BACKGROUND: mRNA decay is central in the regulation of mRNA homeostasis in the cell. The recent discovery of a co-translational mRNA decay pathway (also called CTRD) has changed our understanding of the mRNA decay process. This pathway has emerged as an evolutionarily conversed mechanism essential for specific physiological processes in eukaryotes, especially in plants. In Arabidopsis, this pathway is targeted mainly by the exoribonuclease XRN4. However, the details of the molecular regulation of this pathway are still unclear. RESULTS: In this study, we first tested the role of the 3'-phosphoadenosine 5'-phosphate (PAP), an inhibitor of exoribonucleases in the regulation of CTRD. Using 5'Pseq approach, we discovered that FRY1 inactivation impaired XRN4-CTRD activity. Based on this finding, we demonstrated that exogenous PAP treatment stabilizes CTRD mRNA targets. Furthermore, we also tested the implication of the exoribonuclease DXO1 in CTRD regulation. We found that DXO1, another exoribonuclease sensitive to PAP, is also involved in the CTRD pathway, probably by targeting NAD-capped mRNAs. DXO1 specifically targets mRNAs linked to stress response. CONCLUSIONS: Our study provides further insights into the regulation of CTRD in Arabidopsis and demonstrates that other exoribonucleases can be implicated in this pathway.