The Pseudokinase NIPI-4 Is a Novel Regulator of Antimicrobial Peptide Gene Expression

Abstract

Hosts have developed diverse mechanisms to counter the pathogens they face in their natural environment. Throughout the plant and animal kingdoms, the up-regulation of antimicrobial peptides is a common response to infection. In C. elegans , infection with the natural pathogen Drechmeria coniospora leads to rapid induction of antimicrobial peptide gene expression in the epidermis. Through a large genetic screen we have isolated many new mutants that are incapable of upregulating the antimicrobial peptide nlp-29 in response to infection (i.e. with a Nipi or ‘no induction of peptide after infection’ phenotype). More than half of the newly isolated Nipi mutants do not correspond to genes previously associated with the regulation of antimicrobial peptides. One of these, nipi-4 , encodes a member of a nematode-specific kinase family. NIPI-4 is predicted to be catalytically inactive, thus to be a pseudokinase. It acts in the epidermis downstream of the PKC∂ TPA-1, as a positive regulator of nlp antimicrobial peptide gene expression after infection. It also controls the constitutive expression of antimicrobial peptide genes of the cnc family that are targets of TGFß regulation. Our results open the way for a more detailed understanding of how host defense pathways can be molded by environmental pathogens.

CloudMap: A Cloud-Based Pipeline for Analysis of Mutant Genome Sequences

“…Our lab has previously developed single-step SNP mapping strategies coupled with whole genome sequencing as well as software analysis tools (MAQGene) for mutant genome sequence analysis (Bigelow et al 2009). Although MAQGene has been broadly used by labs in the C. elegans community (Flowers et al 2010 2010;Zhang et al 2011;Kim et al 2012;Labed et al 2012), we no longer support it because the pipeline relies on an outdated aligner (MAQ) and requires technical expertise to install, which inevitably limits its general adoption.In an effort to take advantage of cloud computing and many freely available open source tools, we have designed a new mutant genome sequence analysis pipeline to run on the Galaxy platform (Afgan et al 2011). Our pipeline uses custom Python scripts to provide greatly improved mutant mapping tools and relies on the Next Generation Sequencing (NGS) Toolbox software suite in Galaxy, along with other software adapted for Galaxy.…”

“…Our lab has previously developed single-step SNP mapping strategies coupled with whole genome sequencing as well as software analysis tools (MAQGene) for mutant genome sequence analysis (Bigelow et al 2009). Although MAQGene has been broadly used by labs in the C. elegans community (Flowers et al 2010 2010;Zhang et al 2011;Kim et al 2012;Labed et al 2012), we no longer support it because the pipeline relies on an outdated aligner (MAQ) and requires technical expertise to install, which inevitably limits its general adoption.…”

Evaluating alignment and variant-calling software for mutation identification in C. elegans by whole-genome sequencing

“…Hawaiian SNP frequencies are determined by variant calling, and then plotted on the physical map to identify the gap that defines the mutation interval. The density of annotated Hawaiian SNPs (roughly one per kilobase) allows mapping at high resolution, and the method has been widely adopted by the community (e.g., [2, 35–36, 40– 43]).…”

Mapping challenging mutations by whole-genome sequencing

“…successfully to identify a number of recessive mutations (e.g., Doitsidou et al 2010;Labed et al 2012;Liau et al 2013;Connolly et al 2014;Wang et al 2014;Jaramillo-Lambert et al 2015). With the exception of the strains that contain linked morphological markers (see below), we utilized the Hawaiian SNP mapping method described here for the characterization of different categories of mutations.…”