Welcome to the Paull Lab

Research in the Paull lab is focused on the DNA damage response in eukaryotic cells, specifically the checkpoint activation and DNA repair responses that occur immediately after the introduction of chromosomal double-strand breaks. Several components of these DNA damage response systems have been implicated as tumor suppressors in mammals, and nearly all of the proteins we study are involved in the maintenance of genomic stability in eukaryotic organisms. We are also interested in the regulation of redox control and signaling that occurs in response to oxidative stress in human cells. To study these processes, we use biochemistry and molecular biology-based tools to understand how critical proteins in these pathways function and are regulated in response to stress. Learn more...

Recent Publications

Rajashree A. Deshpande, Alberto Marin-Gonzalez, Hannah K. Barnes, Phillip R. Woolley, Taekjip Ha, and Tanya T. Paull. “Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice.” Nature Communications, 14, 1, Pp. 5759. Publisher's Version Abstract
The Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5ʹ strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site—a role we postulate is played by DNA-dependent protein kinase (DNA-PK) in mammals. Here we interrogate sites of MRN-dependent processing by identifying sites of CtIP association and by sequencing DNA-PK-bound DNA fragments that are products of MRN cleavage. These intermediates are generated most efficiently when DNA-PK is catalytically blocked, yielding products within 200 bp of the break site, whereas DNA-PK products in the absence of kinase inhibition show greater dispersal. Use of light-activated Cas9 to induce breaks facilitates temporal resolution of DNA-PK and Mre11 binding, showing that both complexes bind to DNA ends before release of DNA-PK-bound products. These results support a sequential model of double-strand break repair involving collaborative interactions between homologous and non-homologous repair complexes.
Rajashree A Deshpande and Tanya T Paull. “Characterization of DNA-PK-Bound End Fragments Using GLASS-ChIP.” Methods Mol Biol, 2444, Pp. 171-182. Abstract
Endonucleolytic cleavage of DNA ends by the human Mre11-Rad50-Nbs1 (MRN) complex occurs in a manner that is promoted by DNA-dependent protein kinase (DNA-PK). A method is described to isolate DNA-PK-bound fragments released from chromatin in human cells using a modified Gentle Lysis and Size Selection chromatin immunoprecipitation (GLASS-ChIP) protocol. This method, combined with real-time PCR or next-generation sequencing, can identify sites of MRN endonucleolytic cutting adjacent to DNA-PK binding sites in human cells.
Ji-hoon Lee, Seung W Ryu, Nicolette A Ender, and Tanya T Paull. “Poly-ADP-ribosylation drives loss of protein homeostasis in ATM and Mre11 deficiency.” Mol Cell, 81, 7, Pp. 1515-1533.e5. Abstract
Loss of the ataxia-telangiectasia mutated (ATM) kinase causes cerebellum-specific neurodegeneration in humans. We previously demonstrated that deficiency in ATM activation via oxidative stress generates insoluble protein aggregates in human cells, reminiscent of protein dysfunction in common neurodegenerative disorders. Here, we show that this process is driven by poly-ADP-ribose polymerases (PARPs) and that the insoluble protein species arise from intrinsically disordered proteins associating with PAR-associated genomic sites in ATM-deficient cells. The lesions implicated in this process are single-strand DNA breaks dependent on reactive oxygen species, transcription, and R-loops. Human cells expressing Mre11 A-T-like disorder mutants also show PARP-dependent aggregation identical to ATM deficiency. Lastly, analysis of A-T patient cerebellum samples shows widespread protein aggregation as well as loss of proteins known to be critical in human spinocerebellar ataxias that is not observed in neocortex tissues. These results provide a hypothesis accounting for loss of protein integrity and cerebellum function in A-T.
Seung W Ryu, Rose Stewart, Chase D Pectol, Nicolette A Ender, Oshadi Wimalarathne, Ji-hoon Lee, Carlos P Zanini, Antony Harvey, Jon M Huibregtse, Peter Mueller, and Tanya T Paull. “Proteome-wide identification of HSP70/HSC70 chaperone clients in human cells.” PLoS Biol, 18, 7, Pp. e3000606. Abstract
The 70 kDa heat shock protein (HSP70) family of chaperones are the front line of protection from stress-induced misfolding and aggregation of polypeptides in most organisms and are responsible for promoting the stability, folding, and degradation of clients to maintain cellular protein homeostasis. Here, we demonstrate quantitative identification of HSP70 and 71 kDa heat shock cognate (HSC70) clients using a ubiquitin-mediated proximity tagging strategy and show that, despite their high degree of similarity, these enzymes have largely nonoverlapping specificities. Both proteins show a preference for association with newly synthesized polypeptides, but each responds differently to changes in the stoichiometry of proteins in obligate multi-subunit complexes. In addition, expression of an amyotrophic lateral sclerosis (ALS)-associated superoxide dismutase 1 (SOD1) mutant protein induces changes in HSP70 and HSC70 client association and aggregation toward polypeptides with predicted disorder, indicating that there are global effects from a single misfolded protein that extend to many clients within chaperone networks. Together these findings show that the ubiquitin-activated interaction trap (UBAIT) fusion system can efficiently isolate the complex interactome of HSP chaperone family proteins under normal and stress conditions.
Chung-Hsuan Kao, Seung W Ryu, Min J Kim, Xuemei Wen, Oshadi Wimalarathne, and Tanya T Paull. “Growth-Regulated Hsp70 Phosphorylation Regulates Stress Responses and Prion Maintenance.” Mol Cell Biol, 40, 12. Abstract
Maintenance of protein homeostasis in eukaryotes under normal growth and stress conditions requires the functions of Hsp70 chaperones and associated cochaperones. Here, we investigate an evolutionarily conserved serine phosphorylation that occurs at the site of communication between the nucleotide-binding and substrate-binding domains of Hsp70. Ser151 phosphorylation in yeast Hsp70 (Ssa1) is promoted by cyclin-dependent kinase (Cdk1) during normal growth. Phosphomimetic substitutions at this site (S151D) dramatically downregulate heat shock responses, a result conserved with HSC70 S153 in human cells. Phosphomimetic forms of Ssa1 also fail to relocalize in response to starvation conditions, do not associate with Hsp40 cochaperones Ydj1 and Sis1, and do not catalyze refolding of denatured proteins in cooperation with Ydj1 and Hsp104. Despite these negative effects on HSC70/HSP70 function, the S151D phosphomimetic allele promotes survival of heavy metal exposure and suppresses the Sup35-dependent [ ] prion phenotype, consistent with proposed roles for Ssa1 and Hsp104 in generating self-nucleating seeds of misfolded proteins. Taken together, these results suggest that Cdk1 can downregulate Hsp70 function through phosphorylation of this site, with potential costs to overall chaperone efficiency but also advantages with respect to reduction of metal-induced and prion-dependent protein aggregate production.

Contact Us

2500 Speedway, MBB 2.448, Stop A5000, Austin, Texas 78712
e: tpaull@utexas.edu | p: (512) 232-7803 | f: (512) 471-3730

Latest News & Events

Robert and Jeffrey

ILSGP Annual Retreat

September 9, 2023
Robert Marrick and Jeffrey You presented posters at the ILSGP Annual Retreat
Jeffrey You with NEB Award

Jeffrey You wins Forum award

April 14, 2023
Jeffrery You received the New England BioLabs Award for Excellence in Molecular Biology for his presentation Interrogating the Senescence Associated Secretory Phenotype (SASP) and its dependence on the ATM Interacting protein (ATMIN) at the 2023 CNS Undergraduate Research Forum.