Transcriptomic profiling of sex-specific olfactory neurons reveals subset-specific receptor expression in Caenorhabditis elegans.

The nematode Caenorhabditis elegans utilizes chemosensation to navigate an ever-changing environment for its survival. A class of secreted small-molecule pheromones, termed ascarosides, play an important role in olfactory perception by affecting biological functions ranging from development to behavior. The ascaroside #8 (ascr#8) mediates sex-specific behaviors, driving avoidance in hermaphrodites and attraction in males.

Cell-specific proteomic analysis in Caenorhabditis elegans.

Proteomic analysis of rare cells in heterogeneous environments presents difficult challenges. Systematic methods are needed to enrich, identify, and quantify proteins expressed in specific cells in complex biological systems including multicellular plants and animals. Here, we have engineered a Caenorhabditis elegans phenylalanyl-tRNA synthetase capable of tagging proteins with the reactive noncanonical amino acid p-azido-L-phenylalanine.

Analysis of Dom34 and its function in no-go decay.

Eukaryotic mRNAs are subject to quality control mechanisms that degrade defective mRNAs. In yeast, mRNAs with stalls in translation elongation are targeted for endonucleolytic cleavage by No-Go decay (NGD). The cleavage triggered by No-Go decay is dependent on Dom34p and Hbs1p, and Dom34 has been proposed to be the endonuclease responsible for mRNA cleavage.

Chapter 1. Methods to study no-go mRNA decay in Saccharomyces cerevisiae.

In eukaryotic cells, conserved mRNA surveillance systems target and degrade aberrant mRNAs, eliminating translation errors that occur during protein synthesis and thereby imposing quality control of gene expression. Two such cytoplasmic quality control systems, nonsense-mediated mRNA decay and nonstop mRNA decay, have evolved to target mRNAs with aberrancies in translation. A third novel quality control system has been identified for yeast mRNAs with defects in translation elongation due to strong translation pause sites.

RNA quality control in eukaryotes.

Eukaryotic cells contain numerous RNA quality-control systems that are important for shaping the transcriptome of eukaryotic cells. These systems not only prevent accumulation of nonfunctional RNAs but also regulate normal mRNAs, repress viral and parasitic RNAs, and potentially contribute to the evolution of new RNAs and hence proteins. These quality-control circuits can be viewed as a series of kinetic competitions between steps in normal RNA biogenesis or function and RNA degradation pathways.

Revenge of the NRD: preferential degradation of nonfunctional eukaryotic rRNA.

Eukaryotic cells have several quality control systems that monitor the proper processing of RNAs during RNA biogenesis or the function of cytoplasmic mRNAs. A recent study in Molecular Cell by LaRiviere et al. (2006) shows that after production, mature rRNA is also subject to quality control and nonfunctional ribosomes are targeted for destruction by a novel ribosome surveillance mechanism.

Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation.

A fundamental aspect of the biogenesis and function of eukaryotic messenger RNA is the quality control systems that recognize and degrade non-functional mRNAs. Eukaryotic mRNAs where translation termination occurs too soon (nonsense-mediated decay) or fails to occur (non-stop decay) are rapidly degraded. We show that yeast mRNAs with stalls in translation elongation are recognized and targeted for endonucleolytic cleavage, referred to as 'no-go decay'.