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Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of Xenorhabdus griffiniae HGB2511, the bacterial symbiont of the nematode Steinernema hermaphroditum (India). MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000772. [PMID: 37179970 PMCID: PMC10170317 DOI: 10.17912/micropub.biology.000772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]
Abstract
Symbiosis, the beneficial interactions between two organisms, is a ubiquitous feature of all life on Earth, including associations between animals and bacteria. However, the specific molecular and cellular mechanisms which underlie the diverse partnerships formed between animals and bacteria are still being explored. Entomopathogenic nematodes transport bacteria between insect hosts, together they kill the insect, and the bacteria consume the insect and serve as food source for the nematodes. These nematodes, including those in the Steinernema genus, are effective laboratory models for studying the molecular mechanisms of symbiosis because of the natural partnership they form with Xenorhabdus bacteria and their straightforward husbandry. Steinernema hermaphroditum nematodes and their Xenorhabdus griffiniae symbiotic bacteria are being developed as a genetic model pair for studying symbiosis. Our goal in this project was to begin to identify bacterial genes that may be important for symbiotic interactions with the nematode host. Towards this end, we adapted and optimized a protocol for delivery and insertion of a lacZ- promoter-probe transposon for use in the S. hermaphroditum symbiont, X. griffiniae HGB2511 (Cao et al., 2022). We assessed the frequencies at which we obtained exconjugants, metabolic auxotrophic mutants, and active promoter- lacZ fusions. Our data indicate that the Tn 10 transposon inserted relatively randomly based on the finding that 4.7% of the mutants exhibited an auxotrophic phenotype. Promoter-fusions with the transposon-encoded lacZ , which resulted in expression of β-galactosidase activity, occurred in 47% of the strains. To our knowledge, this is the first mutagenesis protocol generated for this bacterial species, and will facilitate the implementation of large scale screens for symbiosis and other phenotypes of interest in X. griffiniae .
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Affiliation(s)
- Omar S. Alani
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, United States
| | - Mengyi Cao
- California Institute of Technology, Pasadena, California, United States
| | - Heidi Goodrich-Blair
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, United States
| | - Jennifer K. Heppert
- Department of Microbiology, University of Tennessee at Knoxville, Knoxville, Tennessee, United States
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Apex Predator Nematodes and Meso-Predator Bacteria Consume Their Basal Insect Prey through Discrete Stages of Chemical Transformations. mSystems 2022; 7:e0031222. [PMID: 35543104 PMCID: PMC9241642 DOI: 10.1128/msystems.00312-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial symbiosis drives physiological processes of higher-order systems, including the acquisition and consumption of nutrients that support symbiotic partner reproduction. Metabolic analytics provide new avenues to examine how chemical ecology, or the conversion of existing biomass to new forms, changes over a symbiotic life cycle. We applied these approaches to the nematode Steinernema carpocapsae, its mutualist bacterium, Xenorhabdus nematophila, and the insects they infect. The nematode-bacterium pair infects, kills, and reproduces in an insect until nutrients are depleted. To understand the conversion of insect biomass over time into either nematode or bacterium biomass, we integrated information from trophic, metabolomic, and gene regulation analyses. Trophic analysis established bacteria as meso-predators and primary insect consumers. Nematodes hold a trophic position of 4.6, indicative of an apex predator, consuming bacteria and likely other nematodes. Metabolic changes associated with Galleria mellonella insect bioconversion were assessed using multivariate statistical analyses of metabolomics data sets derived from sampling over an infection time course. Statistically significant, discrete phases were detected, indicating the insect chemical environment changes reproducibly during bioconversion. A novel hierarchical clustering method was designed to probe molecular abundance fluctuation patterns over time, revealing distinct metabolite clusters that exhibit similar abundance shifts across the time course. Composite data suggest bacterial tryptophan and nematode kynurenine pathways are coordinated for reciprocal exchange of tryptophan and NAD+ and for synthesis of intermediates that can have complex effects on bacterial phenotypes and nematode behaviors. Our analysis of pathways and metabolites reveals the chemistry underlying the recycling of organic material during carnivory. IMPORTANCE The processes by which organic life is consumed and reborn in a complex ecosystem were investigated through a multiomics approach applied to the tripartite Xenorhabdus bacterium-Steinernema nematode-Galleria insect symbiosis. Trophic analyses demonstrate the primary consumers of the insect are the bacteria, and the nematode in turn consumes the bacteria. This suggests the Steinernema-Xenorhabdus mutualism is a form of agriculture in which the nematode cultivates the bacterial food sources by inoculating them into insect hosts. Metabolomics analysis revealed a shift in biological material throughout progression of the life cycle: active infection, insect death, and conversion of cadaver tissues into bacterial biomass and nematode tissue. We show that each phase of the life cycle is metabolically distinct, with significant differences including those in the tricarboxylic acid cycle and amino acid pathways. Our findings demonstrate that symbiotic life cycles can be defined by reproducible stage-specific chemical signatures, enhancing our broad understanding of metabolic processes that underpin a three-way symbiosis.
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Grossman AS, Escobar CA, Mans EJ, Mucci NC, Mauer TJ, Jones KA, Moore CC, Abraham PE, Hettich RL, Schneider L, Campagna SR, Forest KT, Goodrich-Blair H. A Surface Exposed, Two-Domain Lipoprotein Cargo of a Type XI Secretion System Promotes Colonization of Host Intestinal Epithelia Expressing Glycans. Front Microbiol 2022; 13:800366. [PMID: 35572647 PMCID: PMC9100927 DOI: 10.3389/fmicb.2022.800366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/07/2022] [Indexed: 11/17/2022] Open
Abstract
The only known required component of the newly described Type XI secretion system (TXISS) is an outer membrane protein (OMP) of the DUF560 family. TXISSOMPs are broadly distributed across proteobacteria, but properties of the cargo proteins they secrete are largely unexplored. We report biophysical, histochemical, and phenotypic evidence that Xenorhabdus nematophila NilC is surface exposed. Biophysical data and structure predictions indicate that NilC is a two-domain protein with a C-terminal, 8-stranded β-barrel. This structure has been noted as a common feature of TXISS effectors and may be important for interactions with the TXISSOMP. The NilC N-terminal domain is more enigmatic, but our results indicate it is ordered and forms a β-sheet structure, and bioinformatics suggest structural similarities to carbohydrate-binding proteins. X. nematophila NilC and its presumptive TXISSOMP partner NilB are required for colonizing the anterior intestine of Steinernema carpocapsae nematodes: the receptacle of free-living, infective juveniles and the anterior intestinal cecum (AIC) in juveniles and adults. We show that, in adult nematodes, the AIC expresses a Wheat Germ Agglutinin (WGA)-reactive material, indicating the presence of N-acetylglucosamine or N-acetylneuraminic acid sugars on the AIC surface. A role for this material in colonization is supported by the fact that exogenous addition of WGA can inhibit AIC colonization by X. nematophila. Conversely, the addition of exogenous purified NilC increases the frequency with which X. nematophila is observed at the AIC, demonstrating that abundant extracellular NilC can enhance colonization. NilC may facilitate X. nematophila adherence to the nematode intestinal surface by binding to host glycans, it might support X. nematophila nutrition by cleaving sugars from the host surface, or it might help protect X. nematophila from nematode host immunity. Proteomic and metabolomic analyses of wild type X. nematophila compared to those lacking nilB and nilC revealed differences in cell wall and secreted polysaccharide metabolic pathways. Additionally, purified NilC is capable of binding peptidoglycan, suggesting that periplasmic NilC may interact with the bacterial cell wall. Overall, these findings support a model that NilB-regulated surface exposure of NilC mediates interactions between X. nematophila and host surface glycans during colonization. This is a previously unknown function for a TXISS.
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Affiliation(s)
- Alex S. Grossman
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Cristian A. Escobar
- Department of Bacteriology, The University of Wisconsin–Madison, Madison, WI, United States
| | - Erin J. Mans
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Nicholas C. Mucci
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Terra J. Mauer
- Department of Bacteriology, The University of Wisconsin–Madison, Madison, WI, United States
| | - Katarina A. Jones
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Cameron C. Moore
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Liesel Schneider
- Department of Animal Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Shawn R. Campagna
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, Knoxville, TN, United States
- The University of Tennessee Oak Ridge Innovation Institute, Knoxville, TN, United States
| | - Katrina T. Forest
- Department of Bacteriology, The University of Wisconsin–Madison, Madison, WI, United States
- Katrina T. Forest,
| | - Heidi Goodrich-Blair
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Department of Bacteriology, The University of Wisconsin–Madison, Madison, WI, United States
- *Correspondence: Heidi Goodrich-Blair,
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Li JH, Cho W, Hamchand R, Oh J, Crawford JM. A Conserved Nonribosomal Peptide Synthetase in Xenorhabdus bovienii Produces Citrulline-Functionalized Lipopeptides. JOURNAL OF NATURAL PRODUCTS 2021; 84:2692-2699. [PMID: 34581573 PMCID: PMC9970011 DOI: 10.1021/acs.jnatprod.1c00573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The entomopathogenic bacterium Xenorhabdus bovienii exists in a mutualistic relationship with nematodes of the genus Steinernema. Free-living infective juveniles of Steinernema prey on insect larvae and regurgitate X. bovienii within the hemocoel of a host larva. X. bovienii subsequently produces a complex array of specialized metabolites and effector proteins that kill the insect and regulate various aspects of the trilateral symbiosis. While Xenorhabdus species are rich producers of secondary metabolites, many of their biosynthetic gene clusters remain uncharacterized. Here, we describe a nonribosomal peptide synthetase (NRPS) identified through comparative genomics analysis that is widely conserved in Xenorhabdus species. Heterologous expression of this NRPS gene from X. bovienii in E. coli led to the discovery of a family of lipo-tripeptides that chromatographically appear as pairs, containing either a C-terminal carboxylic acid or carboxamide. Coexpression of the NRPS with the leupeptin protease inhibitor pathway enhanced production, facilitating isolation and characterization efforts. The new lipo-tripeptides were also detected in wild-type X. bovienii cultures. These metabolites, termed bovienimides, share an uncommon C-terminal d-citrulline residue. The NRPS lacked a dedicated chain termination domain, resulting in product diversification and release from the assembly line through reactions with ammonia, water, or exogenous alcohols.
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Affiliation(s)
- Jhe-Hao Li
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Wooyoung Cho
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Randy Hamchand
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Joonseok Oh
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, United States
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Sánchez-Romero MA, Casadesús J. Waddington's Landscapes in the Bacterial World. Front Microbiol 2021; 12:685080. [PMID: 34149674 PMCID: PMC8212987 DOI: 10.3389/fmicb.2021.685080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/20/2021] [Indexed: 11/24/2022] Open
Abstract
Conrad Waddington’s epigenetic landscape, a visual metaphor for the development of multicellular organisms, is appropriate to depict the formation of phenotypic variants of bacterial cells. Examples of bacterial differentiation that result in morphological change have been known for decades. In addition, bacterial populations contain phenotypic cell variants that lack morphological change, and the advent of fluorescent protein technology and single-cell analysis has unveiled scores of examples. Cell-specific gene expression patterns can have a random origin or arise as a programmed event. When phenotypic cell-to-cell differences are heritable, bacterial lineages are formed. The mechanisms that transmit epigenetic states to daughter cells can have strikingly different levels of complexity, from the propagation of simple feedback loops to the formation of complex DNA methylation patterns. Game theory predicts that phenotypic heterogeneity can facilitate bacterial adaptation to hostile or unpredictable environments, serving either as a division of labor or as a bet hedging that anticipates future challenges. Experimental observation confirms the existence of both types of strategies in the bacterial world.
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Affiliation(s)
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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