Complex Coding and Regulatory Polymorphisms in a Restriction Factor Determine the Susceptibility of Drosophila to Viral Infection

Abstract

It is common to find that major-effect genes are an important cause of variation in susceptibility to infection. Here we have characterized natural variation in a gene called pastrel that explains over half of the genetic variance in susceptibility to the Drosophila C virus (DCV) in populations of Drosophila melanogaster. We found extensive allelic heterogeneity, with a sample of seven alleles of pastrel from around the world conferring four phenotypically distinct levels of resistance. By modifying candidate SNPs in transgenic flies, we show that the largest effect is caused by an amino acid polymorphism that arose when an ancestral threonine was mutated to alanine, greatly increasing resistance to DCV. Overexpression of the ancestral, susceptible allele provides strong protection against DCV; indicating that this mutation acted to improve an existing restriction factor. The pastrel locus also contains complex structural variation and cis-regulatory polymorphisms altering gene expression. We find that higher expression of pastrel is associated with increased survival after DCV infection. To understand why this variation is maintained in populations, we investigated genetic variation surrounding the amino acid variant that is causing flies to be resistant. We found no evidence of natural selection causing either recent changes in allele frequency or geographical variation in frequency, suggesting that this is an old polymorphism that has been maintained at a stable frequency. Overall, our data demonstrate how complex genetic variation at a single locus can control susceptibility to a virulent natural pathogen.

Natural Variation in Resistance to Virus Infection in Dipteran Insects

“…Resistance to DCV has been mapped to complex polymorphisms at the pastrel ( pst ) locus [ 130 , 133 ]. The primary pst resistance mutation is due to a single amino acid change, although there are multiple structural alleles and cis- regulatory changes that may enhance resistance, resulting in seven alleles with four distinct phenotypes [ 134 ]. Although the function of pst is unknown, overexpression of the susceptible allele provides protection against DCV, and pst is upregulated after intra-abdominal viral injection, indicating that pst is an induced antiviral factor [ 134 ].…”

“…The primary pst resistance mutation is due to a single amino acid change, although there are multiple structural alleles and cis- regulatory changes that may enhance resistance, resulting in seven alleles with four distinct phenotypes [ 134 ]. Although the function of pst is unknown, overexpression of the susceptible allele provides protection against DCV, and pst is upregulated after intra-abdominal viral injection, indicating that pst is an induced antiviral factor [ 134 ]. In addition to pst, polymorphism in Anaphase promoting complex 7, Ubiquitin conjugating enzyme E2H, and 2 QTLs may also underlie genetic variation in DCV resistance, although these await more extensive characterization [ 130 , 133 ].…”

“…These variants are likely under pathogen-mediated selection, and surrounding patterns of polymorphism and divergence have been compared to expected patterns of balancing selection (i.e., selection that maintains genetic variation) or recurrent positive selection (i.e., selection on an advantageous allele), which would be compatible with their involvement in antagonistic coevolution (reviewed in [ 117 , 147 , 148 ]). Although none of the identified resistance loci display significantly increased diversity that is a hallmark of balancing selection, ref(2)P and pastrel have relatively high levels of nonsynonymous or structural polymorphism [ 123 , 130 , 134 , 149 ]. This may be due, in part, to incomplete selective sweeps, whereby a resistance mutation rises to high frequency and subsequently loses the selective benefit through viral counter-adaptation.…”

Defense Mechanisms against Viral Infection in Drosophila: RNAi and Non-RNAi

“…On the other hand, a single gene, pastrel , is the dominant factor that regulates susceptibility to DCV infections [ 95 , 106 ]. In this case, resistance is achieved through higher expression levels of pastrel , independent of which allele was used.…”

Bub1 Facilitates Virus Entry through Endocytosis in a Model of Drosophila Pathogenesis

“…The presence of the S or R allele of the pastrel ( pst ) gene in the genetic background was reported to affect DCV infection ( 25 , 26 ). To further confirm whether Bub1 was necessary for virus infection, precise excision of the inserted piggyBac element by the pBac transposase was performed in bub1 c04512 flies, which restored bub1 expression to the level in wild-type flies (Fig.…”