Balancing selection of the Intracellular Pathogen Response in natural Caenorhabditis elegans populations

Abstract

23 0031317482998 24 Mark.Sterken@wur.nl 25 Our work provides evidence that balancing genetic selection shapes the transcriptional defence against pathogens 48 in C. elegans. The transcriptional and genetic data in this study demonstrate the functional diversity that can 49 develop within antiviral transcriptional responses in natural host populations. 50 Page 3 of 28 Background 51 The continuous battle between host and virus drives host genetic variation to arise in antiviral mechanisms such 52 as transcriptional responses. Regulatory genetic variation affects the viral susceptibility after infection, making 53 some individuals within the population more resistant than others [1-4]. Yet, the universality and mode-of-action 54 of genetic diversity in shaping antiviral transcriptional responses within natural populations remains largely 55 unknown. 56 Caenorhabditis elegans and its natural pathogen Orsay virus (OrV) are used as a powerful genetic 57 model system to study host-virus interactions [5]. OrV is a positive-sense single-stranded RNA virus infecting C. 58 elegans intestinal cells where it causes local disruptions of the cellular structures [5, 6]. Two major groups of 59 antiviral genes respond to viral infection in C. elegans: genes related to the RNA interference (RNAi) pathway 60 [5, 7-12] and genes related to the Intracellular Pathogen Response (IPR) [13-16]. The RNAi pathway activity is 61 controlled by the gene sta-1 which in turn is activated by the viral sensor sid-3 that is hypothesized to directly 62 interact with the Orsay virus [7]. Subsequently, the antiviral RNAi components dcr-1, drh-1, and rde-1 degrade 63 the viral RNA [9], but the RNAi genes themselves remain equally expressed during infection [9, 16]. The IPR 64 counteracts infection by intracellular pathogens (including OrV) and increases the ability to handle proteotoxic 65 stress [13-15]. The gene pals-22 co-operates together with pals-25 to control the IPR pathway by functioning as 66 a molecular switch between growth and antiviral defence. Pals-22 promotes development and lifespan, whereas 67 pals-25 stimulates pathogen resistance. Together pals-22 and pals-25 regulate a set of 80 genes that are 68 upregulated upon intracellular infection including 25 genes in the pals-family and several members of the 69 ubiquitination response [14, 15].. Both pals-22 and pals-25 do not change gene expression following OrV 70 infection. In total, the pals-gene family contains 39 members mostly found in five genetic clusters on 71 chromosome I, III, and V.. Recently, a third antiviral defence was identified which degrades the viral genome 72 after uridylation by the gene cde-1 [17]. Together, these antiviral pathways are key in controlling OrV infection 73 in C. elegans. 74The transcriptional responses following infection have so far been studied in the C. elegans laboratory 75 strain N2, in RNAi deficient mutants in the N2 background such as rde-1 and dcr-1 and in the RNAi-deficient 76 wild isolate JU1580 [7, 9, 10, 13, 14, 16]. These studies indica...

Balancing selection maintains hyper-divergent haplotypes inC. elegans

“…Four genomic regions were originally identified to affect C. elegans susceptibility to N. parisii , all of which overlap with hyper-divergent regions we identified. Subsequent studies showed that the pals genes mediate responses to N. parisii and the Orsay virus 31,[42][43][44][45] , of which 86.8% (33/38) of these genes are located in hyper-divergent regions. The hyper-divergent regions we present here also include other loci previously found to underlie natural resistance to starvation 59 and toxic bacterial metabolite 60 , and genetic incompatibilities in the species 29,61 .…”

“…G-protein coupled receptors, GPCRs) are located in hyper-divergent regions. In addition to GPCRs, 48.2% (124/257) of genes that encode for C-type lectins, 53% (317/598) of the E3 ligase genes, and 86.8% (33/38) of the pals genes, which are involved in response to diverse pathogens 31,[42][43][44][45] , are found in hyper-divergent regions ( Supplementary Fig. 7, Supplementary Data 2).…”

“…It is hypothesized that the evolutionary forces that reduce genetic variation in selfing species have the potential to increase this genomic footprint of loci under balancing selection 27,28 . Intriguingly, genomic loci under long-term balancing selection have also been characterized in C. elegans [29][30][31] , and previous comparisons between the genome of the laboratory reference strain N2 and a de novo genome assembly of a divergent Hawaiian strain (CB4856) led to the discovery of punctuated regions of extremely high divergence 32,33 .…”

Punctuated loci on chromosome IV determine natural variation in Orsay virus susceptibility ofCaenorhabditis elegansstrains Bristol N2 and Hawaiian CB4856

“…Next to this, we observed that infection tended to be more often established in N2 (76% success rate) than in CB4856 (61% success rate) (chi-square test, p = 0.093). Constant exposure to OrV for four days resulted in similar viral loads between N2 and CB4856 [15,26], thus suggesting that multiple rounds of viral replication are necessary to fully infect CB4856 populations. Together, these observations show that CB4856 develops a lower viral load and can suppress a beginning infection better than N2.…”

“…In addition to the natural variation in the RNAi response, genetic variation also determines the Intracellular Pathogen Response (IPR) against OrV infection. The Hawaiian strain CB4856 had higher (basal) expression of multiple IPR genes than N2, potentially resulting in higher resistance to OrV infection observed in CB4856 [26]. However, the genetic and transcriptional networks leading to this difference have not been uncovered.…”