Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium

Self and kin discrimination are observed in most kingdoms of life and are mediated by highly polymorphic plasma membrane proteins. Sequence polymorphism, which is essential for effective recognition, is maintained by balancing selection. Dictyostelium discoideum are social amoebas that propagate as unicellular organisms but aggregate upon starvation and form fruiting bodies with viable spores and dead stalk cells. Aggregative development exposes Dictyostelium to the perils of chimerism, including cheating, which raises questions about how the victims survive in nature and how social cooperation persists. Dictyostelids can minimize the cost of chimerism by preferential cooperation with kin, but the mechanisms of kin discrimination are largely unknown. Dictyostelium lag genes encode transmembrane proteins with multiple immunoglobulin (Ig) repeats that participate in cell adhesion and signaling. Here, we describe their role in kin discrimination. We show that lagB1 and lagC1 are highly polymorphic in natural populations and that their sequence dissimilarity correlates well with wild-strain segregation. Deleting lagB1 and lagC1 results in strain segregation in chimeras with wild-type cells, whereas elimination of the nearly invariant homolog lagD1 has no such consequences. These findings reveal an early evolutionary origin of kin discrimination and provide insight into the mechanism of social recognition and immunity

Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage

The Amoebozoa are a sister clade to the fungi and the animals, but are poorly sampled for completely sequenced genomes. The social amoeba Dictyostelium discoideum and amitochondriate pathogen Entamoeba histolytica are the first Amoebozoa with genomes completely sequenced. Both organisms are classified under the Conosa subphylum. To identify Amoebozoa-specific genomic elements, we compared these two genomes to each other and to other eukaryotic genomes. An expanded phylogenetic tree built from the complete predicted proteomes of 23 eukaryotes places the two amoebae in the same lineage, although the divergence is estimated to be greater than that between animals and fungi, and probably happened shortly after the Amoebozoa split from the opisthokont lineage. Most of the 1,500 orthologous gene families shared between the two amoebae are also shared with plant, animal, and fungal genomes. We found that only 42 gene families are distinct to the amoeba lineage; among these are a large number of proteins that contain repeats of the FNIP domain, and a putative transcription factor essential for proper cell type differentiation in D. discoideum. These Amoebozoa-specific genes may be useful in the design of novel diagnostics and therapies for amoebal pathologies

Conserved developmental transcriptomes in evolutionarily divergent species

Transcriptional profiling of Dictyostelium development reveals significant conservation of transcriptional profiles between evolutionarily divergent species

Genomic Signatures of Cooperation and Conflict in the Social Amoeba

Molecular evolution analyses reveal the history of social conflict Genes that mediate social conflict show signatures of frequency-dependent selection Balanced polymorphisms suggest that cheating may be stable and endemic Cooperative systems are susceptible to invasion by selfish individuals that profit from receiving the social benefits but fail to contribute. These so-called cheaters can have a fitness advantage in the laboratory, but it is unclear whether cheating provides an important selective advantage in nature. We used a population genomic approach to examine the history of genes involved in cheating behaviors in the social amoeba Dictyostelium discoideum, testing whether these genes experience rapid evolutionary change as a result of conflict over spore-stalk fate. Candidate genes and surrounding regions showed elevated polymorphism, unusual patterns of linkage disequilibrium, and lower levels of population differentiation, but they did not show greater between-species divergence. The signatures were most consistent with frequency-dependent selection acting to maintain multiple alleles, suggesting that conflict may lead to stalemate rather than an escalating arms race. Our results reveal the evolutionary dynamics of cooperation and cheating and underscore how sequence-based approaches can be used to elucidate the history of conflicts that are difficult to observe directly

Relationship between host immunity and svRNA abundance.

<p>For each infected mouse, the susceptibility of the mouse strain to influenza virus was plotted against the abundance of svRNA in the PR8 reads for that sample. Lower values indicate that the mouse strain is more susceptible to PR8 (high viral titer, inflammation and weight loss); higher values indicate that the mouse strain is more resistant to PR8 (low viral titer, little inflammation, and weight loss). Pearson’s linear correlation was applied to the dataset to quantify the relationship between the variables, and the line connecting the data points represents the linear regression of the data.</p

A Developmentally Regulated Kinesin-related Motor Protein from Dictyostelium discoideum

The cellular slime mold Dictyostelium discoideum is an attractive system for studying the roles of microtubule-based motility in cell development and differentiation. In this work, we report the first molecular characterization of kinesin-related proteins (KRPs) in Dictyostelium. A PCR-based strategy was used to isolate DNA fragments encoding six KRPs, several of which are induced during the developmental program that is initiated by starvation. The complete sequence of one such developmentally regulated KRP (designated K7) was determined and found to be a novel member of the kinesin superfamily. The motor domain of K7 is most similar to that of conventional kinesin, but unlike conventional kinesin, K7 is not predicted to have an extensive α-helical coiled-coil domain. The nonmotor domain is unusual and is rich in Asn, Gln, and Thr residues; similar sequences are found in other developmentally regulated genes in Dictyostelium. K7, expressed in Escherichia coli, supports plus end–directed microtubule motility in vitro at a speed of 0.14 μm/s, indicating that it is a bona fide motor protein. The K7 motor is found only in developing cells and reaches a peak level of expression between 12 and 16 h after starvation. By immunofluorescence microscopy, K7 localizes to a membranous perinuclear structure. To examine K7 function, we prepared a null cell line but found that these cells show no gross developmental abnormalities. However, when cultivated in the presence of wild-type cells, the K7-null cells are mostly absent from the prestalk zone of the slug. This result suggests that in a population composed largely of wild-type cells, the absence of the K7 motor protein interferes either with the ability of the cells to localize to the prestalk zone or to differentiate into prestalk cells

Repurposed Transcriptomic Data Reveal Small Viral RNA Produced by Influenza Virus during Infection in Mice

<div><p>Influenza virus, a highly infectious ssRNA virus, replicates in the nucleus of host cells. This unusual feature brings the possibility that the virus may hijack host small noncoding RNA metabolism. Influenza small viral RNA production has been examined <i>in vitro</i> but has not yet been studied in an <i>in vivo</i> setting. We assessed small RNA species from influenza virus during mouse infection by mining publicly available mouse small RNA transcriptome data. We uncovered 26 nt reads corresponding to svRNA, a small viral RNA previously detected <i>in vitro</i> that regulates the transition from transcription to replication during infection, and found a strong positive correlation between svRNA production and host susceptibility to influenza virus infection. We also detected significant overrepresentation of a non-coding 23 nt sequence that we speculate may behave like a miRNA and work with influenza protein NS1 to prevent the transcription and maturation of interferon-stimulated mRNAs.</p></div

Segment-specific genome coverage of reads mapped to PR8.

<p>Influenza virus-specific reads were sorted by genomic coordinate. Strand-specific coverage of each base in the reference sequence was quantified and base coverage values for the seven infected mouse samples were normalized for the total number of PR8-specific reads in the respective sample and displayed as base coverage per thousand reads. For each position in the PR8 genome, the mean and 95% CI of the normalized coverage of the vRNA were calculated and are displayed as black and red, respectively. Nucleotide position is counted from the 5’ end of the vRNA.</p

Evaluation of total and PR8-specific reads in infected and mock-infected mice.

<p>(A) Total small RNA reads detected in mock-infected and infected mouse lungs. Lung samples were taken at two days post infection with influenza A virus PR8. Small RNAs were purified and sequenced on an Illumina Genome Analyzer IIx system. The infected mouse group contained two replicates from each mouse strain (129, CAST, PWK, WSB) and the mock-infected group contained a single sample from each mouse strain. Groups were compared with a Mann-Whitney test. (B) Percentage of influenza virus-specific reads in each mouse group. Adaptor-trimmed reads mapping uniquely to the PR8 genome are shown as a percentage of total RNA reads. Mock-infected and infected groups were compared with a Mann-Whitney test. The data are presented in a box-and-whiskers plot that uses the centerline to indicate median, the box to indicate quartiles, and the whiskers to indicate range.</p