Faculty & Staff

  • Image of Heidi Goodrich-Blair

    Heidi Goodrich-Blair

    Professor of Bacteriology
    Office: 865-974-6358

Start and Promotion Dates

  • Assistant Professor: 1997
  • Associate Professor: 2003
  • Full Professor: 2009


B.S., Biology, University at Albany, SUNY 1987
Ph.D., Molecular Biology, University of Albany, SUNY 1993
Postdoctoral Research: Microbial Genetics, University at Albany, SUNY;
Harvard Medical School

Areas of Study

Molecular mechanisms of bacteria-nematode-insect symbiosis

Research Overview

Our research is aimed at understanding, at a molecular level, how microbes survive and flourish in the environments they occupy. Survival for many microbes is dependent upon their ability to interact with other organisms. To understand host-microbe interactions, our lab focuses on a gamma-proteobacterium, Xenorhabdus nematophila. This bacterium is a symbiont of the insect-infecting nematode Steinernema carpocapsae and is responsible for killing the insect larvae that this pair infects.

X. nematophila resides as a symbiont within a specialized intestinal vesicle of the insect-infecting nematode. Each of these two organisms requires the other to grow and reproduce, a process that occurs within the insect. The bacterium, X. nematophila, is the actual insect pathogen; it produces exo- and endo-toxins that can rapidly kill an insect host. In addition, once inside an insect host, X. nematophila expresses degradative functions such as proteases and lipases that convert insect host tissues into products that can be utilized by the nematode. Thus, X. nematophila is essential for both insect host killing and nematode development.

X. nematophila is a model for both positive and negative host-microbe interactions, knowledge of which will improve our ability to combat and/or utilize microorganisms to our own benefit. Furthermore, X. nematophila is part of a tripartite system (insect, nematode, and bacterium) that has potential use as an alternative to insecticides. Understanding the relationship between the members of this system will greatly improve their use in biocontrol. In our work we use molecular, genetic, and biochemical techniques to ask basic biological questions involving the interaction of X. nematophila with its hosts, examining the interaction from both the bacterium and host sides.

The results of our work will have an impact on our understanding of any system in which microbes interact with a eukaryotic host, including pathogenic and symbiotic associations. It will illustrate the mechanisms by which a single bacterium can form a beneficial association with one organism and a harmful interaction with another. In addition, our findings will have implications in the fields of biocontrol and microbial ecology and development.


  • Microbiology 470: Microbial Genetics & Molecular Machines
  • Microbiology 710: Microbial Symbiosis



  • 2006 - CALS Pound Research Award

Research Papers

  • Murfin KE, Ginete DR, Bashey F, Goodrich-Blair H (2018) Symbiont-mediated competition: Xenorhabdus bovienii confer an advantage to their nematode host Steinernema affine by killing competitor Steinernema feltiae. Environ. Microbiol. : 10.1111/1462-2920.14278 · Pubmed

    Bacterial symbionts can affect several biotic interactions of their hosts, including their competition with other species. Nematodes in the genus Steinernema utilize Xenorhabdus bacterial symbionts for insect host killing and nutritional bioconversion. Here, we establish that the Xenorhabdus bovienii bacterial symbiont (Xb-Sa-78) of Steinernema affine nematodes can impact competition between S. affine and S. feltiae by a novel mechanism, directly attacking its nematode competitor. Through co-injection and natural infection assays we demonstrate the causal role of Xb-Sa-78 in the superiority of S. affine over S. feltiae nematodes during competition. Survival assays revealed that Xb-Sa-78 bacteria kill reproductive life stages of S. feltiae. Microscopy and timed infection assays indicate that Xb-Sa-78 bacteria colonize S. feltiae nematode intestines, which alters morphology of the intestine. These data suggest that Xb-Sa-78 may be an intestinal pathogen of the non-native S. feltiae nematode, although it is a nonharmful colonizer of the native nematode host, S. affine. Screening additional X. bovienii isolates revealed that intestinal infection and killing of S. feltiae is conserved among isolates from nematodes closely related to S. affine, although the underlying killing mechanisms may vary. Together, these data demonstrate that bacterial symbionts can modulate competition between their hosts, and reinforce specificity in mutualistic interactions.

  • Stilwell MD, Cao M, Goodrich-Blair H, Weibel DB (2018) Studying the Symbiotic Bacterium in Individual, Living Nematodes Using Microfluidic Systems. mSphere 3(1): (PMC5750387) 10.1128/mSphere.00530-17 · Pubmed

    Animal-microbe symbioses are ubiquitous in nature and scientifically important in diverse areas, including ecology, medicine, and agriculture. nematodes and bacteria compose an established, successful model system for investigating microbial pathogenesis and mutualism. The bacterium is a species-specific mutualist of insect-infecting nematodes. The bacterium colonizes a specialized intestinal pocket within the infective stage of the nematode, which transports the bacteria between insects that are killed and consumed by the pair for reproduction. Current understanding of the interaction between the infective-stage nematode and its bacterial colonizers is based largely on population-level, snapshot time point studies on these organisms. This limitation arises because investigating temporal dynamics of the bacterium within the nematode is impeded by the difficulty of isolating and maintaining individual living nematodes and tracking colonizing bacterial cells over time. To overcome this challenge, we developed a microfluidic system that enables us to spatially isolate and microscopically observe individual, living nematodes and monitor the growth and development of the associated bacterial communities-starting from a single cell or a few cells-over weeks. Our data demonstrate, to our knowledge, the first direct, temporal, visual analysis of a symbiosis system and the application of this system to reveal continuous dynamics of the symbiont population in the living host animal. This paper describes an experimental system for directly investigating population dynamics of a symbiotic bacterium, , in its host-the infective stage of the entomopathogenic nematode . Tracking individual and groups of bacteria in individual host nematodes over days and weeks yielded insight into dynamic growth and topology changes of symbiotic bacterial populations within infective juvenile nematodes. Our approach for studying symbioses between bacteria and nematodes provides a system to investigate long-term host-microbe interactions in individual nematodes and extrapolate the lessons learned to other bacterium-animal interactions.

  • Kim IH, Aryal SK, Aghai DT, Casanova-Torres ÁM, Hillman K, Kozuch MP, Mans EJ, Mauer TJ, Ogier JC, Ensign JC, Gaudriault S, Goodman WG, Goodrich-Blair H, Dillman AR (2017) The insect pathogenic bacterium Xenorhabdus innexi has attenuated virulence in multiple insect model hosts yet encodes a potent mosquitocidal toxin. BMC Genomics 18(1):927 (PMC5709968) 10.1186/s12864-017-4311-4 · Pubmed

    Xenorhabdus innexi is a bacterial symbiont of Steinernema scapterisci nematodes, which is a cricket-specialist parasite and together the nematode and bacteria infect and kill crickets. Curiously, X. innexi expresses a potent extracellular mosquitocidal toxin activity in culture supernatants. We sequenced a draft genome of X. innexi and compared it to the genomes of related pathogens to elucidate the nature of specialization. Using green fluorescent protein-expressing X. innexi we confirm previous reports using culture-dependent techniques that X. innexi colonizes its nematode host at low levels (~3-8 cells per nematode), relative to other Xenorhabdus-Steinernema associations. We found that compared to the well-characterized entomopathogenic nematode symbiont X. nematophila, X. innexi fails to suppress the insect phenoloxidase immune pathway and is attenuated for virulence and reproduction in the Lepidoptera Galleria mellonella and Manduca sexta, as well as the dipteran Drosophila melanogaster. To assess if, compared to other Xenorhabdus spp., X. innexi has a reduced capacity to synthesize virulence determinants, we obtained and analyzed a draft genome sequence. We found no evidence for several hallmarks of Xenorhabdus spp. toxicity, including Tc and Mcf toxins. Similar to other Xenorhabdus genomes, we found numerous loci predicted to encode non-ribosomal peptide/polyketide synthetases. Anti-SMASH predictions of these loci revealed one, related to the fcl locus that encodes fabclavines and zmn locus that encodes zeamines, as a likely candidate to encode the X. innexi mosquitocidal toxin biosynthetic machinery, which we designated Xlt. In support of this hypothesis, two mutants each with an insertion in an Xlt biosynthesis gene cluster lacked the mosquitocidal compound based on HPLC/MS analysis and neither produced toxin to the levels of the wild type parent. The X. innexi genome will be a valuable resource in identifying loci encoding new metabolites of interest, but also in future comparative studies of nematode-bacterial symbiosis and niche partitioning among bacterial pathogens.

  • Cao M, Goodrich-Blair H (2017) Ready or Not: Microbial Adaptive Responses in Dynamic Symbiosis Environments. J. Bacteriol. 199(15): (PMC5512229) 10.1128/JB.00883-16 · Pubmed

    In mutually beneficial and pathogenic symbiotic associations, microbes must adapt to the host environment for optimal fitness. Both within an individual host and during transmission between hosts, microbes are exposed to temporal and spatial variation in environmental conditions. The phenomenon of phenotypic variation, in which different subpopulations of cells express distinctive and potentially adaptive characteristics, can contribute to microbial adaptation to a lifestyle that includes rapidly changing environments. The environments experienced by a symbiotic microbe during its life history can be erratic or predictable, and each can impact the evolution of adaptive responses. In particular, the predictability of a rhythmic or cyclical series of environments may promote the evolution of signal transduction cascades that allow preadaptive responses to environments that are likely to be encountered in the future, a phenomenon known as adaptive prediction. In this review, we summarize environmental variations known to occur in some well-studied models of symbiosis and how these may contribute to the evolution of microbial population heterogeneity and anticipatory behavior. We provide details about the symbiosis between bacteria and nematodes as a model to investigate the concept of environmental adaptation and adaptive prediction in a microbial symbiosis.

  • Casanova-Torres ÁM, Shokal U, Morag N, Eleftherianos I, Goodrich-Blair H (2017) The Global Transcription Factor Lrp Is both Essential for and Inhibitory to Xenorhabdus nematophila Insecticidal Activity. Appl. Environ. Microbiol. 83(12): (PMC5452817) 10.1128/AEM.00185-17 · Pubmed

    In the entomopathogenic bacterium , cell-to-cell variation in the abundance of the Lrp transcription factor leads to virulence modulation; low Lrp levels are associated with a virulent phenotype and suppression of antimicrobial peptides (AMPs) in insects, while cells that lack or express high Lrp levels are virulence attenuated and elicit AMP expression. To better understand the basis of these phenotypes, we examined strains expressing fixed Lrp levels. Unlike the -null mutant, the high- strain is fully virulent in , suggesting that these two strains have distinct underlying causes of virulence attenuation in Indeed, the -null mutant was defective in cytotoxicity against hemocytes relative to that in the high- and low- strains. Further, supernatant derived from the -null mutant but not from the high- strain was defective in inhibiting weight gain when fed to 1st instar These data suggest that contributors to the -null mutant virulence attenuation phenotype are the lack of Lrp-dependent cytotoxic and extracellular oral growth inhibitory activities, which may be particularly important for virulence in In contrast, the high-Lrp strain was sensitive to the antimicrobial peptide cecropin, had a transient survival defect in , and had reduced extracellular levels of insecticidal activity, measured by injection of supernatant into 4th instar Thus, high- strain virulence attenuation may be explained by its hypersensitivity to host immunity and its inability to secrete one or more insecticidal factors. Adaptation of a bacterial pathogen to host environments can be achieved through the coordinated regulation of virulence factors that can optimize success under prevailing conditions. In the insect pathogen , the global transcription factor Lrp is necessary for virulence when injected into or insect hosts. However, high levels of Lrp, either naturally occurring or artificially induced, cause attenuation of virulence in but not Here, we present evidence suggesting that the underlying cause of high-Lrp-dependent virulence attenuation in is hypersensitivity to host immune responses and decreased insecticidal activity and that high-Lrp virulence phenotypes are insect host specific. This knowledge suggests that faces varied challenges depending on the type of insect host it infects and that its success in these environments depends on Lrp-dependent control of a multifactorial virulence repertoire.

  • Cao M, Patel T, Rickman T, Goodrich-Blair H, Hussa EA (2017) High Levels of the Xenorhabdus nematophila Transcription Factor Lrp Promote Mutualism with the Steinernema carpocapsae Nematode Host. Appl. Environ. Microbiol. 83(12): (PMC5452812) 10.1128/AEM.00276-17 · Pubmed

    bacteria are mutualistic symbionts of nematodes and pathogens of insects. The global regulator Lrp controls the expression of many genes involved in both mutualism and pathogenic activities, suggesting a role in the transition between the two host organisms. We previously reported that natural populations of exhibit various levels of Lrp expression and that cells expressing relatively low levels of Lrp are optimized for virulence in the insect The adaptive advantage of the high-Lrp-expressing state was not established. Here we used strains engineered to express constitutively high or low levels of Lrp to test the model in which high-Lrp-expressing cells are adapted for mutualistic activities with the nematode host. We demonstrate that high-Lrp cells form more robust biofilms in laboratory media than do low-Lrp cells, which may reflect adherence to host tissues. Also, our data showed that nematodes cultivated with high-Lrp strains are more frequently colonized than are those associated with low-Lrp strains. Taken together, these data support the idea that high-Lrp cells have an advantage in tissue adherence and colonization initiation. Furthermore, our data show that high-Lrp-expressing strains better support nematode reproduction than do their low-Lrp counterparts under both and conditions. Our data indicate that heterogeneity of Lrp expression in populations provides diverse cell populations adapted to both pathogenic (low-Lrp) and mutualistic (high-Lrp) states. Host-associated bacteria experience fluctuating conditions during both residence within an individual host and transmission between hosts. For bacteria that engage in evolutionarily stable, long-term relationships with particular hosts, these fluctuations provide selective pressure for the emergence of adaptive regulatory mechanisms. Here we present evidence that the bacterium uses various levels of the transcription factor Lrp to optimize its association with its two animal hosts, nematodes and insects, with which it behaves as a mutualist and a pathogen, respectively. Building on our previous finding that relatively low cellular levels of Lrp are optimal for pathogenesis, we demonstrate that, conversely, high levels of Lrp promote mutualistic activities with the nematode host. These data suggest that has evolved to utilize phenotypic variation between high- and low-Lrp-expression states to optimize its alternating behaviors as a mutualist and a pathogen.

  • Engel Y, Windhorst C, Lu X, Goodrich-Blair H, Bode HB (2017) The Global Regulators Lrp, LeuO, and HexA Control Secondary Metabolism in Entomopathogenic Bacteria. Front Microbiol 8:209 (PMC5313471) 10.3389/fmicb.2017.00209 · Pubmed

    TTO1 and HGB081 are insect pathogenic bacteria and producers of various structurally diverse bioactive natural products. In these entomopathogenic bacteria we investigated the role of the global regulators Lrp, LeuO, and HexA in the production of natural products. Lrp is a general activator of natural product biosynthesis in and for most compounds in TTO1. Microarray analysis confirmed these results in and enabled the identification of additional biosynthesis gene clusters (BGC) regulated by Lrp. Moreover, when promoters of two BGC were analyzed, transcriptional activation by Lrp was observed. In contrast, LeuO in and has both repressing and activating features, depending on the natural product examined. Furthermore, heterologous overexpression of from in the closely related resulted in overproduction of several natural products including novel compounds. The presented findings could be of importance for establishing a tool for overproduction of secondary metabolites and subsequent identification of novel compounds.

  • Ciezki K, Murfin K, Goodrich-Blair H, Stock SP, Forst S (2016) R-type bacteriocins in related strains of Xenorhabdus bovienii: Xenorhabdicin tail fiber modularity and contribution to competitiveness. FEMS Microbiol. Lett. 364(1): 10.1093/femsle/fnw235 · Pubmed

    R-type bacteriocins are contractile phage tail-like structures that are bactericidal towards related bacterial species. The C-terminal region of the phage tail fiber protein determines target-binding specificity. The mutualistic bacteria Xenorhabdus nematophila and X. bovienii produce R-type bacteriocins (xenorhabdicins) that are selectively active against different Xenorhabdus species. We analyzed the P2-type remnant prophage clusters in draft sequences of nine strains of X. bovienii The C-terminal tail fiber region in each of the respective strains was unique and consisted of mosaics of modular units. The region between the main tail fiber gene (xbpH1) and the sheath gene (xbpS1) contained a variable number of modules encoding tail fiber fragments. DNA inversion and module exchange between strains was involved in generating tail fiber diversity. Xenorhabdicin-enriched fractions from three different X. bovienii strains isolated from the same nematode species displayed distinct activities against each other. In one set of strains, the strain that produced highly active xenorhabdicin was able to eliminate a sensitive strain. In contrast, xenorhabdicin activity was not a determining factor in the competitive fitness of a second set of strains. These findings suggest that related strains of X. bovienii use xenorhabdicin and additional antagonistic molecules to compete against each other.

  • Hillman K, Goodrich-Blair H (2016) Are you my symbiont? Microbial polymorphic toxins and antimicrobial compounds as honest signals of beneficial symbiotic defensive traits. Curr. Opin. Microbiol. 31:184-190 · Pubmed

    In defensive symbioses where microbes benefit their host by killing competitors, predators or parasites, natural selection should favor the transmission of microbes with the most beneficial defensive traits. During the initiation of symbiosis, the host's ability to accurately pre-assess a symbiont's beneficial traits would be a selective advantage. We propose that one mechanism by which a host could recognize and select a beneficial partner would be if the latter displayed an honest signal of its defensive or other symbiotic capabilities. As one example, we suggest that polymorphic toxins and their surface receptors, which are involved in inter-microbial competition and predator killing activities, can be honest signals that facilitate partner choice in defensive symbioses.

  • Morran LT, Penley MJ, Byrd VS, Meyer AJ, O'Sullivan TS, Bashey F, Goodrich-Blair H, Lively CM (2016) Nematode-bacteria mutualism: Selection within the mutualism supersedes selection outside of the mutualism. Evolution 70(3):687-95 (PMC4801668) · Pubmed

    The coevolution of interacting species can lead to codependent mutualists. Little is known about the effect of selection on partners within verses apart from the association. Here, we determined the effect of selection on bacteria (Xenorhabdus nematophila) both within and apart from its mutualistic partner (a nematode, Steinernema carpocapsae). In nature, the two species cooperatively infect and kill arthropods. We passaged the bacteria either together with (M+), or isolated from (M-), nematodes under two different selection regimes: random selection (S-) and selection for increased virulence against arthropod hosts (S+). We found that the isolated bacteria evolved greater virulence under selection for greater virulence (M-S+) than under random selection (M-S-). In addition, the response to selection in the isolated bacteria (M-S+) caused a breakdown of the mutualism following reintroduction to the nematode. Finally, selection for greater virulence did not alter the evolutionary trajectories of bacteria passaged within the mutualism (M+S+ = M+S-), indicating that selection for the maintenance of the mutualism was stronger than selection for increased virulence. The results show that selection on isolated mutualists can rapidly breakdown beneficial interactions between species, but that selection within a mutualism can supersede external selection, potentially generating codependence over time.

  • Murfin KE, Whooley AC, Klassen JL, Goodrich-Blair H (2015) Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions. BMC Genomics 16:889 (PMC4630870) · Pubmed

    Xenorhabdus bacteria engage in a beneficial symbiosis with Steinernema nematodes, in part by providing activities that help kill and degrade insect hosts for nutrition. Xenorhabdus strains (members of a single species) can display wide variation in host-interaction phenotypes and genetic potential indicating that strains may differ in their encoded symbiosis factors, including secreted metabolites. To discern strain-level variation among symbiosis factors, and facilitate the identification of novel compounds, we performed a comparative analysis of the genomes of 10 Xenorhabdus bovienii bacterial strains. The analyzed X. bovienii draft genomes are broadly similar in structure (e.g. size, GC content, number of coding sequences). Genome content analysis revealed that general classes of putative host-microbe interaction functions, such as secretion systems and toxin classes, were identified in all bacterial strains. In contrast, we observed diversity of individual genes within families (e.g. non-ribosomal peptide synthetase clusters and insecticidal toxin components), indicating the specific molecules secreted by each strain can vary. Additionally, phenotypic analysis indicates that regulation of activities (e.g. enzymes and motility) differs among strains. The analyses presented here demonstrate that while general mechanisms by which X. bovienii bacterial strains interact with their invertebrate hosts are similar, the specific molecules mediating these interactions differ. Our data support that adaptation of individual bacterial strains to distinct hosts or niches has occurred. For example, diverse metabolic profiles among bacterial symbionts may have been selected by dissimilarities in nutritional requirements of their different nematode hosts. Similarly, factors involved in parasitism (e.g. immune suppression and microbial competition factors), likely differ based on evolution in response to naturally encountered organisms, such as insect hosts, competitors, predators or pathogens. This study provides insight into effectors of a symbiotic lifestyle, and also highlights that when mining Xenorhabdus species for novel natural products, including antibiotics and insecticidal toxins, analysis of multiple bacterial strains likely will increase the potential for the discovery of novel molecules.

  • Hussa EA, Casanova-Torres ÁM, Goodrich-Blair H (2015) The Global Transcription Factor Lrp Controls Virulence Modulation in Xenorhabdus nematophila. J. Bacteriol. 197(18):3015-25 (PMC4542165) · Pubmed

    The bacterium Xenorhabdus nematophila engages in phenotypic variation with respect to pathogenicity against insect larvae, yielding both virulent and attenuated subpopulations of cells from an isogenic culture. The global regulatory protein Lrp is necessary for X. nematophila virulence and immunosuppression in insects, as well as colonization of the mutualistic host nematode Steinernema carpocapsae, and mediates expression of numerous genes implicated in each of these phenotypes. Given the central role of Lrp in X. nematophila host associations, as well as its involvement in regulating phenotypic variation pathways in other bacteria, we assessed its function in virulence modulation. We discovered that expression of lrp varies within an isogenic population, in a manner that correlates with modulation of virulence. Unexpectedly, although Lrp is necessary for optimal virulence and immunosuppression, cells expressing high levels of lrp were attenuated in these processes relative to those with low to intermediate lrp expression. Furthermore, fixed expression of lrp at high and low levels resulted in attenuated and normal virulence and immunosuppression, respectively, and eliminated population variability of these phenotypes. These data suggest that fluctuating lrp expression levels are sufficient to drive phenotypic variation in X. nematophila. Many bacteria use cell-to-cell phenotypic variation, characterized by distinct phenotypic subpopulations within an isogenic population, to cope with environmental change. Pathogenic bacteria utilize this strategy to vary antigen or virulence factor expression. Our work establishes that the global transcription factor Lrp regulates phenotypic variation in the insect pathogen Xenorhabdus nematophila, leading to attenuation of virulence and immunosuppression in insect hosts. Unexpectedly, we found an inverse correlation between Lrp expression levels and virulence: high levels of expression of Lrp-dependent putative virulence genes are detrimental for virulence but may have an adaptive advantage in other aspects of the life cycle. Investigation of X. nematophila phenotypic variation facilitates dissection of this phenomenon in the context of a naturally occurring symbiosis.

  • Dillman AR, Macchietto M, Porter CF, Rogers A, Williams B, Antoshechkin I, Lee MM, Goodwin Z, Lu X, Lewis EE, Goodrich-Blair H, Stock SP, Adams BJ, Sternberg PW, Mortazavi A (2015) Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks. Genome Biol. 16:200 (PMC4578762) · Pubmed

    Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, and S. glaseri). We used these genomes to establish phylogenetic relationships, explore gene conservation across species, and identify genes uniquely expanded in insect parasites. Protein domain analysis in Steinernema revealed a striking expansion of numerous putative parasitism genes, including certain protease and protease inhibitor families, as well as fatty acid- and retinol-binding proteins. Stage-specific gene expression of some of these expanded families further supports the notion that they are involved in insect parasitism by Steinernema. We show that sets of novel conserved non-coding regulatory motifs are associated with orthologous genes in Steinernema and Caenorhabditis. We have identified a set of expanded gene families that are likely to be involved in parasitism. We have also identified a set of non-coding motifs associated with groups of orthologous genes in Steinernema and Caenorhabditis involved in neurogenesis and embryonic development that are likely part of conserved protein-DNA relationships shared between these two genera.

  • Murfin KE, Lee MM, Klassen JL, McDonald BR, Larget B, Forst S, Stock SP, Currie CR, Goodrich-Blair H (2015) Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts. MBio 6(3):e00076 (PMC4462624) · Pubmed

    Microbial symbionts provide benefits that contribute to the ecology and fitness of host plants and animals. Therefore, the evolutionary success of plants and animals fundamentally depends on long-term maintenance of beneficial associations. Most work investigating coevolution and symbiotic maintenance has focused on species-level associations, and studies are lacking that assess the impact of bacterial strain diversity on symbiotic associations within a coevolutionary framework. Here, we demonstrate that fitness in mutualism varies depending on bacterial strain identity, and this is consistent with variation shaping phylogenetic patterns and maintenance through fitness benefits. Through genome sequencing of nine bacterial symbiont strains and cophylogenetic analysis, we demonstrate diversity among Xenorhabdus bovienii bacteria. Further, we identified cocladogenesis between Steinernema feltiae nematode hosts and their corresponding X. bovienii symbiont strains, indicating potential specificity within the association. To test the specificity, we performed laboratory crosses of nematode hosts with native and nonnative symbiont strains, which revealed that combinations with the native bacterial symbiont and closely related strains performed significantly better than those with more divergent symbionts. Through genomic analyses we also defined potential factors contributing to specificity between nematode hosts and bacterial symbionts. These results suggest that strain-level diversity (e.g., subspecies-level differences) in microbial symbionts can drive variation in the success of host-microbe associations, and this suggests that these differences in symbiotic success could contribute to maintenance of the symbiosis over an evolutionary time scale. Beneficial symbioses between microbes and plant or animal hosts are ubiquitous, and in these associations, microbial symbionts provide key benefits to their hosts. As such, host success is fundamentally dependent on long-term maintenance of beneficial associations. Prolonged association between partners in evolutionary time is expected to result in interactions in which only specific partners can fully support symbiosis. The contribution of bacterial strain diversity on specificity and coevolution in a beneficial symbiosis remains unclear. In this study, we demonstrate that strain-level differences in fitness benefits occur in beneficial host-microbe interactions, and this variation likely shapes phylogenetic patterns and symbiotic maintenance. This highlights that symbiont contributions to host biology can vary significantly based on very-fine-scale differences among members of a microbial species. Further, this work emphasizes the need for greater phylogenetic resolution when considering the causes and consequences of host-microbe interactions.

  • Nollmann FI, Heinrich AK, Brachmann AO, Morisseau C, Mukherjee K, Casanova-Torres ÁM, Strobl F, Kleinhans D, Kinski S, Schultz K, Beeton ML, Kaiser M, Chu YY, Phan Ke L, Thanwisai A, Bozhüyük KA, Chantratita N, Götz F, Waterfield NR, Vilcinskas A, Stelzer EH, Goodrich-Blair H, Hammock BD, Bode HB (2015) A Photorhabdus natural product inhibits insect juvenile hormone epoxide hydrolase. Chembiochem 16(5):766-71 (PMC4486325) · Pubmed

    Simple urea compounds ("phurealipids") have been identified from the entomopathogenic bacterium Photorhabdus luminescens, and their biosynthesis was elucidated. Very similar analogues of these compounds have been previously developed as inhibitors of juvenile hormone epoxide hydrolase (JHEH), a key enzyme in insect development and growth. Phurealipids also inhibit JHEH, and therefore phurealipids might contribute to bacterial virulence.

  • Veesenmeyer JL, Andersen AW, Lu X, Hussa EA, Murfin KE, Chaston JM, Dillman AR, Wassarman KM, Sternberg PW, Goodrich-Blair H (2014) NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes. Mol. Microbiol. 93(5):1026-42 (PMC4152777) · Pubmed

    The bacterium Xenorhabdus nematophila is a mutualist of entomopathogenic Steinernema carpocapsae nematodes and facilitates infection of insect hosts. X. nematophila colonizes the intestine of S. carpocapsae which carries it between insects. In the X. nematophila colonization-defective mutant nilD6::Tn5, the transposon is inserted in a region lacking obvious coding potential. We demonstrate that the transposon disrupts expression of a single CRISPR RNA, NilD RNA. A variant NilD RNA also is expressed by X. nematophila strains from S. anatoliense and S. websteri nematodes. Only nilD from the S. carpocapsae strain of X. nematophila rescued the colonization defect of the nilD6::Tn5 mutant, and this mutant was defective in colonizing all three nematode host species. NilD expression depends on the presence of the associated Cas6e but not Cas3, components of the Type I-E CRISPR-associated machinery. While cas6e deletion in the complemented strain abolished nematode colonization, its disruption in the wild-type parent did not. Likewise, nilD deletion in the parental strain did not impact colonization of the nematode, revealing that the requirement for NilD is evident only in certain genetic backgrounds. Our data demonstrate that NilD RNA is conditionally necessary for mutualistic host colonization and suggest that it functions to regulate endogenous gene expression.

  • Singh S, Reese JM, Casanova-Torres AM, Goodrich-Blair H, Forst S (2014) Microbial population dynamics in the hemolymph of Manduca sexta infected with Xenorhabdus nematophila and the entomopathogenic nematode Steinernema carpocapsae. Appl. Environ. Microbiol. 80(14):4277-85 (PMC4068695) · Pubmed

    Xenorhabdus nematophila engages in a mutualistic association with the nematode Steinernema carpocapsae. The nematode invades and traverses the gut of susceptible insects. X. nematophila is released in the insect blood (hemolymph), where it suppresses host immune responses and functions as a pathogen. X. nematophila produces diverse antimicrobials in laboratory cultures. The natural competitors that X. nematophila encounters in the hemolymph and the role of antimicrobials in interspecies competition in the host are poorly understood. We show that gut microbes translocate into the hemolymph when the nematode penetrates the insect intestine. During natural infection, Staphylococcus saprophyticus was initially present and subsequently disappeared from the hemolymph, while Enterococcus faecalis proliferated. S. saprophyticus was sensitive to X. nematophila antibiotics and was eliminated from the hemolymph when coinjected with X. nematophila. In contrast, E. faecalis was relatively resistant to X. nematophila antibiotics. When injected by itself, E. faecalis persisted (~10(3) CFU/ml), but when coinjected with X. nematophila, it proliferated to ~10(9) CFU/ml. Injection of E. faecalis into the insect caused the upregulation of an insect antimicrobial peptide, while the transcript levels were suppressed when E. faecalis was coinjected with X. nematophila. Its relative antibiotic resistance together with suppression of the host immune system by X. nematophila may account for the growth of E. faecalis. At higher injected levels (10(6) CFU/insect), E. faecalis could kill insects, suggesting that it may contribute to virulence in an X. nematophila infection. These findings provide new insights into the competitive events that occur early in infection after S. carpocapsae invades the host hemocoel.

  • Chaston JM, Murfin KE, Heath-Heckman EA, Goodrich-Blair H (2013) Previously unrecognized stages of species-specific colonization in the mutualism between Xenorhabdus bacteria and Steinernema nematodes. Cell. Microbiol. 15(9):1545-59 (PMC3740033) · Pubmed

    The specificity of a horizontally transmitted microbial symbiosis is often defined by molecular communication between host and microbe during initial engagement, which can occur in discrete stages. In the symbiosis between Steinernema nematodes and Xenorhabdus bacteria, previous investigations focused on bacterial colonization of the intestinal lumen (receptacle) of the nematode infective juvenile (IJ), as this was the only known persistent, intimate and species-specific contact between the two. Here we show that bacteria colonize the anterior intestinal cells of other nematode developmental stages in a species-specific manner. Also, we describe three processes that only occur in juveniles that are destined to become IJs. First, a few bacterial cells colonize the nematode pharyngeal-intestinal valve (PIV) anterior to the intestinal epithelium. Second, the nematode intestine constricts while bacteria initially remain in the PIV. Third, anterior intestinal constriction relaxes and colonizing bacteria occupy the receptacle. At each stage, colonization requires X. nematophila symbiosis region 1 (SR1) genes and is species-specific: X. szentirmaii, which naturally lacks SR1, does not colonize unless SR1 is ectopically expressed. These findings reveal new aspects of Xenorhabdus bacteria interactions with and transmission by theirSteinernema nematode hosts, and demonstrate that bacterial SR1 genes aid in colonizing nematode epithelial surfaces.

  • Reimer D, Cowles KN, Proschak A, Nollmann FI, Dowling AJ, Kaiser M, ffrench-Constant R, Goodrich-Blair H, Bode HB (2013) Rhabdopeptides as insect-specific virulence factors from entomopathogenic bacteria. Chembiochem 14(15):1991-7 · Pubmed

    Six novel linear peptides, named "rhabdopeptides", have been identified in the entomopathogenic bacterium Xenorhabdus nematophila after the discovery of the corresponding rdp gene cluster by using a promoter trap strategy for the detection of insect-inducible genes. The structures of these rhabdopeptides were deduced from labeling experiments combined with detailed MS analysis. Detailed analysis of an rdp mutant revealed that these compounds participate in virulence towards insects and are produced upon bacterial infection of a suitable insect host. Furthermore, two additional rhabdopeptide derivatives produced by Xenorhabdus cabanillasii were isolated, these showed activity against insect hemocytes thereby confirming the virulence of this novel class of compounds.

  • Hussa EA, Goodrich-Blair H (2013) It takes a village: ecological and fitness impacts of multipartite mutualism. Annu. Rev. Microbiol. 67:161-78 · Pubmed

    Microbial symbioses, in which microbes have either positive (mutualistic) or negative (parasitic) impacts on host fitness, are integral to all aspects of biology, from ecology to human health. In many well-studied cases, microbial symbiosis is characterized by a specialized association between a host and a specific microbe that provides it with one or more beneficial functions, such as novel metabolic pathways or defense against pathogens. Even in relatively simple associations, symbiont-derived benefits can be context dependent and influenced by other host-associated or environmental microbes. Furthermore, naturally occurring symbioses are typically complex, in which multiple symbionts exhibit coordinated, competing, or independent influences on host physiology, or in which individual symbionts affect multiple interacting hosts. Here we describe research on the mechanisms and consequences of multipartite symbioses, including consortia in which multiple organisms interact with the host and one another, and on conditional mutualists whose impact on the host depends on additional interacting organisms.

  • Hussa E, Goodrich-Blair H (2012) Rearing and injection of Manduca sexta larvae to assess bacterial virulence. J Vis Exp (70):e4295 · Pubmed

    Manduca sexta, commonly known as the tobacco hornworm, is considered a significant agricultural pest, feeding on solanaceous plants including tobacco and tomato. The susceptibility of M. sexta larvae to a variety of entomopathogenic bacterial species(1-5), as well as the wealth of information available regarding the insect's immune system(6-8), and the pending genome sequence(9) make it a good model organism for use in studying host-microbe interactions during pathogenesis. In addition, M. sexta larvae are relatively large and easy to manipulate and maintain in the laboratory relative to other susceptible insect species. Their large size also facilitates efficient tissue/hemolymph extraction for analysis of the host response to infection. The method presented here describes the direct injection of bacteria into the hemocoel (blood cavity) of M. sexta larvae. This approach can be used to analyze and compare the virulence characteristics of various bacterial species, strains, or mutants by simply monitoring the time to insect death after injection. This method was developed to study the pathogenicity of Xenorhabdus and Photorhabdus species, which typically associate with nematode vectors as a means to gain entry into the insect. Entomopathogenic nematodes typically infect larvae via natural digestive or respiratory openings, and release their symbiotic bacterial contents into the insect hemolymph (blood) shortly thereafter(10). The injection method described here bypasses the need for a nematode vector, thus uncoupling the effects of bacteria and nematode on the insect. This method allows for accurate enumeration of infectious material (cells or protein) within the inoculum, which is not possible using other existing methods for analyzing entomopathogenesis, including nicking(11) and oral toxicity assays(12). Also, oral toxicity assays address the virulence of secreted toxins introduced into the digestive system of larvae, whereas the direct injection method addresses the virulence of whole-cell inocula. The utility of the direct injection method as described here is to analyze bacterial pathogenesis by monitoring insect mortality. However, this method can easily be expanded for use in studying the effects of infection on the M. sexta immune system. The insect responds to infection via both humoral and cellular responses. The humoral response includes recognition of bacterial-associated patterns and subsequent production of various antimicrobial peptides(7); the expression of genes encoding these peptides can be monitored subsequent to direct infection via RNA extraction and quantitative PCR(13). The cellular response to infection involves nodulation, encapsulation, and phagocytosis of infectious agents by hemocytes(6). To analyze these responses, injected insects can be dissected and visualized by microscopy(13, 14).

  • Murfin KE, Chaston J, Goodrich-Blair H (2012) Visualizing bacteria in nematodes using fluorescent microscopy. J Vis Exp (68): (PMC3490300) · Pubmed

    Symbioses, the living together of two or more organisms, are widespread throughout all kingdoms of life. As two of the most ubiquitous organisms on earth, nematodes and bacteria form a wide array of symbiotic associations that range from beneficial to pathogenic (1-3). One such association is the mutually beneficial relationship between Xenorhabdus bacteria and Steinernema nematodes, which has emerged as a model system of symbiosis (4). Steinernema nematodes are entomopathogenic, using their bacterial symbiont to kill insects (5). For transmission between insect hosts, the bacteria colonize the intestine of the nematode's infective juvenile stage (6-8). Recently, several other nematode species have been shown to utilize bacteria to kill insects (9-13), and investigations have begun examining the interactions between the nematodes and bacteria in these systems (9). We describe a method for visualization of a bacterial symbiont within or on a nematode host, taking advantage of the optical transparency of nematodes when viewed by microscopy. The bacteria are engineered to express a fluorescent protein, allowing their visualization by fluorescence microscopy. Many plasmids are available that carry genes encoding proteins that fluoresce at different wavelengths (i.e. green or red), and conjugation of plasmids from a donor Escherichia coli strain into a recipient bacterial symbiont is successful for a broad range of bacteria. The methods described were developed to investigate the association between Steinernema carpocapsae and Xenorhabdus nematophila (14). Similar methods have been used to investigate other nematode-bacterium associations (9) (,) (15-18)and the approach therefore is generally applicable. The method allows characterization of bacterial presence and localization within nematodes at different stages of development, providing insights into the nature of the association and the process of colonization (14) (,) (16) (,) (19). Microscopic analysis reveals both colonization frequency within a population and localization of bacteria to host tissues (14) (,) (16) (,) (19-21). This is an advantage over other methods of monitoring bacteria within nematode populations, such as sonication (22)or grinding (23), which can provide average levels of colonization, but may not, for example, discriminate populations with a high frequency of low symbiont loads from populations with a low frequency of high symbiont loads. Discriminating the frequency and load of colonizing bacteria can be especially important when screening or characterizing bacterial mutants for colonization phenotypes (21) (,) (24). Indeed, fluorescence microscopy has been used in high throughput screening of bacterial mutants for defects in colonization (17) (,) (18), and is less laborious than other methods, including sonication (22) (,) (25-27)and individual nematode dissection (28) (,) (29).

  • Murfin KE, Dillman AR, Foster JM, Bulgheresi S, Slatko BE, Sternberg PW, Goodrich-Blair H (2012) Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age. Biol. Bull. 223(1):85-102 (PMC3508788) · Pubmed

    Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, "omics"' studies in nematode-bacterial systems, and the wider implications of the findings.

  • Sugar DR, Murfin KE, Chaston JM, Andersen AW, Richards GR, deLéon L, Baum JA, Clinton WP, Forst S, Goldman BS, Krasomil-Osterfeld KC, Slater S, Stock SP, Goodrich-Blair H (2012) Phenotypic variation and host interactions of Xenorhabdus bovienii SS-2004, the entomopathogenic symbiont of Steinernema jollieti nematodes. Environ. Microbiol. 14(4):924-39 (PMC3307839) · Pubmed

    Xenorhabdus bovienii (SS-2004) bacteria reside in the intestine of the infective-juvenile (IJ) stage of the entomopathogenic nematode, Steinernema jollieti. The recent sequencing of the X. bovienii genome facilitates its use as a model to understand host - symbiont interactions. To provide a biological foundation for such studies, we characterized X. bovienii in vitro and host interaction phenotypes. Within the nematode host X. bovienii was contained within a membrane bound envelope that also enclosed the nematode-derived intravesicular structure. Steinernema jollieti nematodes cultivated on mixed lawns of X. bovienii expressing green or DsRed fluorescent proteins were predominantly colonized by one or the other strain, suggesting the colonizing population is founded by a few cells. Xenorhabdus bovienii exhibits phenotypic variation between orange-pigmented primary form and cream-pigmented secondary form. Each form can colonize IJ nematodes when cultured in vitro on agar. However, IJs did not develop or emerge from Galleria mellonella insects infected with secondary form. Unlike primary-form infected insects that were soft and flexible, secondary-form infected insects retained a rigid exoskeleton structure. Xenorhabdus bovienii primary and secondary form isolates are virulent towards Manduca sexta and several other insects. However, primary form stocks present attenuated virulence, suggesting that X. bovienii, like Xenorhabdus nematophila may undergo virulence modulation.

  • Bhasin A, Chaston JM, Goodrich-Blair H (2012) Mutational analyses reveal overall topology and functional regions of NilB, a bacterial outer membrane protein required for host association in a model of animal-microbe mutualism. J. Bacteriol. 194(7):1763-76 (PMC3302474) · Pubmed

    The gammaproteobacterium Xenorhabdus nematophila is a mutualistic symbiont that colonizes the intestine of the nematode Steinernema carpocapsae. nilB (nematode intestine localization) is essential for X. nematophila colonization of nematodes and is predicted to encode an integral outer membrane beta-barrel protein, but evidence supporting this prediction has not been reported. The function of NilB is not known, but when expressed with two other factors encoded by nilA and nilC, it confers upon noncognate Xenorhabdus spp. the ability to colonize S. carpocapsae nematodes. We present evidence that NilB is a surface-exposed outer membrane protein whose expression is repressed by NilR and growth in nutrient-rich medium. Bioinformatic analyses reveal that NilB is the only characterized member of a family of proteins distinguished by N-terminal region tetratricopeptide repeats (TPR) and a conserved C-terminal domain of unknown function (DUF560). Members of this family occur in diverse bacteria and are prevalent in the genomes of mucosal pathogens. Insertion and deletion mutational analyses support a beta-barrel structure model with an N-terminal globular domain, 14 transmembrane strands, and seven extracellular surface loops and reveal critical roles for the globular domain and surface loop 6 in nematode colonization. Epifluorescence microscopy of these mutants demonstrates that NilB is necessary at early stages of colonization. These findings are an important step in understanding the function of NilB and, by extension, its homologs in mucosal pathogens.

  • Dillman AR, Chaston JM, Adams BJ, Ciche TA, Goodrich-Blair H, Stock SP, Sternberg PW (2012) An entomopathogenic nematode by any other name. PLoS Pathog. 8(3):e1002527 (PMC3291613) · Pubmed

    No abstract available.

  • Chaston JM, Suen G, Tucker SL, Andersen AW, Bhasin A, Bode E, Bode HB, Brachmann AO, Cowles CE, Cowles KN, Darby C, de Léon L, Drace K, Du Z, Givaudan A, Herbert Tran EE, Jewell KA, Knack JJ, Krasomil-Osterfeld KC, Kukor R, Lanois A, Latreille P, Leimgruber NK, Lipke CM, Liu R, Lu X, Martens EC, Marri PR, Médigue C, Menard ML, Miller NM, Morales-Soto N, Norton S, Ogier JC, Orchard SS, Park D, Park Y, Qurollo BA, Sugar DR, Richards GR, Rouy Z, Slominski B, Slominski K, Snyder H, Tjaden BC, van der Hoeven R, Welch RD, Wheeler C, Xiang B, Barbazuk B, Gaudriault S, Goodner B, Slater SC, Forst S, Goldman BS, Goodrich-Blair H (2011) The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. PLoS ONE 6(11):e27909 (PMC3220699) · Pubmed

    Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points.

  • Lu X, Goodrich-Blair H, Tjaden B (2011) Assessing computational tools for the discovery of small RNA genes in bacteria. RNA 17(9):1635-47 (PMC3162329) · Pubmed

    Over the past decade, a number of biocomputational tools have been developed to predict small RNA (sRNA) genes in bacterial genomes. In this study, several of the leading biocomputational tools, which use different methodologies, were investigated. The performance of the tools, both individually and in combination, was evaluated on ten sets of benchmark data, including data from a novel RNA-seq experiment conducted in this study. The results of this study offer insight into the utility as well as the limitations of the leading biocomputational tools for sRNA identification and provide practical guidance for users of the tools.

  • Ogier JC, Calteau A, Forst S, Goodrich-Blair H, Roche D, Rouy Z, Suen G, Zumbihl R, Givaudan A, Tailliez P, Médigue C, Gaudriault S (2010) Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus. BMC Genomics 11:568 (PMC3091717) · Pubmed

    Flexible genomes facilitate bacterial evolution and are classically organized into polymorphic strain-specific segments called regions of genomic plasticity (RGPs). Using a new web tool, RGPFinder, we investigated plasticity units in bacterial genomes, by exhaustive description of the RGPs in two Photorhabdus and two Xenorhabdus strains, belonging to the Enterobacteriaceae and interacting with invertebrates (insects and nematodes). RGPs account for about 60% of the genome in each of the four genomes studied. We classified RGPs into genomic islands (GIs), prophages and two new classes of RGP without the features of classical mobile genetic elements (MGEs) but harboring genes encoding enzymes catalyzing DNA recombination (RGPmob), or with no remarkable feature (RGPnone). These new classes accounted for most of the RGPs and are probably hypervariable regions, ancient MGEs with degraded mobilization machinery or non canonical MGEs for which the mobility mechanism has yet to be described. We provide evidence that not only the GIs and the prophages, but also RGPmob and RGPnone, have a mosaic structure consisting of modules. A module is a block of genes, 0.5 to 60 kb in length, displaying a conserved genomic organization among the different Enterobacteriaceae. Modules are functional units involved in host/environment interactions (22-31%), metabolism (22-27%), intracellular or intercellular DNA mobility (13-30%), drug resistance (4-5%) and antibiotic synthesis (3-6%). Finally, in silico comparisons and PCR multiplex analysis indicated that these modules served as plasticity units within the bacterial genome during genome speciation and as deletion units in clonal variants of Photorhabdus. This led us to consider the modules, rather than the entire RGP, as the true unit of plasticity in bacterial genomes, during both short-term and long-term genome evolution.

  • Chaston J, Goodrich-Blair H (2010) Common trends in mutualism revealed by model associations between invertebrates and bacteria. FEMS Microbiol. Rev. 34(1):41-58 (PMC2794943) · Pubmed

    Mutually beneficial interactions between microorganisms and animals are a conserved and ubiquitous feature of biotic systems. In many instances animals, including humans, are dependent on their microbial associates for nutrition, defense, or development. To maintain these vital relationships, animals have evolved processes that ensure faithful transmission of specific microbial symbionts between generations. Elucidating mechanisms of transmission and symbiont specificity has been aided by the study of experimentally tractable invertebrate animals with diverse and highly evolved associations with microorganisms. Here, we review several invertebrate model systems that contribute to our current understanding of symbiont transmission, recognition, and specificity. Although the details of transmission and symbiont selection vary among associations, comparisons of diverse mutualistic associations are revealing a number of common themes, including restriction of symbiont diversity during transmission and glycan-lectin interactions during partner selection and recruitment.

  • Richards GR, Goodrich-Blair H (2010) Examination of Xenorhabdus nematophila lipases in pathogenic and mutualistic host interactions reveals a role for xlpA in nematode progeny production. Appl. Environ. Microbiol. 76(1):221-9 (PMC2798643) · Pubmed

    Xenorhabdus nematophila is a gammaproteobacterium and broad-host-range insect pathogen. It is also a symbiont of Steinernema carpocapsae, the nematode vector that transports the bacterium between insect hosts. X. nematophila produces several secreted enzymes, including hemolysins, lipases, and proteases, which are thought to contribute to virulence or nutrient acquisition for the bacterium and its nematode host in vivo. X. nematophila has two lipase activities with distinct in vitro specificities for Tween and lecithin. The gene encoding the Tween-specific lipase, xlpA, has been identified and is not required for X. nematophila virulence in one insect host, the tobacco hornworm Manduca sexta. However, the gene encoding the lecithin-specific lipase activity is not currently known. Here, we identify X. nematophila estA, a gene encoding a putative lecithinase, and show that an estA mutant lacks in vitro lipase activity against lecithin but has wild-type virulence in Manduca sexta. X. nematophila secondary-form phenotypic variants have higher in vitro lecithinase activity and estA transcript levels than do primary-form variants, and estA transcription is negatively regulated by NilR, a repressor of nematode colonization factors. We establish a role for xlpA, but not estA, in supporting production of nematode progeny during growth in Galleria mellonella insects. Future research is aimed at characterizing the biological roles of estA and xlpA in other insect hosts.

  • Richards GR, Vivas EI, Andersen AW, Rivera-Santos D, Gilmore S, Suen G, Goodrich-Blair H (2009) Isolation and characterization of Xenorhabdus nematophila transposon insertion mutants defective in lipase activity against Tween. J. Bacteriol. 191(16):5325-31 (PMC2725573) · Pubmed

    We identified Xenorhabdus nematophila transposon mutants with defects in lipase activity. One of the mutations, in yigL, a conserved gene of unknown function, resulted in attenuated virulence against Manduca sexta insects. We discuss possible connections between lipase production, YigL, and specific metabolic pathways.

  • Richards GR, Goodrich-Blair H (2009) Masters of conquest and pillage: Xenorhabdus nematophila global regulators control transitions from virulence to nutrient acquisition. Cell. Microbiol. 11(7):1025-33 (PMC2811582) · Pubmed

    Invertebrate animal models are experimentally tractable and have immunity and disease symptoms that mirror those of vertebrates. Therefore they are of particular utility in understanding fundamental aspects of pathogenesis. Indeed, artificial models using human pathogens and invertebrate hosts have revealed conserved and novel molecular mechanisms of bacterial infection and host immune responses. Additional insights may be gained from investigating interactions between invertebrates and pathogens they encounter in their natural environments. For example, enteric bacteria in the genera Photorhabdus and Xenorhabdus are pathogens of insects that also mutualistically associate with nematodes in the genera Heterorhabditis and Steinernema respectively. These bacteria serve as models to understand naturally occurring symbiotic associations that result in disease in or benefit for animals. Xenorhabdus nematophila is the best-studied species of its genus with regard to the molecular mechanisms of its symbiotic associations. In this review, we summarize recent advances in understanding X. nematophila-host interactions. We emphasize regulatory cascades involved in coordinating transitions between various stages of the X. nematophila life cycle: infection, reproduction and transmission.

  • Herbert Tran EE, Goodrich-Blair H (2009) CpxRA contributes to Xenorhabdus nematophila virulence through regulation of lrhA and modulation of insect immunity. Appl. Environ. Microbiol. 75(12):3998-4006 (PMC2698343) · Pubmed

    The gammaproteobacterium Xenorhabdus nematophila is a blood pathogen of insects that requires the CpxRA signal transduction system for full virulence (E. E. Herbert et al., Appl. Environ. Microbiol. 73:7826-7836, 2007). We show here that the DeltacpxR1 mutant has altered localization, growth, and immune suppressive activities relative to its wild-type parent during infection of Manduca sexta insects. In contrast to wild-type X. nematophila, which were recovered throughout infection, DeltacpxR1 cells did not accumulate in hemolymph until after insect death. In vivo imaging of fluorescently labeled bacteria within live insects showed that DeltacpxR1 displayed delayed accumulation and also occasionally were present in isolated nodes rather than systemically throughout the insect as was wild-type X. nematophila. In addition, in contrast to its wild-type parent, the DeltacpxR1 mutant elicited transcription of an insect antimicrobial peptide, cecropin. Relative to phosphate-buffered saline-injected insects, cecropin transcript was induced 21-fold more in insects injected with DeltacpxR1 and 2-fold more in insects injected with wild-type X. nematophila. These data suggest that the DeltacpxR1 mutant has a defect in immune suppression or has an increased propensity to activate M. sexta immunity. CpxR regulates, directly or indirectly, genes known or predicted to be involved in virulence (E. E. Herbert et al., Appl. Environ. Microbiol. 73:7826-7836, 2007), including lrhA, encoding a transcription factor necessary for X. nematophila virulence, motility, and lipase production (G. R. Richards et al., J. Bacteriol. 190:4870-4879, 2008). CpxR positively regulates lrhA transcript, and we have shown that altered regulation of lrhA in the DeltacpxR1 mutant causes this strain's virulence defect. The DeltacpxR1 mutant expressing lrhA from a constitutive lac promoter showed wild-type virulence in M. sexta. These data suggest that CpxR contributes to X. nematophila virulence through the regulation of lrhA, immune suppression, and growth in Insecta.

  • Herbert Tran EE, Andersen AW, Goodrich-Blair H (2009) CpxRA influences Xenorhabdus nematophila colonization initiation and outgrowth in Steinernema carpocapsae nematodes through regulation of the nil locus. Appl. Environ. Microbiol. 75(12):4007-14 (PMC2698367) · Pubmed

    The gammaproteobacterium Xenorhabdus nematophila mutualistically colonizes an intestinal region of a soil-dwelling nematode and is a blood pathogen of insects. The X. nematophila CpxRA two-component regulatory system is necessary for both of these host interactions (E. Herbert et al., Appl. Environ. Microbiol. 73:7826-7836, 2007). Mutualistic association of X. nematophila with its nematode host consists of two stages: initiation, where a small number of bacterial cells establish themselves in the colonization site, and outgrowth, where these cells grow to fill the space. In this study, we show that the Cpx system is necessary for both of these stages. X. nematophila DeltacpxR1 colonized fewer nematodes than its wild-type parent and did not achieve as high a density as did the wild type within a portion of the colonized nematodes. To test whether the DeltacpxR1 host interaction phenotypes are due to its overexpression of mrxA, encoding the type I pilin subunit protein, we assessed the colonization phenotype of a DeltacpxR1 DeltamrxA1 double mutant. This mutant displayed the same colonization defect as DeltacpxR1, indicating that CpxR negative regulation of mrxA does not play a detectable role in X. nematophila-host interactions. CpxR positively regulates expression of nilA, nilB, and nilC genes necessary for nematode colonization. Here we show that the nematode colonization defect of the DeltacpxR1 mutant is rescued by elevating nil gene expression through mutation of nilR, a negative regulator of nilA, nilB, and nilC. These data suggest that the nematode colonization defect previously observed in DeltacpxR1 is caused, at least in part, by altered regulation of nilA, nilB, and nilC.

  • Richards GR, Herbert EE, Park Y, Goodrich-Blair H (2008) Xenorhabdus nematophila lrhA is necessary for motility, lipase activity, toxin expression, and virulence in Manduca sexta insects. J. Bacteriol. 190(14):4870-9 (PMC2447004) · Pubmed

    The gram-negative insect pathogen Xenorhabdus nematophila possesses potential virulence factors including an assortment of toxins, degradative enzymes, and regulators of these compounds. Here, we describe the lysR-like homolog A (lrhA) gene, a gene required by X. nematophila for full virulence in Manduca sexta insects. In several other gram-negative bacteria, LrhA homologs are transcriptional regulators involved in the expression (typically repression) of virulence factors. Based on phenotypic and genetic evidence, we report that X. nematophila LrhA has a positive effect on transcription and expression of certain potential virulence factors, including a toxin subunit-encoding gene, xptD1. Furthermore, an lrhA mutant lacks in vitro lipase activity and has reduced swimming motility compared to its wild-type parent. Quantitative PCR revealed that transcript levels of flagellar genes, a lipase gene, and xptD1 were significantly lower in the lrhA mutant than in the wild type. In addition, lrhA itself is positively regulated by the global regulator Lrp. This work establishes a role for LrhA as a vital component of a regulatory hierarchy necessary for X. nematophila pathogenesis and expression of surface-localized and secreted factors. Future research is aimed at identifying and characterizing virulence factors within the LrhA regulon.

  • Cowles CE, Goodrich-Blair H (2008) The Xenorhabdus nematophila nilABC genes confer the ability of Xenorhabdus spp. to colonize Steinernema carpocapsae nematodes. J. Bacteriol. 190(12):4121-8 (PMC2446770) · Pubmed

    Members of the Steinernema genus of nematodes are colonized mutualistically by members of the Xenorhabdus genus of bacteria. In nature, Steinernema carpocapsae nematodes are always found in association with Xenorhabdus nematophila bacteria. Thus, this interaction, like many microbe-host associations, appears to be species specific. X. nematophila requires the nilA, nilB, and nilC genes to colonize S. carpocapsae. In this work, we showed that of all the Xenorhabdus species examined, only X. nematophila has the nilA, nilB, and nilC genes. By exposing S. carpocapsae to other Xenorhabdus spp., we established that only X. nematophila is able to colonize S. carpocapsae; therefore, the S. carpocapsae-X. nematophila interaction is species specific. Further, we showed that introduction of the nilA, nilB, and nilC genes into other Xenorhabdus species enables them to colonize the same S. carpocapsae host tissue that is normally colonized by X. nematophila. Finally, sequence analysis supported the idea that the nil genes were horizontally acquired. Our findings indicate that a single genetic locus determines host specificity in this bacteria-animal mutualism and that host range expansion can occur through the acquisition of a small genetic element.

  • Herbert EE, Cowles KN, Goodrich-Blair H (2007) CpxRA regulates mutualism and pathogenesis in Xenorhabdus nematophila. Appl. Environ. Microbiol. 73(24):7826-36 (PMC2168154) · Pubmed

    The CpxRA signal transduction system, which in Escherichia coli regulates surface structure assembly and envelope maintenance, is involved in the pathogenic and mutualistic interactions of the entomopathogenic bacterium Xenorhabdus nematophila. When DeltacpxR1 cells were injected into Manduca sexta insects, the time required to kill 50% of the insects was twofold longer than the time observed for wild-type cells and the DeltacpxR1 cells ultimately killed 16% fewer insects than wild-type cells killed. During mutualistic colonization of Steinernema carpocapsae nematodes, the DeltacpxR1 mutant achieved colonization levels that were only 38% of the wild-type levels. DeltacpxR1 cells exhibited an extended lag phase when they were grown in liquid LB or hemolymph, formed irregular colonies on solid medium, and had a filamentous cell morphology. A mutant with a cpxRp-lacZ fusion had peaks of expression in the log and stationary phases that were conversely influenced by CpxR; the DeltacpxR1 mutant produced 130 and 17% of the wild-type beta-galactosidase activity in the log and stationary phases, respectively. CpxR positively influences motility and secreted lipase activity, as well as transcription of genes necessary for mutualistic colonization of nematodes. CpxR negatively influences the production of secreted hemolysin, protease, and antibiotic activities, as well as the expression of mrxA, encoding the pilin subunit. Thus, X. nematophila CpxRA controls expression of envelope-localized and secreted products, and its activity is necessary for both mutualistic and pathogenic functions.

  • Latreille P, Norton S, Goldman BS, Henkhaus J, Miller N, Barbazuk B, Bode HB, Darby C, Du Z, Forst S, Gaudriault S, Goodner B, Goodrich-Blair H, Slater S (2007) Optical mapping as a routine tool for bacterial genome sequence finishing. BMC Genomics 8:321 (PMC2045679) · Pubmed

    In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila. Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished. Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly.

  • Herbert EE, Goodrich-Blair H (2007) Friend and foe: the two faces of Xenorhabdus nematophila. Nat. Rev. Microbiol. 5(8):634-46 · Pubmed

    Comparisons of mutualistic and pathogenic relationships are necessary to decipher the common language of microorganism-host interactions, as well as the subtle differences in dialect that distinguish types of symbiosis. One avenue towards making such comparisons is to study a single organism that speaks both dialects, such as the gamma-proteobacterium Xenorhabdus nematophila. X. nematophila inhabits and influences the lives of two host animals, helping one to reproduce optimally while killing the other.

  • Goodrich-Blair H (2007) They've got a ticket to ride: Xenorhabdus nematophila-Steinernema carpocapsae symbiosis. Curr. Opin. Microbiol. 10(3):225-30 · Pubmed

    The association between the bacterium Xenorhabdus nematophila and the nematode Steinernema carpocapsae is emerging as a model system to understand mutually beneficial symbioses. X. nematophila, but not other Xenorhabdus species, colonize a discrete region of a specific developmental stage of S. carpocapsae nematodes. Recent progress has led to the identification of bacterial genes necessary for colonization. Furthermore, new details have been elucidated regarding the morphology and physiology of the colonization site and the bacteria within it. A deeper understanding of the molecular mechanisms underlying the association of X. nematophila will undoubtedly yield insights into fundamental processes underlying the ubiquitous association of microbes with animals.

  • Flores-Lara Y, Renneckar D, Forst S, Goodrich-Blair H, Stock P (2007) Influence of nematode age and culture conditions on morphological and physiological parameters in the bacterial vesicle of Steinernema carpocapsae (Nematoda: Steinernematidae). J. Invertebr. Pathol. 95(2):110-8 · Pubmed

    Steinernema spp. third-stage infective juveniles (IJs) play a key role in the symbiotic partnership between these entomopathogenic nematodes and Xenorhabdus bacteria. Recent studies suggest that Steinernema carpocapsae IJs contribute to the nutrition and growth of their symbionts in the colonization site (vesicle) [Martens, E.C. and Goodrich-Blair, H., 2005. The S. carpocapsae intestinal vesicle contains a sub-cellular structure with which Xenorhabdus nematophila associates during colonization initiation. Cellular Microbiol. 7, 1723-1735.]. However, the morphological and physiological interactions between Xenorhabdus symbionts and Steinernema IJs are not understood in depth. This study was undertaken to assess the influence of culture conditions and IJ age on the structure, nutrition, and symbiont load (colonization level) of S. carpocapsae vesicles. Our observations indicate the vesicles of axenic IJs are shorter and wider than those of colonized IJs. Moreover, as colonized IJs age the vesicle becomes shorter and narrower and bacterial load declines. The colonization proficiency of several bacterial metabolic mutants was compared between two cultivation conditions: in vitro on lipid agar and in vivo in Galleria mellonella insects. Colonization defects were generally less severe in IJs cultivated in vivo versus those cultivated in vitro. However, IJs from both cultivation conditions exhibited similar declining bacterial load over time. These results suggest that although the vesicle forms in the absence of bacteria, the presence of symbionts within the vesicle may influence its fine structure. Moreover, these studies provide further evidence in support of the concept that the conditions under which steinernematid nematodes are cultivated and stored affect the nutritive content of the vesicle and the bacterial load, and therefore have an impact on the quality of the nematodes for their application as biological control agents.

  • Cowles KN, Cowles CE, Richards GR, Martens EC, Goodrich-Blair H (2007) The global regulator Lrp contributes to mutualism, pathogenesis and phenotypic variation in the bacterium Xenorhabdus nematophila. Cell. Microbiol. 9(5):1311-23 · Pubmed

    Xenorhabdus nematophila is a Gram-negative bacterium that leads both pathogenic and mutualistic lifestyles. In this study, we examine the role of Lrp, the leucine-responsive regulatory protein, in regulating both of these lifestyles. lrp mutants have attenuated virulence towards Manduca sexta insects and are defective in suppression of both cellular and humoral insect immunity. In addition, an lrp mutant is deficient in initiating colonization of and growth within mutualistic host nematodes. Furthermore, nematodes reared on lrp mutant lawns exhibit decreased overall numbers of nematode progeny. To our knowledge, this is the first demonstration of virulence attenuation associated with an lrp mutation in any bacterium, as well as the first report of a factor involved in both X. nematophila symbioses. Protein profiles of wild-type and mutant cells indicate that Lrp is a global regulator of expression in X. nematophila, affecting approximately 65% of 290 proteins. We show that Lrp binds to the promoter regions of genes known to be involved in basic metabolism, mutualism and pathogenesis, demonstrating that the regulation of at least some host interaction factors is likely direct. Finally, we demonstrate that Lrp influences aspects of X. nematophila phenotypic variation, a spontaneous process that occurs during prolonged growth in stationary phase.

  • Goodrich-Blair H, Clarke DJ (2007) Mutualism and pathogenesis in Xenorhabdus and Photorhabdus: two roads to the same destination. Mol. Microbiol. 64(2):260-8 · Pubmed

    Photorhabdus and Xenorhabdus bacteria colonize the intestines of the infective soil-dwelling stage of entomophagous nematodes, Heterorhabditis and Steinernema, respectively. These nematodes infect susceptible insect larvae and release the bacteria into the insect blood. The bacteria kill the insect larvae and convert the cadaver into a food source suitable for nematode growth and development. After several rounds of reproduction the nematodes are recolonized by the bacteria before emerging from the insect cadaver into the soil to search for a new host. Photorhabdus and Xenorhabdus bacteria therefore engage in both pathogenic and mutualistic interactions with different invertebrate hosts as obligate components of their life cycle. In this review we aim to describe current knowledge of the molecular mechanisms utilized by Photorhabdus and Xenorhabdus to control their host-dependent interactions. Recent work has established that there is a trade-off between pathogenicity and mutualism in both these species of bacteria suggesting that the transition between these interactions must be under regulatory control. Despite the superficial similarity between the life cycles of these bacteria, it is now apparent that the molecular components of the regulatory networks controlling pathogenicity and mutualism in Photorhabdus and Xenorhabdus are very different.

  • Park Y, Herbert EE, Cowles CE, Cowles KN, Menard ML, Orchard SS, Goodrich-Blair H (2007) Clonal variation in Xenorhabdus nematophila virulence and suppression of Manduca sexta immunity. Cell. Microbiol. 9(3):645-56 · Pubmed

    Virulence of the insect pathogen Xenorhabdus nematophila is attributed in part to its ability to suppress immunity. For example, X. nematophila suppresses transcripts encoding several antimicrobial proteins, even in the presence of Salmonella enterica, an inducer of these transcripts. We show here that virulence and immune suppression phenotypes can be lost in a subpopulation of X. nematophila. Cells that have undergone 'virulence modulation' (vmo) have attenuated virulence and fail to suppress antimicrobial transcript levels, haemocyte aggregation and nodulation in Manduca sexta insects. When plated on certain media, vmo cells have a higher proportion of translucent (versus opaque) colonies compared with non-vmo cells. Like vmo strains, translucent colony isolates are defective in virulence and immune suppression. The X. nematophila genome encodes two 'opacity' genes with similarity to the Ail/PagC/Rck family of outer membrane proteins involved in adherence, invasion and serum resistance. Quantitative polymerase chain reaction analysis shows that RNA levels of one of these opacity genes, opaB, are higher in opaque relative to translucent colonies. We propose that in X. nematophila opaB may be one of several factors involved in immune suppression during infection, and expression of these factors can be co-ordinately eliminated in a subpopulation, possibly through a phase variation mechanism.

  • Cowles CE, Goodrich-Blair H (2006) nilR is necessary for co-ordinate repression of Xenorhabdus nematophila mutualism genes. Mol. Microbiol. 62(3):760-71 · Pubmed

    The bacterial mutualist Xenorhabdus nematophila colonizes a specific region of its nematode host Steinernema carpocapsae. We previously reported the identification of a chromosomal locus encoding three X. nematophila genes of unknown function, nilA, B and C, that are each necessary for colonization. Subsequent work indicated the global regulator Lrp is a repressor of nilC: nilC transcription is elevated in an lrp mutant and Lrp interacts directly with the nilC promoter. In this manuscript, we report the identification of an additional gene, nilR, required for repression of nilC transcription. We show that nilR and lrp mutants also have elevated expression of nilA and nilB, demonstrating that nilA, B and C are co-ordinately regulated. nil gene expression is derepressed most strongly when both nilR and lrp are lacking, suggesting NilR and Lrp synergistically repress nil transcription. NilR contains a helix-turn-helix-type DNA binding domain and likely acts directly at promoters. A comparison of the wild type and nilR proteomes indicates that NilR, unlike Lrp, regulates a small number of genes. Finally, X. nematophila carrying an ectopic copy of nilR colonizes at approximately 60-fold lower levels than the control strain, suggesting that derepression of nil gene expression is necessary for nematode colonization.

  • Martens EC, Goodrich-Blair H (2005) The Steinernema carpocapsae intestinal vesicle contains a subcellular structure with which Xenorhabdus nematophila associates during colonization initiation. Cell. Microbiol. 7(12):1723-35 · Pubmed

    Steinernema carpocapsae infective juvenile (IJ) nematodes are intestinally colonized by mutualistic Xenorhabdus nematophila bacteria. During IJ development, a small number of ingested X. nematophila cells initiate colonization in an anterior region of the intestine termed the vesicle and subsequently multiply within this host niche. We hypothesize that efficient colonization of a high percentage of S. carpocapsae individuals (typically>85%) is facilitated by bacterial adherence to a site(s) in the nematode intestine. We provide evidence that the adherence site is a structure in the lumen of the IJ vesicle that we have termed the intravesicular structure (IVS). The IVS is an untethered cluster of anucleate spherical bodies that co-localizes with colonizing X. nematophila cells, but does not require X. nematophila for its formation. Colocalization with the IVS is readily apparent in IJs colonized by X. nematophila mutants that initiate intestinal colonization but fail to proliferate normally, suggesting that bacterial-IVS interaction occurs early in the colonization process. Treatment with insect haemolymph induces anal release of X. nematophila from colonized IJs and induces release of the IVS from uncolonized S. carpocapsae IJs. Released IVS were probed with several carbohydrate-specific lectins. One lectin, wheat-germ agglutinin, reacts strongly with a mucus-like substance that is present around individual spheres in the aggregate IVS. Potential roles for the IVS in mediating X. nematophila colonization of the nematode intestine are discussed.

  • Orchard SS, Goodrich-Blair H (2005) Pyrimidine nucleoside salvage confers an advantage to Xenorhabdus nematophila in its host interactions. Appl. Environ. Microbiol. 71(10):6254-9 (PMC1265980) · Pubmed

    Xenorhabdus nematophila is a mutualist of entomopathogenic nematodes and a pathogen of insects. To begin to examine the role of pyrimidine salvage in nutrient exchange between X. nematophila and its hosts, we identified and mutated an X. nematophila tdk homologue. X. nematophila tdk mutant strains had reduced virulence toward Manduca sexta insects and a competitive defect for nematode colonization in plate-based assays. Provision of a wild-type tdk allele in trans corrected the defects of the mutant strain. As in Escherichia coli, X. nematophila tdk encodes a deoxythymidine kinase, which converts salvaged deoxythymidine and deoxyuridine nucleosides to their respective nucleotide forms. Thus, nucleoside salvage may confer a competitive advantage to X. nematophila in the nematode intestine and be important for normal entomopathogenicity.

  • Martens EC, Russell FM, Goodrich-Blair H (2005) Analysis of Xenorhabdus nematophila metabolic mutants yields insight into stages of Steinernema carpocapsae nematode intestinal colonization. Mol. Microbiol. 58(1):28-45 · Pubmed

    Xenorhabdus nematophila colonizes the intestinal tract of infective-juvenile (IJ) stage Steinernema carpocapsae nematodes. During colonization, X. nematophila multiplies within the lumen of a discrete region of the IJ intestine termed the vesicle. To begin to understand bacterial nutritional requirements during multiplication in the IJ vesicle, we analysed the colonization behaviour of several X. nematophila metabolic mutants, including amino acid and vitamin auxotrophs. X. nematophila mutants defective for para-aminobenzoate, pyridoxine or l-threonine biosynthesis exhibit substantially decreased colonization of IJs (0.1-50% of wild-type colonization). Analysis of gfp-labelled variants revealed that those mutant cells that can colonize the IJ vesicle differ noticeably from wild-type X. nematophila. One aberrant colonization phenotype exhibited by the metabolic mutants tested, but not wild-type X. nematophila, is a spherical shape indicative of apparently non-viable X. nematophila cells within the vesicle. Because these spherical cells appear to have initiated colonization but failed to proliferate, we term this type of colonization 'abortive'. In a portion of IJs grown on para-aminobenzoate auxotrophs, X. nematophila does not exhibit abortive colonization but rather reduced growth and filamentous cell morphology. Several mutants with defects in other amino acid, vitamin and nutrient metabolism pathways colonize IJs to wild-type levels suggesting that the IJ vesicle is replete with respect to a number of nutrients.

  • Orchard SS, Goodrich-Blair H (2005) An encoded N-terminal extension results in low levels of heterologous protein production in Escherichia coli. Microb. Cell Fact. 4:22 (PMC1190211) · Pubmed

    The tdk gene (encoding deoxythymidine kinase) of the gamma-proteobacterium Xenorhabdus nematophila has two potential translation start sites. The promoter-distal start site was predicted to be functional based on amino acid sequence alignment with closely related Tdk proteins. However, to experimentally determine if either of the two possible start codons allows production of a functional Tdk, we expressed the "long-form" (using the promoter-proximal start codon) and "short-form" (using the promoter-distal start codon) X. nematophila tdk genes from the T7 promoter of the pET-28a(+) vector. We assessed Tdk production and activity using a functional assay in an Escherichia coli tdk mutant, which, since it lacks functional Tdk, is able to grow in 5-fluorodeoxyuridine (FUdR)-containing medium. Short-form Tdk complemented the E. coli tdk mutant strain, resulting in FUdR sensitivity of the strain. However, the E. coli tdk mutant expressing the long form of tdk remained FUdR resistant, indicating it did not have a functional deoxythymidine kinase enzyme. We report that long-form Tdk is at least 13-fold less abundant than short-form Tdk, the limited protein produced was as stable as short-form Tdk and the long-form transcript was 1.7-fold less abundant than short-form transcript. Additionally, we report that the long-form extension was sufficient to decrease heterologous production of a different X. nematophila protein, NilC. We conclude that the difference in the FUdR growth phenotype between the E. coli tdk mutant carrying the long-or short-form X. nematophila tdk is due to a difference in Tdk levels. The lower long-form protein level does not result from protein instability, but instead from reduced transcript levels possibly combined with reduced translation efficiency. Because the observed effect of the encoded N-terminal extension is not specific to Tdk production and can be overcome with induction of gene expression, these results may have particular relevance to researchers attempting to limit production of toxic proteins under non-inducing conditions.

  • Cowles KN, Goodrich-Blair H (2005) Expression and activity of a Xenorhabdus nematophila haemolysin required for full virulence towards Manduca sexta insects. Cell. Microbiol. 7(2):209-19 · Pubmed

    As an insect pathogen, the gamma-proteobacterium Xenorhabdus nematophila likely possesses an arsenal of virulence factors, one of which is described in this work. We present evidence that the X . nematophilahaemolysin XhlA is required for full virulence towards Manduca sexta larvae. Lrp (leucine-responsive regulatory protein), FlhDC (regulator of flagella synthesis), and iron (II) limitation positively influenced xhlA transcript levels, suggesting XhlA expression is linked with nutrient acquisition and motility regulons. To help understand the role of XhlA in virulence, we examined its cellular targets and found that XhlA was a cell-surface associated haemolysin that lysed the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes. Taken together, the need for xhlA for full virulence and XhlA activity towards insect immune cells suggest this haemolysin functions in X. nematophila immune evasion during infection. Analysis of a gene located immediately upstream of the xhlA locus, hcp (haemolysin co-regulated protein) revealed that its transcript levels were elevated during iron (III) limitation and its expression was Lrp-dependent. Further characterization of xhlA, hcp, and lrp will clarify their regulatory and functional relationships and their individual roles during the infectious process.

  • Cowles CE, Goodrich-Blair H (2004) Characterization of a lipoprotein, NilC, required by Xenorhabdus nematophila for mutualism with its nematode host. Mol. Microbiol. 54(2):464-77 · Pubmed

    Xenorhabdus nematophila is a gamma-proteobacterial mutualist of an insect-pathogenic nematode, Steinernema carpocapsae. X. nematophila requires nilC, a gene predicted to encode an outer membrane lipoprotein of unknown function, for colonization of its nematode host. Characterization of NilC, described here, demonstrated it is a 28 kDa lipoprotein directed to the periplasm by an N-terminal signal sequence. Lipidation and processing of NilC occurs by a mechanism that is conserved in proteobacteria. This work also showed NilC is membrane associated and oriented towards the periplasm of X. nematophila and is produced as an outer membrane-associated protein when expressed in Escherichia coli. Expression analyses revealed that nilC transcription is directly or indirectly repressed by Lrp, and this regulatory link may explain the nematode mutualism defect of a previously identified lrp::Tn5 mutant. An lrp::Tn5 mutant produces an additional nilC transcript, not observed in wild-type cells growing in vitro, and produces approximately 75-fold more nilC than wild-type cells in late stationary phase. These fundamental characterizations of nilC expression and nilC localization and processing events have provided firm bases for understanding the role of this colonization factor in the X. nematophila/S. carpocapsae microbe-host interaction.

  • Orchard SS, Goodrich-Blair H (2004) Identification and functional characterization of a Xenorhabdus nematophila oligopeptide permease. Appl. Environ. Microbiol. 70(9):5621-7 (PMC520880) · Pubmed

    The bacterium Xenorhabdus nematophila is a mutualist of Steinernema carpocapsae nematodes and a pathogen of insects. Presently, it is not known what nutrients the bacterium uses to thrive in these host environments. In other symbiotic bacteria, oligopeptide permeases have been shown to be important in host interactions, and we therefore sought to determine if oligopeptide uptake is essential for growth or symbiotic functions of X. nematophila in laboratory or host environments. We identified an X. nematophila oligopeptide permease (opp) operon of two sequential oppA genes, predicted to encode oligopeptide-binding proteins, and putative permease-encoding genes oppB, oppC, oppD, and oppF. Peptide-feeding studies indicated that this opp operon encodes a functional oligopeptide permease. We constructed strains with mutations in oppA(1), oppA(2), or oppB and examined the ability of each mutant strain to grow in a peptide-rich laboratory medium and to interact with the two hosts. We found that the opp mutant strains had altered growth phenotypes in the laboratory medium and in hemolymph isolated from larval insects. However, the opp mutant strains were capable of initiating and maintaining both mutualistic and pathogenic host interactions. These data demonstrate that the opp genes allow X. nematophila to utilize peptides as a nutrient source but that this function is not essential for the existence of X. nematophila in either of its host niches. To our knowledge, this study represents the first experimental analysis of the role of oligopeptide transport in mediating a mutualistic invertebrate-bacterium interaction.

  • Martens EC, Gawronski-Salerno J, Vokal DL, Pellitteri MC, Menard ML, Goodrich-Blair H (2003) Xenorhabdus nematophila requires an intact iscRSUA-hscBA-fdx operon to colonize Steinernema carpocapsae nematodes. J. Bacteriol. 185(12):3678-82 (PMC156225) · Pubmed

    An insertion between iscA and hscB of the Xenorhabdus nematophila iscRSUA-hscBA-fdx locus, predicted to encode Fe-S assembly machinery, prevented colonization of Steinernema carpocapsae nematodes. The insertion disrupted cotranscription of iscA and hscB, but did not reduce hscBA expression, suggesting that X. nematophila requires coordinated expression of the isc-hsc-fdx locus for colonization.

  • Martens EC, Heungens K, Goodrich-Blair H (2003) Early colonization events in the mutualistic association between Steinernema carpocapsae nematodes and Xenorhabdus nematophila bacteria. J. Bacteriol. 185(10):3147-54 (PMC154081) · Pubmed

    The bacterium Xenorhabdus nematophila is a mutualist of the entomopathogenic nematode Steinernema carpocapsae. During its life cycle, the bacterium exists both separately from the nematode and as an intestinal resident of a nonfeeding nematode form, the infective juvenile (IJ). The progression of X. nematophila from an ex vivo existence to a specific and persistent colonization of IJs is a model to understand the mechanisms mediating the initiation and maintenance of benign host-microbe interactions. To help characterize this process, we constructed an X. nematophila strain that constitutively expresses green fluorescent protein, which allowed its presence to be monitored within IJs. Using this strain, we showed that few bacterial cells initiate colonization of an individual IJ and that these grow inside the lumen of the IJ intestine in a reproducible polyphasic pattern during colonization. In accordance with these two observations, we demonstrated that the final population of bacteria in a nematode is of predominantly monoclonal origin, suggesting that only one or two bacterial clones initiate or persist during colonization of an individual nematode. These data suggest that X. nematophila initiates IJ colonization by competing for limited colonization sites or resources within the nematode intestine. This report represents the first description of the biological interactions occurring between X. nematophila and S. carpocapsae during the early stages of the colonization process, provides insights into the physiology of X. nematophila in its host niche, and will facilitate interpretation of future data regarding the molecular events mediating this process.

  • Zhou X, Kaya HK, Heungens K, Goodrich-Blair H (2002) Response of ants to a deterrent factor(s) produced by the symbiotic bacteria of entomopathogenic nematodes. Appl. Environ. Microbiol. 68(12):6202-9 (PMC134438) · Pubmed

    The production of an ant-deterrent factor(s) (ADF) by Xenorhabdus nematophila and Photorhabdus luminescens, the symbiotic bacteria of the nematodes Steinernema carpocapsae and Heterorhabditis bacteriophora, respectively, was examined. In addition to an in vivo assay in which bacteria were tested for their ability to produce ADF within insect cadavers (M.E. Baur, H. K. Kaya, and D. R. Strong, Biol. Control 12:231-236, 1998), an in vitro microtiter dish assay was developed to monitor ADF activity produced by bacteria grown in cultures. Using these methods, we show that ADF activity is present in the supernatants of bacterial cultures, is filterable, heat stable, and acid sensitive, and passes through a 10-kDa-pore-size membrane. Thus, ADF appears to be comprised of a small, extracellular, and possibly nonproteinaceous compound(s). The amount of ADF repellency detected depends on the ant species being tested, the sucrose concentration (in vitro assays), and the strain, form, and age of the ADF-producing bacteria. These findings demonstrate that the symbiotic bacteria of some species of entomopathogenic nematodes produce a compound(s) that deters scavengers such as ants and thus could protect nematodes from being eaten during reproduction within insect cadavers.

  • Heungens K, Cowles CE, Goodrich-Blair H (2002) Identification of Xenorhabdus nematophila genes required for mutualistic colonization of Steinernema carpocapsae nematodes. Mol. Microbiol. 45(5):1337-53 · Pubmed

    One stage in the symbiotic interaction between the bacterium Xenorhabdus nematophila and its nematode host, Steinernema carpocapsae, involves the species-specific colonization of the nematode intestinal vesicle by the bacterium. To characterize the bacterial molecular determinants that are essential for vesicle colonization, we adapted and applied a signature-tagged mutagenesis (STM) screen to this system. We identified 15 out of 3000 transposon mutants of X. nematophila with at least a 15-fold reduction in average vesicle colonization. These 15 mutants harbour disruptions in nine separate loci. Three of these loci have predicted open reading frames (ORFs) with similarity to genes (rpoS, rpoE, lrp) encoding regulatory proteins; two have predicted ORFs with similarity to genes (aroA, serC) encoding amino acid biosynthetic enzymes; one, designated nilB (nematode intestine localization), has an ORF with similarity to a gene encoding a putative outer membrane protein (OmpU) in Neisseria; and three, nilA, nilC and nilD, have no apparent homologues in the public database. nilA, nilB and nilC are linked on a single 4 kb locus. nilB and nilC are > 104-fold reduced in their ability to colonize the nematode vesicle and are predicted to encode membrane-localized proteins. The nilD locus contains an extensive repeat region and several small putative ORFs. Other than reduced colonization, the nilB, nilC and nilD mutants did not display alterations in any other phenotype tested, suggesting a specific role for these genes in allowing X. nematophila to associate with the nematode host.

  • Vivas EI, Goodrich-Blair H (2001) Xenorhabdus nematophilus as a model for host-bacterium interactions: rpoS is necessary for mutualism with nematodes. J. Bacteriol. 183(16):4687-93 (PMC99521) · Pubmed

    Xenorhabdus nematophilus, a gram-negative bacterium, is a mutualist of Steinernema carpocapsae nematodes and a pathogen of larval-stage insects. We use this organism as a model of host-microbe interactions to identify the functions bacteria require for mutualism, pathogenesis, or both. In many gram-negative bacteria, the transcription factor sigma(S) controls regulons that can mediate stress resistance, survival, or host interactions. Therefore, we examined the role of sigma(S) in the ability of X. nematophilus to interact with its hosts. We cloned, sequenced, and disrupted the X. nematophilus rpoS gene that encodes sigma(S). The X. nematophilus rpoS mutant pathogenized insects as well as its wild-type parent. However, the rpoS mutant could not mutualistically colonize nematode intestines. To our knowledge, this is the first report of a specific allele that affects the ability of X. nematophilus to exist within nematode intestines, an important step in understanding the molecular mechanisms of this association.

  • Goodrich-Blair H, Kolter R (2000) Homocysteine thiolactone is a positive effector of sigma(S) levels in Escherichia coli. FEMS Microbiol. Lett. 185(2):117-21 · Pubmed

    sigma(S) is a regulator of the stationary phase response in Escherichia coli. Multi-copy suppressors were sought in a strain with decreased levels of sigma(S) and one such suppressor was found to encode HsrA, a putative efflux pump. Multi-copy expression of hsrA was shown to lead to accumulation of homocysteine, which is predicted to cause an increase in homocysteine thiolactone (HCTL) levels. A direct correlation between HCTL levels and sigma(S) accumulation was observed both in mutants and during normal cell growth, leading to the hypothesis that HCTL is a physiologically relevant positive effector of sigma(S) levels in vivo.

  • Goodrich-Blair H, Shub DA (1996) Beyond homing: competition between intron endonucleases confers a selective advantage on flanking genetic markers. Cell 84(2):211-21 · Pubmed

    The closely related B. subtilis bacteriophages SPO1 and SP82 have similar introns inserted into a conserved domain of their DNA polymerase genes. These introns encode endonucleases with unique properties. Other intron-encoded "homing" endonucleases cleave both strands of intronless DNA; subsequent repair results in unidirectional gene conversion to the intron-containing allele. In contrast, the enzymes described here cleave one strand on both intron-containing and intronless targets at different distances from their common intron insertion site. Most surprisingly, each enzyme prefers DNA of the heterologous phage. The SP82-encoded endonuclease is responsible for exclusion of the SPO1 intron and flanking genetic markers from the progeny of mixed infections, a novel selective advantage imparted by an intron to the genome in which it resides.

  • Shub DA, Goodrich-Blair H, Eddy SR (1994) Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends Biochem. Sci. 19(10):402-4 · Pubmed

    No abstract available.

  • Goodrich-Blair H, Shub DA (1994) The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames. Nucleic Acids Res. 22(18):3715-21 (PMC308352) · Pubmed

    A previous report described the discovery of a group I, self-splicing intron in the DNA polymerase gene of the Bacillus subtilis bacteriophage SPO1 (1). In this study, the DNA polymerase genes of three close relatives of SPO1: SP82, 2C and phi e, were also found to be interrupted by an intron. All of these introns have group I secondary structures that are extremely similar to one another in primary sequence. Each is interrupted by an open reading frame (ORF) that, unlike the intron core or exon sequences, are highly diverged. Unlike the relatives of Escherichia coli bacteriophage T4, most of which do not have introns (2), this intron seems to be common among the relatives of SPO1.

  • Shub DA, Goodrich-Blair H (1992) Protein introns: a new home for endonucleases. Cell 71(2):183-6 · Pubmed

    No abstract available.

  • Xu MQ, Kathe SD, Goodrich-Blair H, Nierzwicki-Bauer SA, Shub DA (1990) Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria. Science 250(4987):1566-70 · Pubmed

    A self-splicing group I intron has been found in the gene for a leucine transfer RNA in two species of Anabaena, a filamentous nitrogen-fixing cyanobacterium. The intron is similar to one that is found at the identical position in the same transfer RNA gene of chloroplasts of land plants. Because cyanobacteria were the progenitors of chloroplasts, it is likely that group I introns predated the endosymbiotic association of these eubacteria with eukaryotic cells.

  • Goodrich-Blair H, Scarlato V, Gott JM, Xu MQ, Shub DA (1990) A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1. Cell 63(2):417-24 · Pubmed

    We report a self-splicing intron in bacteriophage SPO1, whose host is the gram-positive Bacillus subtilis. The intron contains all the conserved features of primary sequence and secondary structure previously described for the group IA introns of eukaryotic organelles and the gram-negative bacteriophage T4. The SPO1 intron contains an open reading frame of 522 nucleotides. As in the T4 introns, this open reading frame begins in a region that is looped out of the secondary structure, but ends in a highly conserved region of the intron core. The exons encode SPO1 DNA polymerase, which is highly similar to E. coli DNA polymerase I. The demonstration of self-splicing introns in viruses of both gram-positive and gram-negative eubacteria lends further evidence for their early origin in evolution.