Cooling-induced SUMOylation of EXOSC10 down-regulates ribosome biogenesis

Abstract

The RNA exosome is essential for 3 ′ processing of functional RNA species and degradation of aberrant RNAs in eukaryotic cells. Recent reports have defined the substrates of the exosome catalytic domains and solved the multimeric structure of the exosome complex. However, regulation of exosome activity remains poorly characterized, especially in response to physiological stress. Following the observation that cooling of mammalian cells results in a reduction in 40S:60S ribosomal subunit ratio, we uncover regulation of the nuclear exosome as a result of reduced temperature. Using human cells and an in vivo model system allowing whole-body cooling, we observe reduced EXOSC10 (hRrp6, Pm/Scl-100) expression in the cold. In parallel, both models of cooling increase global SUMOylation, leading to the identification of specific conjugation of SUMO1 to EXOSC10, a process that is increased by cooling. Furthermore, we define the major SUMOylation sites in EXOSC10 by mutagenesis and show that overexpression of SUMO1 alone is sufficient to suppress EXOSC10 abundance. Reducing EXOSC10 expression by RNAi in human cells correlates with the 3 ′ preribosomal RNA processing defects seen in the cold as well as reducing the 40S:60S ratio, a previously uncharacterized consequence of EXOSC10 suppression. Together, this work illustrates that EXOSC10 can be modified by SUMOylation and identifies a physiological stress where this regulation is prevalent both in vitro and in vivo.

EXOSC10/Rrp6 is post-translationally regulated in male germ cells and controls the onset of spermatogenesis

“…This is interesting in light of Rrp6’s essential role for processing 5.8S rRNA in yeast 24 . It is also noteworthy that stress-induced down-regulation of EXOSC10 in a cultured cell system negatively affects ribosome biosynthesis, and that the protein interacts with MPHOSPH6, an enzyme associated with the exosome that is involved in processing 7S precursor rRNA into mature 5.8S rRNA 52 – 54 . Taken together, the results support the notion that protein translation in male germline development might at least in part be down-regulated via progressive depletion of EXOSC10.…”

Suboptimal T-cell receptor signaling compromises protein translation, ribosome biogenesis, and proliferation of mouse CD8 T cells

“…Methods were adapted and modified from a previous study (56). Cycloheximide (Sigma) was added to the media at 100 μg/mL for 10 min at 37°C at the end of the culture.…”

“…The experimental procedure was adapted from a previous publication (56). Total RNA was extracted from cells using an RNeasy kit (Qiagen) supplemented with 5 × 10 −5 M 2β-ME during the lysing step.…”

“…The procedure was adapted from a previous publication (56). For naive T cells, 32 P orthophosphate was added to the media to a final concentration of 20 μCi/mL, and the cells were cultured for 1 h before being stimulated with the SIINFEKL peptide.…”

EXOSC10 sculpts the transcriptome during the growth-to-maturation transition in mouse oocytes

“…EXOSC10 is a nuclear RNase, the absence of which causes RNA processing defects in yeast (Carneiro et al, 2007) and increased sensitivity to DNA damage in fly and human cells (Domingo-Prim et al, 2019;Rolfsmeier et al, 2011). EXOSC10 has been documented to promote mRNA turnover (van Dijk et al, 2007), 3' pre-rRNA processing (Knight et al, 2016) and long noncoding/enhancer RNA degradation (Pefanis et al, 2015). It also has been reported to control the onset of spermatogenesis in male germ cells (Jamin et al, 2017).…”