Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress‐dependent mRNAs

RNA‐binding proteins (RBPs) participate in all steps of gene expression, underscoring their potential as regulators of RNA homeostasis. We structurally and functionally characterize Mip6, a four‐RNA recognition motif (RRM)‐containing RBP, as a functional and physical interactor of the export factor Mex67. Mip6‐RRM4 directly interacts with the ubiquitin‐associated (UBA) domain of Mex67 through a loop containing tryptophan 442. Mip6 shuttles between the nucleus and the cytoplasm in a Mex67‐dependent manner and concentrates in cytoplasmic foci under stress. Photoactivatable ribonucleoside‐enhanced crosslinking and immunoprecipitation experiments show preferential binding of Mip6 to mRNAs regulated by the stress‐response Msn2/4 transcription factors. Consistent with this binding, MIP6 deletion affects their export and expression levels. Additionally, Mip6 interacts physically and/or functionally with proteins with a role in mRNA metabolism and transcription such as Rrp6, Xrn1, Sgf73, and Rpb1. These results reveal a novel role for Mip6 in the homeostasis of Msn2/4‐dependent transcripts through its direct interaction with the Mex67 UBA domain. Synopsis The RNA binding protein Mip6 interacts with the ubiquitin‐associated domain of Mex67 and attenuates the nuclear export of mRNAs regulated by the stress response Msn2/4 transcription factors. The key elements involved in Mip6/Mex67 interaction are a loop in Mip6 RRM4 containing tryptophan 442, and helix H2 of the Mex67 UBA domain. Mip6 binds to Msn2/4‐regulated transcripts attenuating their expression and export under non‐stress. Mip6 shuttles between the nucleus and the cytoplasm in a Mex67‐dependent manner and interacts with Rpb1, Sgf73, Rrp6 and Xrn1 along the gene expression pathway. Graphical Abstract The RNA binding protein Mip6 interacts with the ubiquitin‐associated domain of Mex67 and attenuates the nuclear export of mRNAs regulated by the stress response Msn2/4 transcription factors.