The nuclear export of mRNAs is one of the key steps in eukaryotic gene expression, and involves the formation of mature and export competent mRNA ribonucleoparticles (mRNPs). Growing evidence indicates that post-translational modifications targeting different processing and export factors may play a role in regulating and remodeling the assembly of these mRNP complexes along the export pathway. Here, we show that Yra1 ubiquitination varies in a cell cycle dependent manner and we propose that the heterodimeric Slx5/Slx8 E3 ligase is involved in Yra1 ubiquitination. Notably, Slx5/Slx8 has been proposed to ubiquitinating SUMOylated and polySUMOylated proteins targeting them to degradation by the proteasome. Consistently, we find that Yra1 is also SUMOylated and that this modification, like ubiquitination, takes place at the C-terminal part of the protein. Interestingly, the absence of Slx5 or Slx8 seems not to impair mRNA export. However, loss of Slx5 and Slx8 has been shown to affect genome stability and several studies have linked Yra1 to replication. Consistent with a role of Yra1 in replication related functions, we found Cdc55, a phosphatase implicated in cell cycle regulation, as a high copy suppressor of the non ubiquitinated and non sumoylated Yra1 KR-all mutant. All together our observations indicate that, besides mRNA export, Yra1 may also contribute to cell cycle progression and that both functions may be regulated through different E3 ubiquitin ligases.