Cooperative predation in the social amoebae Dictyostelium discoideum

Rubin, Michele; Miller, Amber; Katoh-Kurasawa, Mariko; Dinh, Christopher; Kuspa, Adam; Shaulsky, Gad

doi:10.1371/journal.pone.0209438

Cited by 10 publications

(10 citation statements)

References 47 publications

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“…For example, previous approaches to identify mutants that show growth defects have relied on laborious qualitative analysis of large numbers of mutant clones [ 52 ]. Interestingly, many of these are rescued by helper effects in mixed growth with wild-type cells [ 61 ]. The high throughput nature of REMI-seq, together with the fact that the pooled REMI-seq approach is refractive to identifying such mutants, likely explains why a different spectrum of mutants was identified.…”

Section: Discussionmentioning

confidence: 99%

Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology

et al. 2021

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Background Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoeba Dictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in the cell, developmental and evolutionary biology. Results We describe REMI-seq, an adaptation of Tn-seq, which allows high throughput, en masse, and quantitative identification of the genomic site of insertion of a drug resistance marker after restriction enzyme-mediated integration. We use REMI-seq to develop tools which greatly enhance the efficiency with which the sequence, transcriptome or proteome variation can be linked to phenotype in D. discoideum. These comprise (1) a near genome-wide resource of individual mutants and (2) a defined pool of ‘barcoded’ mutants to allow large-scale parallel phenotypic analyses. These resources are freely available and easily accessible through the REMI-seq website that also provides comprehensive guidance and pipelines for data analysis. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified. Conclusions We present methods and resources, generated using REMI-seq, for high throughput gene function analysis in a key model system.

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Section: Discussionmentioning

confidence: 99%

Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology

et al. 2021

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“…In particular, the myxobacteria appear to differ from amoebae in the degree to which germinating spores and vegetative cells continue to interact and to cooperate. Whereas amoebae may live comparatively solitary lives except when they undergo aggregative development (Rubin et al 2019), the myxobacteria remain social throughout their life cycle. For such systems that cooperate extensively during growth, aggregation may have density benefits that extend beyond the formation, survival and dispersal of spores (Ramsey and Dworkin 1968).…”

Section: Life After Aggregationmentioning

confidence: 99%

Why Aggregate? On the Evolution of Aggregative Multicellularity

Fortezza¹,

Schaal²,

Velicer³

2021

Preprint

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Microbes have evolved many fascinating and complex ways of interacting with conspecifics. Perhaps one of the most interesting is aggregative multicellularity, wherein independent cells come together and adhere to one another in order to form a larger entity. The fundamental benefits of active aggregation into multicellular groups generally remain unclear, and there are many open questions about what selective pressures led to the evolution of this behavior in various eukaryotic and prokaryotic taxa, most notably the dictyostelids and the myxobacteria. Aggregative multicellularity can be partitioned into three main phases: coming together, staying together as a group, and disaggregation. Different selective pressures may have led to adaptations unique to each phase. While aggregative microbial systems generally form elevated multicellular structures such as fruiting bodies, these can vary in complexity and morphology even among closely related species. What evolutionary forces shaped such morphological diversification remains unknown. Strains that are not genetically identical can coaggregate, which can impact group-level function either positively through functional synergy or negatively through harmful exploitation. Such chimerism within aggregates is likely to have played important roles in shaping the evolution of microbial multicellularity. Much further research is needed into the evolutionary forces and processes leading to and shaping the many forms of microbial aggregation.

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“…A recent study suggests that vegetative growth in D. discoideum while preying on bacteria might not be asocial, but instead may involve cooperative predation (Rubin et al, 2019).They found that D. discoideum growth is positively correlated with amoeba density, and mutants that grow poorly on live bacteria can be rescued by the presence of wild-type amoebas and synergistic mutants. They suggest this is due to the secretion of diffusible factors by wild-type cells that facilitates mutant growth, though the molecule mediating such an interaction has not yet been identified.…”

Section: Cooperative Predationmentioning

confidence: 99%

Cooperation and conflict in the social amoeba Dictyostelium discoideum

Medina¹,

Shreenidhi²,

Larsen³

et al. 2019

Int. J. Dev. Biol.

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The social amoeba Dictyostelium discoideum has provided considerable insight into the evolution of cooperation and conflict. Under starvation, D. discoideum amoebas cooperate to form a fruiting body comprised of hardy spores atop a stalk. The stalk development is altruistic because stalk cells die to aid spore dispersal. The high relatedness of cells in fruiting bodies in nature implies that this altruism often benefits relatives. However, since the fruiting body forms through aggregation there is potential for non-relatives to join the aggregate and create conflict over spore and stalk fates. Cheating is common in chimeras of social amoebas, where one genotype often takes advantage of the other and makes more spores. This social conflict is a significant force in nature as indicated by rapid rates of adaptive evolution in genes involved in cheating and its resistance. However, cheating can be prevented by high relatedness, allorecognition via tgr genes, pleiotropy and evolved resistance. Future avenues for the study of cooperation and conflict in D. discoideum include the sexual cycle as well as the relationship between D. discoideum and its bacterial symbionts. D. discoideum's tractability in the laboratory as well as its uncommon mode of aggregative multicellularity have established it as a promising model for future studies of cooperation and conflict.

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Cooperative predation in the social amoebae Dictyostelium discoideum

Cited by 10 publications

References 47 publications

Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology

Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology

Why Aggregate? On the Evolution of Aggregative Multicellularity

Cooperation and conflict in the social amoeba Dictyostelium discoideum

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