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Fishburn, J.

Publications and source records attributed to Fishburn, J..

3 recordsLinked to original sources

Senataxin loss induces cGAS–STING-mediated mitochondrial dysfunction

Ataxia with oculomotor apraxia type 2 (AOA2) is a rare neurodegenerative disease caused by loss-of-function mutations in Senataxin, which encodes an RNA:DNA helicase. Many studies on Senataxin loss focus on its putative roles in regulating transcription and RNA transcript localization. However, several phenotypes remain underexplored, including metabolic dysregulation associated with ataxias. Using Senataxin-deficient mouse cells, we observed increased nuclear and genomic instability, as well as innate immune activation via the cGAS-STING axis. We also observed elevated ROS levels, decreased mitochondrial function, and hyperfused mitochondria. Importantly, mitochondrial dysfunction depends on cGAS/STING activity, indicating that the two phenotypes are functionally connected. Senataxin-deficient mice and AOA2 patient cells similarly exhibit spontaneous innate immune activation, and AOA2 patient cells also show decreased mitochondrial function. Our work identifies a previously unseen phenotype for AOA2 in which loss of Senataxin results in mitochondrial dysfunction promoted by cGAS and STING. SummaryThis study demonstrates a previously unidentified phenotype in AOA2 and Senataxin research in which cGAS-STING promotes mitochondrial dysregulation in Setx-/- MEFs. Further, these innate immune activation and mitochondrial dysregulated phenotypes are recapitulated in AOA2 patient cells.

Cell Biology↗

The role of XPB/Ssl2 double-stranded DNA translocase processivity in transcription start-site scanning.

The general transcription factor TFIIH contains three ATP-dependent catalytic activities. TFIIH functions in nucleotide excision repair primarily as a DNA helicase and in Pol II transcription initiation as a dsDNA translocase and protein kinase. During initiation, the XPB/Ssl2 subunit of TFIIH couples ATP hydrolysis to dsDNA translocation facilitating promoter opening and the kinase module phosphorylates the C-terminal domain to facilitate the transition to elongation. These functions are conserved between metazoans and yeast; however, yeast TFIIH also drives transcription start-site scanning in which Pol II scans downstream DNA to locate productive start-sites. The ten-subunit holo-TFIIH from S. cerevisiae has a processive dsDNA translocase activity required for scanning and a structural role in scanning has been ascribed to the three-subunit TFIIH kinase module. Here, we assess the dsDNA translocase activity of ten-subunit holo- and core-TFIIH complexes (i.e. seven subunits, lacking the kinase module) from both S. cerevisiae and H. sapiens. We find that neither holo nor core human TFIIH exhibit processive translocation, consistent with the lack of start-site scanning in humans. Furthermore, in contrast to holo-TFIIH, the S. cerevisiae core-TFIIH also lacks processive translocation and its dsDNA-stimulated ATPase activity was reduced ~5-fold to a level comparable to the human complexes, potentially explaining the reported upstream shift in start-site observed in the absence of the S. cerevisiae kinase module. These results suggest that neither human nor S. cerevisiae core-TFIIH can translocate efficiently, and that the S. cerevisiae kinase module functions as a processivity factor to allow for robust transcription start-site scanning.

biochemistry↗

A high-throughput screen for transcription activation domains reveals their sequence characteristics and permits reliable prediction by deep learning

Transcription activation domains (ADs) are encoded by a wide range of seemingly unrelated amino acid sequences, making it difficult to recognize features that permit their dynamic behavior, fuzzy interactions and target specificity. We screened a large set of random 30-mer peptides for AD function and trained a deep neural network (ADpred) on the AD-positive and negative sequences. ADpred correctly identifies known ADs within protein sequences and accurately predicts the consequences of mutations. We show that functional ADs are (1) located within intrinsically disordered regions with biased amino acid composition, (2) contain clusters of hydrophobic residues near acidic side chains, (3) are enriched or depleted for particular dipeptide sequences, and (4) have higher helical propensity than surrounding regions. Taken together, our findings fit the model of "fuzzy" binding through hydrophobic protein-protein interfaces, where activator-coactivator binding takes place in a dynamic hydrophobic environment rather than through combinations of sequence-specific interactions.

molecular biology↗