Regulation by the RNA-binding protein Unkempt at its effector interface.

How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here, we document the existence and functions of a multivalent RBP-effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of 'dual-purpose' peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP-effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for the reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP-effector interface.

A paradigm for regulation at the effector interface with RNA-binding proteins.

RNA-binding proteins (RBPs) are key regulators of gene expression, but how RBPs convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP-effector interface. We show that the effector interface of a deeply conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of 'dual-purpose' peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by the recruiting RBP. Systems analyses reveal that multivalent RBP-effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP-effector interface, with implications for the evolution and function of RBP-operated regulatory networks.

RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation.

The CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated mRNA degradation upon HDAC inhibition. Here, we explored acetylation-induced changes in the composition of the CCR4-NOT complex by purification of the endogenously tagged scaffold subunit NOT1 and identified RNF219 as an acetylation-regulated cofactor. We demonstrate that RNF219 is an active RING-type E3 ligase which stably associates with CCR4-NOT via NOT9 through a short linear motif (SLiM) embedded within the C-terminal low-complexity region of RNF219. By using a reconstituted six-subunit human CCR4-NOT complex, we demonstrate that RNF219 inhibits deadenylation through the direct interaction of the α-helical SLiM with the NOT9 module. Transcriptome-wide mRNA half-life measurements reveal that RNF219 attenuates global mRNA turnover in cells, with differential requirement of its RING domain. Our results establish RNF219 as an inhibitor of CCR4-NOT-mediated deadenylation, whose loss upon HDAC inhibition contributes to accelerated mRNA turnover.

Reduced brain cell proliferation following somatic injury is buffered by social interaction in electric fish, Apteronotus leptorhynchus.

In many species, the negative effects of aversive stimuli are mitigated by social interactions, a phenomenon termed social buffering. In one form of social buffering, social interactions reduce the inhibition of brain cell proliferation during stress. Indirect predator stimuli (e.g., olfactory or visual cues) are known to decrease brain cell proliferation, but little is known about how somatic injury, as might occur from direct predator encounter, affects brain cell proliferation and whether this response is influenced by conspecific interactions. Here, we assessed the social buffering of brain cell proliferation in an electric fish, Apteronotus leptorhynchus, by examining the separate and combined effects of tail injury and social interactions. We mimicked a predator-induced injury by amputating the caudal tail tip, exposed fish to paired interactions that varied in timing, duration and recovery period, and measured brain cell proliferation and the degree of social affiliation. Paired social interaction mitigated the negative effects of tail amputation on cell proliferation in the forebrain but not the midbrain. Social interaction either before or after tail amputation reduced the effect of tail injury and continuous interaction both before and after caused an even greater buffering effect. Social interaction buffered the proliferation response after short-term (1 d) or long-term recovery (7 d) from tail amputation. This is the first report of social buffering of brain cell proliferation in a non-mammalian model. Despite the positive association between social stimuli and brain cell proliferation, we found no evidence that fish affiliate more closely following tail injury.

Predation drives the evolution of brain cell proliferation and brain allometry in male Trinidadian killifish, Rivulus hartii.

The external environment influences brain cell proliferation, and this might contribute to brain plasticity underlying adaptive behavioural changes. Additionally, internal genetic factors influence the brain cell proliferation rate. However, to date, researchers have not examined the importance of environmental versus genetic factors in causing natural variation in brain cell proliferation. Here, we examine brain cell proliferation and brain growth trajectories in free-living populations of Trinidadian killifish, Rivulus hartii, exposed to contrasting predation environments. Compared to populations without predators, populations in high predation (HP) environments exhibited higher rates of brain cell proliferation and a steeper brain growth trajectory (relative to body size). To test whether these differences in the wild persist in a common garden environment, we reared first-generation fish originating from both predation environments in uniform laboratory conditions. Just as in the wild, brain cell proliferation and brain growth in the common garden were greater in HP populations than in no predation populations. The differences in cell proliferation observed across the brain in both the field and common garden studies indicate that the differences are probably genetically based and are mediated by evolutionary shifts in overall brain growth and life-history traits.