The Caenorhabditis elegans ekl (Enhancer of ksr-1 Lethality) Genes Include Putative Components of a Germline Small RNA Pathway

Abstract

A canonical Ras-ERK signaling pathway specifies the fate of the excretory duct cell during Caenorhabditis elegans embryogenesis. The paralogs ksr-1 and ksr-2 encode scaffolding proteins that facilitate signaling through this pathway and that act redundantly to promote the excretory duct fate. In a genomewide RNAi screen for genes that, like ksr-2, are required in combination with ksr-1 for the excretory duct cell fate, we identified 16 ''ekl '' (enhancer of ksr-1 lethality) genes that are largely maternally required and that have molecular identities suggesting roles in transcriptional or post-transcriptional gene regulation. These include the Argonaute gene csr-1 and a specific subset of other genes implicated in endogenous small RNA processes, orthologs of multiple components of the NuA4/Tip60 histone acetyltransferase and CCR4/NOT deadenylase complexes, and conserved enzymes involved in ubiquitination and deubiquitination. The identification of four small RNA regulators (csr-1, drh-3, ego-1, and ekl-1) that share the Ekl phenotype suggests that these genes define a functional pathway required for the production and/or function of particular germline small RNA(s). These small RNAs and the other ekl genes likely control the expression of one or more regulators of Ras-ERK signaling that function at or near the level of kinase suppressor of Ras (KSR).

Neuronal Migration Is Regulated by Endogenous RNAi and Chromatin-Binding Factor ZFP-1/AF10 in Caenorhabditis elegans

“…Similar to the regulation of embryonic HSN migration described here, both CSR-1 and DRH-3 have been implicated in another embryonic process: the specification of the excretory duct cell, a component of the worm's renal system (Rocheleau et al 2008). A genome-wide RNAi screen identified these RNAi pathway genes to act redundantly with the KSR-1 (kinase suppressor of Ras) scaffolding protein in Rasmediated excretory duct cell specification (Rocheleau et al 2008).…”

A Genomewide RNAi Screen for Genes That Affect the Stability, Distribution and Function of P Granules in Caenorhabditis elegans

“…Next we examined GFPTPGL-1 in drh-3(RNAi) germ lines. drh-3 encodes a DExH-box helicase that is required for RdRP activity and shares several phenotypes with ego-1 and csr-1 (Duchaine et al 2006;Yigit et al 2006;Aoki et al 2007;Rocheleau et al 2008;She et al 2009). Depletion of drh-3 phenocopied the PGL-1 phenotype observed in ego-1 and csr-1 RNAi germ lines ( Figure 8B), providing further evidence that DRH-3 functions in a pathway with EGO-1 and CSR-1.…”

“…CSR-1, EGO-1, and DRH-3 are thought to work together in a germ-line-specific endogenous siRNA pathway Robert et al 2005;Duchaine et al 2006;Yigit et al 2006;Aoki et al 2007;Rocheleau et al 2008;She et al 2009). Argonautes, like CSR-1, have been identified as germ granule components from worms to mammals (Kotaja et al 2006;Batista et al 2008;Wang and Reinke 2008).…”

“…csr-1 worms are also partially deficient in RNAi (Yigit et al 2006). It was recently discovered that csr-1 shares multiple phenotypes with ego-1 and drh-3, which encode an RdRP and an RdRP interacting factor required for small endogenous RNAi in the germ line (Aoki et al 2007;Rocheleau et al 2008;She et al 2009). …”

MAP Kinase Signaling Antagonizes PAR-1 Function During Polarization of the Early Caenorhabditis elegans Embryo

“…ntl-2 encodes a protein similar to NOT2, a component of the transcriptional regulatory complex CCR4/NOT. Reduction of function of ntl-2 is synthetic lethal with a mutation in ksr-1, a gene in the MAP kinase signaling pathway, indicating that this gene may impinge on MAP kinase signaling (Rocheleau et al 2008). Finally, mpk-1, the gene encoding the central kinase of the highly conserved MAP kinase pathway (Figure 2A), also suppressed embryonic lethality in a par-1 mutant background.…”