bioRxiv Science⌕ Search

Biology subjects

Mistry, A.

Publications and source records attributed to Mistry, A..

10 recordsLinked to original sources

A novel mechanism of ubiquitin-charging a bivalent E2:RING E3 complex

Protein ubiquitination results from a cascade of enzyme interactions that transfer ubiquitin from one covalent bond to another. First, an E1 is activated by attaching ubiquitin to itself through a thioester bond. Next, in E2 charging, activated E1 interacts with an E2 and transfers ubiquitin to a thioester bond on the E2. Finally, an E3 mediates the transfer of ubiquitin from a charged E2 to an isopeptide bond on a protein target. RING E3s, the largest E3 family in eukaryotes, function as scaffolds rather than enzymes and facilitate direct transfer of ubiquitin from a charged E2 to a protein target by simultaneously engaging both. All RING E3s engage an E2 at an interface that overlaps with the E1-binding site and several form stable, bivalent complexes with an E2 through additional binding surfaces. How E2 charging proceeds within these complexes remains unclear.Here, we utilize human Rad6(Rad18)2 as a model bivalent E2:RING E3 complex to delineate the interplay of protein{middle dot}protein interactions among the primary human E1 (Uba1), an E2 (Rad6), and a RING E3 (Rad18) during E2 charging. Collectively, the results reveal a novel mechanism that is not directed by ubiquitin thioester affinity switches. Rather, interactions of Rad18 with Rad6 slow the chemistry step and all preceding steps of the Uba1 catalytic cycle via competitive inhibition but accelerate release of charged Rad6 from Uba1, ultimately stimulating Rad6 charging overall. To the best of our knowledge, this represents the first example of a RING E3 stimulating Uba1-dependent charging of an E2.

biochemistry↗

Structural elements required for the efficient loading and activation of HELB on RPA-coated single-stranded DNA

HELB is a human helicase involved in DNA repair and replication that interacts physically with the single-stranded DNA binding protein RPA. ATP-dependent translocation of HELB along ssDNA results in the active displacement of RPA molecules and the formation of ssDNA loops, suggesting that HELB contains at least two DNA binding sites. In this work, we investigated the role of HELB-specific structural elements in facilitating interactions between HELB and RPA-coated DNA. We show that a predicted OB-fold in the N-terminal region of the protein is important both for loop extrusion and RPA displacement. We confirm that a HELB-specific-motif within the RecA-like helicase/translocase domains is critical for binding RPA in solution but that, once HELB is bound to ssDNA, is dispensable for RPA displacement. We propose a model for RPA displacement in which both structural elements play important roles in the recruitment and activation of HELB at RPA-ssDNA filaments. SIGNIFICANCE STATEMENTSingle-stranded DNA generated during replication and repair is rapidly coated by replication protein A (RPA), creating a protected filament that must nevertheless remain accessible to DNA-processing enzymes. We show that the human DNA helicase HELB uses two specialised structural elements to overcome this problem. A HELB-specific RPA-binding motif promotes recruitment, whereas a predicted OB domain enables DNA looping and efficient RPA displacement. Removing these elements modestly enhances activity on naked ssDNA while impairing loading and activation on RPA- coated DNA. This reveals how helicase accessory domains restrain inappropriate motor activity while targeting the intended nucleoprotein substrate. Human HELB variants linked to reproductive ageing map to these regulatory regions, suggesting a connection between impaired RPA dynamics and reproductive health.

biochemistry↗

Dissecting the role of PCNA and Pif1 in replication of individual DNA molecules by DNA polymerase δ.

PCNA loading and stabilization at primer-template junctions is crucial for processive DNA synthesis by replicative polymerases. It is also essential for strand displacement synthesis during Break Induced Replication (BIR). In this study, we employed a single molecule approach to directly visualize the role of PCNA, DNA polymerase {delta} and the Pif1 DNA helicase in these pathways. We first dissected the preferential loading of PCNA by RFC to 3-junctions of gaps, nicks and flapped substrates. Moreover, we found that Pol {delta} and Pif1 both stabilize loaded PCNA and reduce its diffusion coefficient along DNA. We further show that the interaction of PCNA with Pol {delta} is essential for gap-filling synthesis. On a 5-flapped substrate, we show that both Pol {delta} and Pif1 are required for strand displacement synthesis, while PCNA is not; although, it stimulates the process.

biochemistry↗

Impact of integration on persistent homology clustering and biological signal detection in scRNA-seq data

BackgroundAs the availability of single-cell RNA sequencing (scRNA-seq) data expands, there is a growing need for robust methods that enable integration and comparison across diverse biological conditions and experimental protocols. Persistent homology (PH), a technique from topological data analysis (TDA), provides a deformation-invariant framework for capturing structural patterns in high-dimensional data. MethodsIn this study, PH was applied to a diverse collection of scRNA-seq datasets spanning eight tissue types to investigate how data integration affects the topological features and biological interpretability of the resulting representations. Clustering was performed based on PH-derived pairwise distances and global topological structure was assessed through Betti curves, Euler characteristics, and persistence landscapes. By comparing these summaries across raw, normalized, and integrated datasets, we examined whether integration enhances the detection of biologically meaningful patterns, or, conversely, obscures fine-scale structure. ResultsThis approach demonstrates that PH can serve as a powerful complementary strategy for evaluating the impact of integration and reveals how topological summaries can help disentangle biological signal from batch-related noise in single-cell data. This work establishes a framework for using topological methods to assess integration quality and highlights new avenues for interpreting complex transcriptomic landscapes beyond conventional clustering.

bioinformatics↗

Mechanism of RPA phosphocode priming and tuning by Cdk1/Wee1 signaling circuit

Replication protein A (RPA) is a heterotrimeric single-strand DNA binding protein that is integral to DNA metabolism. Segregation of RPA functions in response to DNA damage is fine-tuned by hyperphosphorylation of the RPA32 subunit that is dependent on Cyclin-dependent kinase (Cdk)-mediated priming phosphorylation at the Ser-23 and Ser-29 sites. However, the mechanism of priming-driven hyperphosphorylation of RPA remains unresolved. Furthermore, the modulation of cell cycle progression by the RPA-Cdk axis is not clearly understood. Here, we uncover that the RPA70 subunit is also phosphorylated by Cdk1 at Thr-191. This modification is crucial for the G2 to M phase transition. This function is enacted through reciprocal regulation of Cdk1 activity through a feedback circuit espoused by stabilization of Wee1 kinase. The Thr-191 phosphosite on RPA70 is also crucial for priming hyperphosphorylation of RPA32 in response to DNA damage. Structurally, phosphorylation by Cdk1 primes RPA by reconfiguring the domains to release the N-terminus of RPA32 and the two protein-interaction domains that markedly enhances the efficiency of multisite phosphorylation by other kinases. Our findings establish a unique phosphocode-dependent feedback mechanism between RPA and RPA-regulating kinases that is fine-tuned to enact bipartite functions in cell cycle progression and DNA damage response.

biochemistry↗

Rad52 sorts and stacks Rad51 at the DNA junction to promote homologous recombination

Homologous recombination (HR) repairs double-stranded DNA breaks (DSBs). The DSBs are resected to yield single-stranded DNA (ssDNA) that are coated by Replication Protein A (RPA). Rad51 is a recombinase and catalyzes strand invasion and the search for homology. However, it binds to ssDNA with lower affinity than RPA. Thus, mediator proteins such as Rad52/BRCA2 are required to promote Rad51 binding to RPA-coated ssDNA, but the underlying mechanisms remain poorly understood. Saccharomyces cerevisiae Rad52 interacts with Rad51 through two distinct binding modes. We here uncover that the Rad51-binding site in the disordered C-terminus of Rad52 (mode-1) sorts polydisperse Rad51 into discrete monomers. The second Rad51 binding site resides in the ordered N-terminal ring of Rad52 (mode-2), but this interaction occurs at only one position on the ring. In single molecule confocal fluorescence microscopy combined with optical tweezer analysis, we directly visualize filament formation using fluorescent-Rad51. Rad52 catalyzes Rad51 loading onto RPA-coated ssDNA, with a distinct preference for junctions, but no filament growth is observed. Deletion of the C-terminus of Rad52 results in loss of Rad51 sorting and abrogates Rad51 binding to RPA-coated DNA. While BRCA2 and Rad52 are structurally unrelated, many of these functional features are conserved. We describe a concerted Sort & Stack mechanism for mediator proteins in promoting HR.

biochemistry↗

Mechanisms of action and synergies of a novel lipid IVA biosynthesis inhibitor

The development of novel antimicrobials provides additional treatment options for infectious diseases, including antimicrobial resistant infections. There are many hurdles to antimicrobial development and identifying an antimicrobials mechanism of action is a crucial step in progressing candidate molecules through the drug discovery pipeline. We used the genome wide screening method TraDIS-Xpress to identify genes in two model Gram-negative bacteria that affected sensitivity to three analogues of a novel antimicrobial compound (OPT-2U1). TraDIS-Xpress identified that all three analogues targeted the lipid IVA biosynthetic pathway in E. coli and Salmonella Typhimurium. Specifically, we determined that the antimicrobial target was likely to be LpxD, and validated this by finding a 5 log2-fold increase in the MIC of the OPT-2U1 analogues in E. coli when lpxD was overexpressed. Synergies were identified between OPT-2U1 analogues combined with rifampicin or colistin, to varying strengths, in both E. coli and S. Typhimurium. LPS composition was a likely reason for differences between E. coli and S.Typhimurium, as perturbation of LPS synthesis affected synergy between antibiotics and OPT-2U1 analogues. Finally, genes involved in ATP synthesis and membrane signalling functions were also found to affect the synergy between colistin and OPT-2U1 analogues. TraDIS-Xpress has proven a powerful tool to rapidly assay all genes (and notably, essential genes) within a bacterium for roles in dictating antimicrobial sensitivity. This study has confirmed the predicted target pathway of OPT-2U1 and identified synergies which could be investigated for development of novel antimicrobial formulations. Data SummaryNucleotide sequence data supporting the analysis in this study has been deposited in ArrayExpress under the accession number E-MTAB-13250. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

molecular biology↗

Pan-cancer Analysis Predicts Kindlin-associated Global Mechanochemical Perturbation

Kindlins are mechanosensitive adapter proteins that connect extracellular mechanical cues to intracellular chemical events. Any alterations in these proteins thus alter cellular signaling, which could result in cancer progression. However, their involvement in global mechanochemical signals remains elusive in cancers. Here we analyze pan-cancer samples to decipher how kindlin alterations aid cancer progression. We show that kindlin alterations, at both the genetic and mRNA level, dysregulates cellular behavior which significantly correlate with poor survival. We find that while these alterations are cancer-specific, they are prevalent in advanced tumor stages and metastatic onset. We observe that kindlins co-alter with a substantial fraction of human mechanochemical proteome in various tumors. Our analysis suggests how kindlin alterations aid tumor-promoting signals with a synergistic effect from alterations of cancer-hallmark genes. Notably, we demonstrate a consistent alteration of epithelial-mesenchymal-transition markers with kindlin activity. Overall, our study highlights how kindlin alterations could affect metabolism, genomic instability, and signal disruption via their interactome network, causing cancer and suggests targeting them as a therapeutic strategy.

cancer biology↗

Trimethylamine N-oxide (TMAO) enhances substrate mechanical stability probed by single molecule magnetic tweezers

Trimethylamine N-oxide (TMAO) is a well-known osmolyte to stabilize the folded proteins through a variety of mechanisms. Since mechanical strength of proteins is a critical determinant of its stabilization, TMAO might play a relevant role by favoring its folding dynamics or by enhancing its mechanical stability. To address this question, we have performed the single-molecule magnetic tweezers experiment to explore the TMAO effect on two structurally distinct substrates-protein L and talin. We observed that TMAO increases the mechanical stability of these proteins through increasing their unfolding force. Additionally, we are able to demonstrate that TMAO retards the unfolding kinetics, while accelerating the refolding kinetics under force; which eventually tilts the energy landscape towards the folded state. Interestingly, this TMAO-enhanced protein folding generates mechanical work output upto [~]67 zJ, allowing the protein folding under higher force regime. Overall this TMAO-enhanced mechanical stability provides a significant implication to folding-induced structural stability of proteins.

biophysics↗

Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation

Dosage compensation between the sexes has emerged independently multiple times during evolution, often harnessing long noncoding RNAs (lncRNAs) to alter gene expression on the sex chromosomes. In eutherian mammals, X chromosome inactivation (XCI) in females proceeds via the lncRNA Xist, which coats one of the two X chromosomes and recruits repressive proteins to epigenetically silence gene expression in cis1,2. How Xist evolved new functional RNA domains to recruit ancient, pleiotropic protein partners is of great interest. Here we show that Spen, an Xist-binding repressor protein essential for XCI3-7, binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation leads to de-repression of a subset of endogenous retroviral (ERV) elements in embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A-repeat of Xist, a region critical for Xist-mediated gene silencing8-9. ERV RNA and Xist A-repeat bind the RRM3 domain of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in local gene silencing in cis. These results suggest that insertion of an ERV element into proto-Xist may have been a critical evolutionary event, which allowed Xist to coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.

genomics↗