High-throughput analysis of spatio-temporal dynamics in Dictyostelium

Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
Genome biology (Impact Factor: 10.81). 02/2007; 8(7):R144. DOI: 10.1186/gb-2007-8-7-r144
Source: PubMed


We demonstrate a time-lapse video approach that allows rapid examination of the spatio-temporal dynamics of Dictyostelium cell populations. Quantitative information was gathered by sampling life histories of more than 2,000 mutant clones from a large mutagenesis collection. Approximately 4% of the clonal lines showed a mutant phenotype at one stage. Many of these could be ordered by clustering into functional groups. The dataset allows one to search and retrieve movies on a gene-by-gene and phenotype-by-phenotype basis.

Download full-text


Available from: Adam Kuspa
  • Source
    • "The majority of microbial genotype-to-phenotype studies focus on a single characteristic, growth rate (Liu et al., 2010; North et al., 2012), but a few have attempted to characterize more complex multicellular traits. In Pseudomonas aeruginosa, confocal microscopy was used to study biofilm density patterns in mutant strains using a high-throughput assay (Pommerenke et al., 2010), and in Dictyostelium discoideum, time lapse images of ~2000 mutant strains were used to identify and characterize changes in the formation of fruiting bodies (Sawai et al., 2007). In both of these studies, despite the acquisition of detailed image data, the percentage of strains displaying discernably mutant traits remained below 10%. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Information about a gene sometimes can be deduced by examining the impact of its mutation on phenotype. However, the genome-scale utility of the method is limited because, for nearly all model organisms, the majority of mutations result in little or no observable phenotypic impact. The cause of this is often attributed to robustness or redundancy within the genome, but that is only one plausible hypothesis. We examined a standard set of phenotypic traits, and applied statistical methods commonly used in the study of natural variants to an engineered mutant strain collection representing disruptions in 180 of the 192 ABC transporters within the bacterium Myxococcus xanthus. These strains display continuous variation in their phenotypic distributions, with a small number of "outlier" strains at both phenotypic extremes, and the majority within a confidence interval about the mean that always includes wild type. Correlation analysis reveals substantial pleiotropy, indicating that the traits do not represent independent variables. The traits measured in this study co-cluster with expression profiles, thereby demonstrating that these changes in phenotype correspond to changes at the molecular level, and therefore can be indirectly connected to changes in the genome. However, the continuous distributions, the pleiotropy, and the placement of wild type always within the confidence interval all indicate that this standard set of M. xanthus phenotypic assays is measuring a narrow range of partially overlapping traits that do not directly reflect fitness. This is likely a significant cause of the observed small phenotypic impact from mutation, and is unrelated to robustness and redundancy.
    Full-text · Article · Jul 2014 · Frontiers in Microbiology
  • Source
    • "Roco7 and Roco9 are expressed mostly during aggregation, similar to GbpC. Although roco5-null cells were previously identified in a large screen for mutants with defects in the developmental cycle (Sawai et al., 2007), they did not show any recognizable developmental phenotype. In the contrary roco11- null cells show mild developmental defects: these cells develop significantly larger fruiting bodies; in particular, the multicellular structures have longer stalks compared to wild-type cells, re-expression of Roco11 in roco11-null cells rescues this defect. "

    Full-text · Chapter · Feb 2012
  • Source
    • "In addition, no caspases or metacaspases are encoded by the D. discoideum genome (Eichinger et al., 2005). On the other hand, the MAPK proteins ErkA and ErkB have been implicated in various growth, developmental, and defense functions in the D. discoideum life-cycle (Sawai et al., 2007; Segall et al., 1995). Interestingly, recent evidence indicates that the D. discoideum MAPK response is also involved in host responses to the pathogen L. pneumophila (Li et al., 2009). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Innate immune cells respond to invading microbes upon detection of pathogen-associated molecular patterns (PAMPS). PAMP-recognition machinery is evolutionarily conserved, allowing for characterization in model organisms. The model organism Dictyostelium discoideum can exist as single-celled amoebae, which phagocytize bacteria for nutrients. Although D. discoideum is used extensively to study phagocytosis, it has not been determined if D. discoideum detects bacterial PAMPs using pattern-recognition machinery. Here we show that D. discoideum mounts responses against the bacterial cell wall PAMP, lipopolysaccharide (LPS). Upon treatment with LPS or its active component Lipid A, D. discoideum cells more efficiently clear phagocytized bacteria. LPS-enhanced bactericidal activity appears dependent both on MAPK signaling pathways as well as on the D. discoideum toll/interleukin-1 receptor domain-containing protein, TirA. These findings indicate that pattern-recognition machinery required to detect and respond to bacterial PAMPs may be conserved in D. discoideum.
    Full-text · Article · Aug 2011 · Developmental and comparative immunology
Show more