Elaboration, Diversification and Regulation of the Sir1 Family of Silencing Proteins in Saccharomyces |
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| Authors: | Jennifer E. G. Gallagher Joshua E. Babiarz Leonid Teytelman Kenneth H. Wolfe Jasper Rine |
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| Affiliation: | Field of Genetics and Development, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853 |
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| Abstract: | This study quantifies the effects of naturally occurring X-linked variation on immune response in Drosophila melanogaster to assess associations between immunity genotypes and innate immune response. We constructed a set of 168 X-chromosomal extraction lines, incorporating X chromosomes from a natural population into co-isogenic autosomal backgrounds, and genotyped the lines at 88 SNPs in 20 X-linked immune genes. We find that genetic variation in many of the genes is associated with immune response phenotypes, including bacterial load and immune gene expression. Many of the associations act in a sex-specific or sexually antagonistic manner, supporting the theory that with the selective pressures facing genes on the X chromosome, sexually antagonistic variation may be more easily maintained.THE deep evolutionary conservation of many specific genes in innate immunity underscores the potent forces of natural selection maintaining this vital function. While it is widely accepted as the ancestral form of immune response, its role in the activation of adaptive immune response further motivates investigation into variation in its function (Medzhitov and Janeway 1997). Drosophila has been used as a valuable model organism to identify and characterize functions of the components of innate immune pathways as well as the evolutionary patterns present among the genes comprising these pathways (reviewed in Brennan and Anderson 2004; Irving et al. 2004; Ferrandon et al. 2007). The humoral response, resulting in the production of antimicrobial peptides in response to bacterial or fungal infection, relies mainly on Toll and imd signal transduction pathways, both of which are highly homologous to pathways in mammalian immunity (reviewed in Kimbrell and Beutler 2001). The cellular component, on the other hand, incorporates phagocytic engulfment as well as melanization and encapsulation of infecting particles. While less well defined in the Drosophila model, portions of other systems also appear to affect the effectiveness of immune response, including JAK/STAT and JNK signaling pathways, hematopoesis, and iron metabolism.Population genetic analysis can be used to determine whether sequence polymorphism and divergence patterns among Drosophila genes in innate immune pathways are consistent with signatures of selection acting within and between species of flies. If, for example, the innate immune pathways are involved in an evolutionary “arms race” with pathogenic organisms, genes in these pathways would be expected to show signs of positive selection driven by evolutionary pressure to counter virulence mechanisms of invading microbes. When signs of selection (as inferred from sequence comparisons within Drosophila simulans populations and between D. simulans and D. melanogaster) in immune genes and nonimmune genes were evaluated, immune genes as a group were found to have higher KA/KS ratios than nonimmune genes, providing evidence for elevated adaptive evolution (Schlenke and Begun 2003). Since receptor, effector, and signaling proteins function in different portions of the immune response pathways, these may be exposed to differing levels of contact with invading microbes and may display nonuniform levels of functional redundancy or pleiotropy. Thus, genes from different functional groups may be exposed to distinct selective pressures. Antimicrobial peptides, which might be expected to encounter unique selective pressures due to their direct interactions with invading microbes, have shown little sign of positive selection, bearing low levels of amino acid divergence (Clark and Wang 1997; Date et al. 1998; Ramos-Onsins and Aguadé 1998; Lazzaro and Clark 2003). Furthermore, sequence analyses of immune-related receptors have shown evidence for purifying selection in peptidoglycan recognition proteins (PGRPs), while others, including some scavenger receptors (SRs), appear to be rapidly evolving under pressures consistent with positive selection (Jiggins and Hurst 2003; Lazzaro 2005). On a deeper evolutionary timescale, sequence comparisons between immune genes in multiple Drosophila species (based on full-genome sequence data) have shown striking differences among functional groups of immune genes, with recognition molecules showing much more positive selection than either signaling or effector genes (Sackton et al. 2007).Beyond using sequence data and the analysis of polymorphism and divergence to infer levels and modes of selection that have previously acted on immune genes (either individually or in functional groups), other studies have investigated correlations between autosomal variation in genotype and immune response phenotype in natural populations of Drosophila (Lazzaro et al. 2004, 2006). These experiments tested associations between naturally occurring genetic variation in immune-related genes and postinfection bacterial load. In these studies, genetic variation in many of the immune genes was found to associate significantly with one or more of the bacterial load phenotypes. Specifically, polymorphisms in autosomal genes encoding recognition and signaling proteins (but not antimicrobial peptides) associate consistently with bacterial load phenotypes, suggesting that not all functional classes of immune-related genes harbor equally influential genetic variation.The focus of this study is X-linked immune genes, which may be under unique regulatory and selective pressures simply because they are hemizygous in males, are dosage compensated, and face elevated influence of random genetic drift due to their smaller effective population size. As a consequence, the X chromosome should favor the more rapid fixation of beneficial recessive alleles and more rapid loss of harmful recessive alleles compared to the autosomes (Charlesworth et al. 1987; Singh et al. 2008). Thus, with different selective pressures compared to autosomal genes, X-linked immunity genes are expected to bear different standing levels of variation, and segregating polymorphisms in these genes may have different impacts on phenotype.Different exposures of X-linked genes to selection in males and females can also contribute to sexual dimorphism. Rice (1984) suggested that X-linked sexually antagonistic alleles may more freely influence sexually dimorphic traits than can those on autosomes. In fact, the X chromosome appears to favor the maintenance of sexually antagonistic variation (Gibson et al. 2002); if a given allele is slightly deleterious in one sex, it may be maintained in the population by being beneficial to the other sex. Immune-related genes may be particularly prone to bearing sexual dimorphism in Drosophila, since males and females have been shown to have different evolutionary optima for energetic expenditure on immune response, and thus their respective immune responses may differ on the basis of conditions such as food or reproductive resource availability (McKean and Nunney 2001, 2005). If sexually antagonistic traits are responsible for some of the observed sexual dimorphism, variation in X-linked genes could contribute to phenotypic differences, and so X-linked variation in immune genes could face unique selective pressures.In this report we investigate the standing levels of variation in X-linked immune genes in natural populations of D. melanogaster and quantify the impacts of that variation on immune response phenotypes. We genotyped 168 lines at single-nucleotide polymorphisms (SNPs) across 20 X-linked immunity loci and quantified postinfection bacterial load and immune gene expression phenotypes. We found significant variation across the lines for bacterial load after infection, and we were able to identify polymorphisms in immune-related genes that associate with immune response phenotypes individually and in interacting pairs of SNPs. Additionally, some of the genetic variation was found to associate with a sex difference in immune competence, with alleles acting in either a sex-specific or a sexually antagonistic manner. This provides evidence for X-linked genetic variation in immune-related loci associating with both phenotypic variation among lines and sex differences in these phenotypes. |
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