark J. Banfield
- Department of Biological Chemistry, John Innes Centre, NR4 7UH, Norwich, United Kingdom
| | - Ascel Samba-Louaka
- INRA, UMR1225, Toulouse, France
- Université de Toulouse, ENVT, UMR 1225, Toulouse, France
| | - Rika Nobe
- INRA, UMR1225, Toulouse, France
- Université de Toulouse, ENVT, UMR 1225, Toulouse, France
| | | | - Robert Zumbihl
- INRA, UMR 1133 Laboratoire EMIP, Montpellier, France
- Université Montpellier 2, UMR 1133 Laboratoire EMIP, Montpellier, France
| | - Alain Givaudan
- INRA, UMR 1133 Laboratoire EMIP, Montpellier, France
- Université Montpellier 2, UMR 1133 Laboratoire EMIP, Montpellier, France
| | - Jean-Michel Escoubas
- INRA, UMR 1133 Laboratoire EMIP, Montpellier, France
- Université Montpellier 2, UMR 1133 Laboratoire EMIP, Montpellier, France
| | - Eric Oswald
- INRA, UMR1225, Toulouse, France
- Université de Toulouse, ENVT, UMR 1225, Toulouse, France
- * E-mail:
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