An anti-inflammatory phenotype with pronounced immunosuppression develops during sepsis, during which time neutrophils and monocytes/macrophages limit their Toll-like receptor 4 responses to bacterial lipopolysaccharide (LPS/endotoxin). We previously reported that during this endotoxin-tolerant state, distinct signaling pathways differentially repress transcription and translation of proinflammatory cytokines such as TNFα and IL-6. Sustained endotoxin tolerance contributes to sepsis mortality. While transcription repression requires chromatin modifications, a translational repressor complex of Argonaute 2 (Ago2) and RNA-binding motif protein 4 (RBM4), which bind the 3′-UTR of TNFα and IL-6 mRNA, limits protein synthesis. Here, we show that Dcp1 supports the assembly of the Ago2 and RBM4 repressor complex into cytoplasmic processing bodies (p-bodies) in endotoxin-tolerant THP-1 human monocytes following stimulation with LPS, resulting in translational repression and limiting protein synthesis. Importantly, this translocation process is reversed by Dcp1 knockdown, which restores TNFα and IL-6 protein levels. We also find this translational repression mechanism in primary macrophages of septic mice. Because p-body formation is a critical step in mRNA translation repression, we conclude that Dcp1 is a major component of the translational repression machinery of endotoxin tolerance and may contribute to sepsis outcome.

mRNA decay is an important step in gene regulation, environmental responsiveness, and mRNA quality control. One such quality control pathway, Nonsense-mediated mRNA Decay (NMD), targets transcripts whose translation terminates prematurely. However, the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. The vast majority of NMD-regulated transcripts are normal-looking protein-coding mRNAs. Our bioinformatics analyses reveal that this set of NMD-regulated transcripts generally have lower translational efficiency, lower average codon optimality scores, and higher ratios of out-of-frame translation. General mRNA decay is predominantly mediated by decapping by the Dcp1-Dcp2 complex and 5' to 3' decay by Xrn1, but the exact mechanism of decapping regulation has remained largely unknown. Several in vitro and in vivo studies have revealed the importance of the C-terminal extension of Dcp2 and the identities of many decapping regulators that interact with the decapping complex. To better understand how decapping regulation is achieved by the C-terminal extension of Dcp2 we generated RNA-Seq libraries from a Dcp2 allele that lacks this portion of Dcp2 along with libraries from strains that contain single deletions of several decapping activators. Our transcriptome-wide results indicate that the C-terminal extension of Dcp2 is crucial for efficient regulation of decapping, and different decapping activators are responsible for targeting different sets of mRNAs. Considering the limited pool of Dcp1-Dcp2 in the cell decapping activators might be in competition for decapping complex binding. Collectively, our results yield valuable insights into the mechanism of substrate selection for mRNA quality control and decay in yeast.