Contrasting invertebrate immune defense behaviors caused by a single gene, the Caenorhabditis elegans neuropeptide receptor gene npr-1. Caenorhabditis elegans

The nematode Caenorhabditis elegans feeds on microbes in its natural environment. Some of these microbes are pathogenic and thus harmful to C. elegans. To minimize resulting fitness reductions, C. elegans has evolved various defence mechanisms including behavioural responses (e.g. avoidance behaviour) that reduce contact with the infectious microbes. In this study, we characterized the genetic architecture of natural variation in C. elegans avoidance behaviour against the infectious stages of the Gram-positive bacterium Bacillus thuringiensis. We performed an analysis of quantitative trait loci (QTLs) using recombinant inbred lines (RILs) and introgression lines (ILs) generated from a cross of two genetically as well as phenotypically distinct natural isolates N2 and CB4856. The analysis identified several QTLs that underlie variation in the behavioural response to pathogenic and/or non-pathogenic bacteria. One of the candidates is the npr-1 gene. This gene encodes a homolog of the mammalian neuropeptide receptor. Npr-1 was previously indicated to fully contribute to behavioural defence against the Gram-negative bacterium Pseudomonas aeruginosa and food patch-leaving behaviour on Escherichia coli. Interestingly, in our study, npr-1 is not the only gene mediating avoidance behaviour toward Bacillus thuringiensis. Moreover, our functional analyses show that npr-1 alleles appear to influence survival and avoidance behaviour toward Bacillus thuringiensis in exactly the opposite way than toward Pseudomonas aeruginosa. Our findings highlight the role of npr-1 in fine-tuning nematode behaviour in an ecological context depending on the microbe to which C. elegans is exposed. These opposite phenotypes reflect the diversity in innate immunity to pathogens. To understand the mechanism involved in these opposite phenotypes, we carried out a whole-genome transcriptomics study by RNA-Sequencing. This study includes two pathogens: Pseudomonas aeruginosa PA14 and Bacillus thuringiensis B-18247 (BT247), two strains: N2 and npr-1 (ur89), two time points (12 and 24h) and standard lab food E. coli OP50 as control. Overall design: mRNA profiles of wild type (WT) and npr-1 (ur89) C.elegans exposed to either Bacillus thuringiensis B-18247, Pseudomonas aeruginosa PA14 or standard lab food E. coli OP50 at 12h or 24h were generated by deep sequencing, in double or triplicate, using Illumina HiSeq2000.

秀丽隐杆线虫（Caenorhabditis elegans，C. elegans）在其自然生境中以微生物为食。其中部分微生物具有致病性，会对秀丽隐杆线虫造成伤害。为尽可能降低由此带来的适合度下降，秀丽隐杆线虫演化出了多种防御机制，包括可减少与传染性微生物接触的行为响应（如回避行为）。
本研究针对秀丽隐杆线虫对革兰氏阳性菌苏云金芽孢杆菌（Bacillus thuringiensis）感染阶段的回避行为的自然变异遗传结构进行了表征。我们利用由两个遗传与表型均存在显著差异的野生自然分离株N2与CB4856杂交获得的重组自交系（recombinant inbred lines，RILs）和导入系（introgression lines，ILs），开展了定量性状位点（quantitative trait loci，QTLs）分析。本次分析鉴定出了多个与秀丽隐杆线虫对致病性和/或非致病性细菌的行为响应变异相关的QTL。
候选基因之一为npr-1基因。该基因编码哺乳动物神经肽受体的同源蛋白。既往研究表明，npr-1基因在秀丽隐杆线虫对抗革兰氏阴性菌铜绿假单胞菌（Pseudomonas aeruginosa）的行为防御，以及在大肠杆菌（Escherichia coli，E. coli）培养基上的食物斑块撤离行为中发挥了完全的调控作用。有趣的是，在本研究中，介导秀丽隐杆线虫对苏云金芽孢杆菌回避行为的基因并非仅有npr-1。此外，我们的功能分析结果显示，npr-1等位基因对秀丽隐杆线虫在苏云金芽孢杆菌胁迫下的存活与回避行为的影响，与在铜绿假单胞菌胁迫下的影响恰好相反。
本研究结果凸显了npr-1在生态场景下，根据秀丽隐杆线虫所接触的微生物种类精细调控线虫行为的作用。这些相反的表型反映了宿主对病原体先天免疫的多样性。为解析这些相反表型背后的分子机制，我们通过RNA测序（RNA-Sequencing）开展了全基因组转录组学研究。本次研究涵盖两类病原体：铜绿假单胞菌PA14（Pseudomonas aeruginosa PA14）与苏云金芽孢杆菌B-18247（BT247）；两种实验菌株：野生型N2与npr-1（ur89）突变株；两个取样时间点（12h与24h），并以标准实验室食物大肠杆菌OP50（E. coli OP50）作为对照。
实验整体设计：本研究通过Illumina HiSeq2000测序平台进行深度测序，对暴露于苏云金芽孢杆菌B-18247、铜绿假单胞菌PA14或标准实验室食物大肠杆菌OP50的野生型（wild type，WT）与npr-1（ur89）秀丽隐杆线虫，在12h与24h两个时间点的mRNA转录组图谱进行了构建，每个样本设置2次或3次生物学重复。