Full-length NF-κB repressing factor contains an XRN2 binding domain.

Jana Alexandrova,David Piñeiro,Mark Stoneley,Rebekah Jukes-Jones,Ryan Mordue,Anne E Willis

doi:10.1042/bcj20190733

Jana Alexandrova, David Piñeiro + Show 4 more

Open Access

https://doi.org/10.1042/bcj20190733

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Abstract

NF-κB repressing factor (NKRF) was recently identified as an RNA binding protein that together with its associated proteins, the 5′–3′ exonuclease XRN2 and the helicase DHX15, is required to process the precursor ribosomal RNA. XRN2 is a multi-functional ribonuclease that is also involved in processing mRNAs, tRNAs and lncRNAs. The activity and stability of XRN2 are controlled by its binding partners, PAXT-1, CDKN2AIP and CDKN2AIPNL. In each case, these proteins interact with XRN2 via an XRN2 binding domain (XTBD), the structure and mode of action of which is highly conserved. Rather surprisingly, although NKRF interacts directly with XRN2, it was not predicted to contain such a domain, and NKRF's interaction with XRN2 was therefore unexplained. We have identified an alternative upstream AUG start codon within the transcript that encodes NKRF and demonstrate that the full-length form of NKRF contains an XTBD that is conserved across species. Our data suggest that NKRF is tethered in the nucleolus by binding directly to rRNA and that the XTBD in the N-terminal extension of NKRF is essential for the retention of XRN2 in this sub-organelle. Thus, we propose NKRF regulates the early steps of pre-rRNA processing during ribosome biogenesis by controlling the spatial distribution of XRN2 and our data provide further support for the XTBD as an XRN2 interacting motif.

Highlights

Ribosomes are complex macromolecular machines that translate the genetic code into functional polypeptides
NF-κB repressing factor (NKRF), which was recently shown to have a role in ribosome biogenesis [8,9], was originally identified as a 43.8 kDa protein that repressed the transcriptional activity of NF-κB and constitutively silenced the IFN-β promoter [16]
Spatial control of multi-functional RNA binding proteins (RBPs) is required for a large number of key cellular processes including ribosome biogenesis, stress signalling and cell cycle progression [19,20,21,22,23]

Summary

Introduction

Ribosomes are complex macromolecular machines that translate the genetic code into functional polypeptides. Shifts AUG2 in the longer NKRF mRNA into the same reading frame as the previously identified coding region, extending the open reading frame to encode a 784 amino acid protein with a predicted molecular mass of 88 kDa. Importantly, the amino acid sequence of this N-terminal extension is highly conserved between mammalian species (Supplementary Figure S1C) with all corresponding genomic sequences containing an additional cytosine when compared with the human reference sequence.

Results

Conclusion