Identification of Compounds with Bioactivity against the Nematode Caenorhabditis elegans by a Screen Based on the Functional Genomics of the Marine Bacterium Pseudoalteromonas tunicata D2

Marine bacteria are a rich, yet underexplored, resource of compounds with inhibitory bioactivity against a range of eukaryotic target organisms. Identification of those inhibitors, however, requires a culturable or genetically tractable producer strain, a prerequisite that is not often fulfilled. This study describes a novel functional genomic screen that is based on expression of inhibitors in a heterogeneous recombinant host (i.e., Escherichia coli). Functional libraries were screened by selective grazing by the nematode Caenorhabditis elegans, in a simple, rapid, high-throughput manner. We applied our approach to discover inhibitors of C. elegans produced by the marine bacterium Pseudoalteromonas tunicata D2, a model organism for exploring a range of antagonistic activities between bacteria and eukaryotes and a known producer of several toxic compounds. Expression of P. tunicata DNA in E. coli and grazing selection by the nematode Caenorhabditis elegans identified two clones, with slow- and fast-killing modes of action. Genomic analysis of the slow-killing clone revealed that the activity was due to a small molecule, tambjamine, while the fast-killing activity involved a gene encoding for a novel protein. Microscopic analysis showed substantial colonization of the intestinal lumen, or rapid death of the nematode without colonization, for the two activities, respectively. The novel functional genomic screen presented here therefore detects new eukaryotic inhibitors with different chemical structures, kinetics, and predicted modes of actions.Marine environments harbor highly diverse microbial communities, with an estimated more than one million different species (60). The vast majority of these are still functionally undescribed and unexplored, and only a fraction of the total number of species can currently be investigated by culture-dependent methods (47). Surface-associated marine microorganisms thrive in challenging habitats, often characterized by space and nutrient limitation, competition with other microorganisms, and colonizing higher organisms, as well as the targeted predation pressure by protozoa, nematodes, and other grazers. In response to this highly competitive environment, microorganisms have evolved strategies such as the production of toxins, attachment structures, biofilm formation, and host resilience in order to prevent the settlement and growth of competitive colonizers and for protection against bacterivorous predators. In fact, some of these adaptive traits are now recognized as virulence factors against a range of eukaryotic organisms, including plants, animals, and humans (24, 25, 44, 46). Despite this realization, there is limited information available on the presence and function of virulence factors in marine microbial organisms, nor is the full potential to mine such organisms for novel compounds with bioactivity realized.The marine bacterial genus Pseudoalteromonas contains numerous species, which synthesize biologically active molecules. Many of these species have been demonstrated to produce an array of low- and high-molecular-weight compounds with antimicrobial, algicidal, neurotoxic, and other pharmaceutically relevant activities (7). P. tunicata strain D2 is the most comprehensively studied species within the genus (7). This species colonizes sessile eukaryotes such as algae and tunicates and is a producer of several compounds with inhibitory activities against a range of organisms. Although the identity of several of these compounds remains to be elucidated, they target a range of bacteria, fungi, invertebrate larvae, diatoms, algal spores, and protozoa (15, 28, 29). Furthermore, a recent analysis of the P. tunicata D2 genome revealed properties characteristic of pathogens such as curli, several proteases, and homologs to virulence regulators (59). Hence, P. tunicata D2 is a powerful model system in which to investigate bioactive compounds and their mode of action, including those that serve as virulence factors.In order to detect and identify bacterial bioactive compounds that target multicellular eukaryotes, the nematode Caenorhabditis elegans can be utilized as a model system. This free-living worm provides several practical experimental advantages, including its ability to feed solely on bacteria, a short life cycle, and easy cultivation in large numbers. Comprehensive studies have reported the nematode as a versatile model metazoan in which to assess the virulence of many human, animal, plant, and insect pathogens (53). Some of the characteristics of the C. elegans immune system are conserved in higher eukaryotic organisms; moreover, diverse bacterial virulence factors necessary for killing of the nematode are used as virulence strategies regardless of the host (53). Despite the progress made using this model, current methods that help elucidate microbial genes involved in toxin-mediated killing or virulence are time-consuming or require expensive automation. Furthermore, a large fraction of potentially pathogenic bacteria elude investigations because they are not cultivable by using conventional laboratory techniques (47) or because of incompatible culture conditions for the pathogen and C. elegans (e.g., C. elegans is cultured at 25°C, while the Yersinia pestis virulence factors are upregulated only at 37°C 55]). Therefore, new high-resolution and simple methods are required to study genes and effector molecules mediating the inhibitory or toxic activity displayed by both cultured and uncultured bacteria.In the present study we investigate the presence and activity of toxins in P. tunicata D2 with a rapid, culture-independent, eukaryotic screening assay. Our novel approach is based on the ability of C. elegans, using a sophisticated chemosensory system, to perceive and behaviorally respond to a range of chemical cues, including deterrence from noxious substances and attraction to nutrients or signals (2, 4, 26, 27, 45, 51, 52, 61, 62). The high-throughput screen successfully detected antinematode bioactive compounds and rapidly identified the responsible P. tunicata D2 genes and gene products in a recombinant Escherichia coli clone library. To our knowledge, this is the first time that a functional genomic library screening has been used to identify antinematode bioactive compounds.