6 research outputs found
Interdomain interactions of the transactive response DNA binding protein 43 kDa (TDP-43)
Transactive response DNA binding protein, 43 kDa (TDP-43) is 416-residue RNA processing and transport protein, observed in insoluble cytoplasmic aggregates within affected neurons in neurodegenerative diseases. TDP-43 has three domains: the N-terminal (N), RNA-binding (R) and unstructured C-terminal domains (G). Unstructured domains often form intramolecular interactions regulating other domains; our goal was to determine if such an interaction occurs in TDP-43. In Far Western blots, tagged NR was observed to bind to G. A 10 residue C-terminal truncation of G virtually abolished binding and introduction of phosphomimetics at Ser409/Ser410 also reduced binding. Sedimentation velocity ultracentrifugation with tagged NR and G also revealed interaction, observed by a shift in sedimentation coefficients when compared to those of the individual polypeptides. In vivo colocalization studies confirmed a cellular interaction between fluorescently labeled NR and G. This interaction has potential implications for the regulation of TDP-43 and the mechanism of generation of aggregative forms
Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation
The E3 ligase parkin ubiquitinates outer mitochondrial membrane
proteins during oxidative stress and is linked to early-onset
Parkinson’s disease. Parkin is autoinhibited but is activated by the
kinase PINK1 that phosphorylates ubiquitin leading to parkin
recruitment, and stimulates phosphorylation of parkin’s N-terminal
ubiquitin-like (pUbl) domain. How these events alter the
structure of parkin to allow recruitment of an E2~Ub conjugate
and enhanced ubiquitination is an unresolved question. We
present a model of an E2~Ub conjugate bound to the phosphoubiquitin-loaded
C-terminus of parkin, derived from NMR chemical
shift perturbation experiments. We show the UbcH7~Ub conjugate
binds in the open state whereby conjugated ubiquitin binds to the
RING1/IBR interface. Further, NMR and mass spectrometry experiments
indicate the RING0/RING2 interface is re-modelled,
remote from the E2 binding site, and this alters the reactivity of
the RING2(Rcat) catalytic cysteine, needed for ubiquitin transfer.
Our experiments provide evidence that parkin phosphorylation
and E2~Ub recruitment act synergistically to enhance a weak
interaction of the pUbl domain with the RING0 domain and rearrange
the location of the RING2(Rcat) domain to drive parkin
activity
Distinct phosphorylation signals drive acceptor versus free ubiquitin chain targeting by Parkin
The RBR E3 ligase parkin is recruited to the outer mitochondrial membrane (OMM) during oxidative stress where it becomes activated and ubiquitinates numerous proteins. Parkin activation involves binding of a phosphorylated ubiquitin (pUb), followed by phosphorylation of the Ubl domain in parkin, both mediated by the OMM kinase, PINK1. How an OMM protein is selected for ubiquitination is unclear. Parkin targeted OMM proteins have little structural or sequence similarity, with the commonality between substrates being proximity to the OMM. Here, we used chimeric proteins, tagged with ubiquitin (Ub), to evaluate parkin ubiquitination of mitochondrial substrates. We find that pUb tethered to the mitochondrial target proteins, Miro1 or CISD1, is necessary for parkin recruitment and essential for target protein ubiquitination. Surprisingly, phosphorylation of parkin is not necessary for the ubiquitination of either Miro1 or CISD1. Thus, parkin lacking its Ubl domain efficiently ubiquitinates a substrate tethered to pUb. Instead, phosphorylated parkin appears to stimulate free Ub-chain formation. We also demonstrate that parkin ubiquitination of pUb-tethered substrates occurs on the substrate, rather than the pUb modification. We propose divergent parkin mechanisms whereby parkin-mediated ubiquitination of acceptor proteins is driven by binding to pre-existing pUb on the OMM protein and subsequent parkin phosphorylation triggers free Ub chain formation. This finding accounts for the broad spectrum of OMM proteins ubiquitinated by parkin and has implications on target design for therapeutics