Gergely Róna

NYU School of Medicine and Howard Hughes Medical Institute

Intracellular degradation of proteins and organelles by the autophagy-lysosome system is essential for cellular quality control and energy homeostasis. Besides degradation, endolysosomal organelles can fuse with the plasma membrane and contribute to unconventional secretion. Here, we identify a function for mammalian SKP1 in endolysosomes that is i...

Immune-checkpoint blockade has revolutionized cancer treatment, but some cancers, such as acute myeloid leukemia (AML), do not respond or develop resistance. A potential mode of resistance is immune evasion of T cell immunity involving aberrant major histocompatibility complex class I (MHC-I) antigen presentation (AP). To map such mechanisms of res...

Small-cell lung cancer (SCLC) is an aggressive neuroendocrine lung cancer. Oncogenic MYC amplifications drive SCLC heterogeneity, but the genetic mechanisms of MYC amplification and phenotypic plasticity, characterized by neuroendocrine and nonneuroendocrine cell states, are not known. Here, we integrate whole-genome sequencing, long-range optical...

Cells must avoid licensing of neosynthesized DNA to prevent rereplication. In this issue of Molecular Cell, Ratnayeke et al. (2022)1 reveal how the licensing factor CDT1, prior to its degradation, inhibits DNA elongation by suppressing CMG helicase progression at replication forks.

The risk of zoonotic coronavirus spillover into the human population, as highlighted by the SARS-CoV-2 pandemic, demands the development of pan-coronavirus antivirals. The efficacy of existing antiviral ribonucleoside/ribonucleotide analogs, such as remdesivir, is decreased by the viral proofreading exonuclease NSP14-NSP10 complex. Here, using a no...

Mammalian development, adult tissue homeostasis and the avoidance of severe diseases including cancer require a properly orchestrated cell cycle, as well as error-free genome maintenance. The key cell-fate decision to replicate the genome is controlled by two major signalling pathways that act in parallel—the MYC pathway and the cyclin D–cyclin-dep...

D-type cyclins are central regulators of the cell division cycle and are among the most frequently deregulated therapeutic targets in human cancer¹, but the mechanisms that regulate their turnover are still being debated2,3. Here, by combining biochemical and genetics studies in somatic cells, we identify CRL4AMBRA1 (also known as CRL4DCAF3) as the...

Significance Understanding the functions of the genes encoded in the SARS-CoV-2 genome is imperative to understanding its pathogenesis. One unique feature of the SARS-CoV-2 genome is ORF10, a small putative protein that was hypothesized to promote infection by hijacking a cellular E3 ubiquitin ligase, CRL2 ZYG11B . Here, we investigate whether ORF1...

DNA damage repair maintains the genetic integrity of cells in a highly reactive environment. Cells may accumulate various types of DNA damage due to both endogenous and exogenous sources such as metabolic activities or UV radiation. Without DNA repair, the cell's genetic code becomes compromised, undermining the structures and functions of proteins...

Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug treatments in human cancer cell...

Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug treatments in human cancer cell...

Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug treatments in human cancer cell...

Background: The SMC5/6 complex, cohesin and condensin are the three mammalian members of the structural maintenance of chromosomes (SMC) family, large ring-like protein complexes that are essential for genome maintenance. The SMC5/6 complex is the least characterized complex in mammals; however, it is known to be involved in homologous recombinati...

Raw, not cropped supporting Western blot files for: Rona, G., ... Pagano, M.: PARP1-dependent recruitment of the FBXL10-RNF68-RNF2 ubiquitin ligase to sites of DNA damage controls H2A.Z loading. Elife 7 (2018). DOI: http://dx.doi.org/10.17632/2k5jvkswvr.2#folder-d87d4fc5-dc24-4b66-9dc8-5914340a56b6

Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug-treatment in human cancer cell-...

Diverse linkage in polyubiquitin chain structure gives cells an unparalleled complexity to virtually modulate all aspects of cell biology. Substrates can be covalently modified by ubiquitin chains of different topology. Proper DNA damage response takes advantage of this regulatory system and heavily relies on ubiquitin-based signaling. Moreover, in...

Epithelial to mesenchymal transition (EMT) is a multipurpose process involved in wound healing, development, and certain pathological processes, such as metastasis formation. The Tks4 scaffold protein has been implicated in cancer progression; however, its role in oncogenesis is not well defined. In this study, the function of Tks4 was investigated...

Sanitization of nucleotide pools is essential for genome maintenance. Deoxyuridine 5′-triphosphate nucleotidohydrolase (dUTPase) is a key enzyme in this pathway since it catalyzes the cleavage of 2′-deoxyuridine 5′-triphosphate (dUTP) into 2′-deoxyuridine 5′-monophosphate (dUMP) and inorganic pyrophosphate. Through its action dUTPase efficiently pr...

The mammalian FBXL10-RNF68-RNF2 ubiquitin ligase complex (FRRUC) mono-ubiquitylates H2A at Lys119 to repress transcription in unstressed cells. We found that the FRRUC is rapidly and transiently recruited to sites of DNA damage in a PARP1- and TIMELESS-dependent manner to promote mono-ubiquitylation of H2A at Lys119, a local decrease of H2A levels,...

Raw data for all graphs in main figures and figure supplements.

Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting techni...

SLBP (stem-loop binding protein) is a highly conserved factor necessary for the processing, translation, and degradation of H2AFX and canonical histone mRNAs. We identified the F-box protein cyclin F, a substrate recognition subunit of an SCF (Skp1-Cul1-F-box protein) complex, as the G2 ubiquitin ligase for SLBP. SLBP interacts with cyclin F via an...

Proteins are translated in the cytoplasm, but many need to access the nucleus to perform their functions. Understanding how these nuclear proteins are transported through the nuclear envelope and how the import processes are regulated is therefore an important aspect of understanding cell function. Structural biology has played a key role in unders...

The role of uracil in genomic DNA has been recently re-evaluated. It is now widely accepted to be a physiologically important DNA element in diverse systems from specific phages to antibody maturation and Drosophila development. Further relevant investigations would largely benefit from a novel reliable and fast method to gain quantitative and qual...

dUTPase is a dNTP sanitizing enzyme that prevents the appearance of the potentially harmful uracil bases in DNA by hydrolyzing cellular dUTP. This function of dUTPase is found to be essential in many organisms including Drosophila melanogaster. Previously we showed that the expression pattern of dUTPase determines the extent of uracil accumulation...

Nucleocytoplasmic trafficking of large macromolecules requires an active transport machinery. In many cases, this is initiated by binding of the nuclear localization signal ( NLS ) peptide of cargo proteins to importin‐α molecules. Fine orchestration of nucleocytoplasmic trafficking is of particularly high importance for proteins involved in mainte...

The authors respond to a comment by Alvisi & Jans [(2014), Acta Cryst. D70, 27752776] on the article Phosphorylation adjacent to the nuclear localization signal of human dUTPase abolishes nuclear import: structural and mechanistic insights[Rna et al. (2013), Acta Cryst. D69, 24952505].

Transfer of phage-related pathogenicity islands of Staphylococcus aureus (SaPI-s) was recently reported to be activated by helper phage dUTPases. This is a novel function for dUTPases otherwise involved in preservation of genomic integrity by sanitizing the dNTP pool. Here we investigated the molecular mechanism of the dUTPase-induced gene expressi...

Abstract Phosphorylation by the cyclin-dependent kinase 1 (Cdk1) adjacent to nuclear localization segments (NLSs) is an important mechanism of regulation of nucleocytoplasmic transport. However, no systematic survey has yet been performed in human cells to analyze this regulatory process, and the corresponding cell-cycle dynamics have not yet been...

Genome integrity requires well controlled cellular pools of nucleotides. dUTPases are responsible for regulating cellular dUTP levels and providing dUMP for dTTP biosynthesis. In Staphylococcus , phage dUTPases are also suggested to be involved in a moonlighting function regulating the expression of pathogenicity-island genes. Staphylococcal phage...

Phosphorylation adjacent to nuclear localization signals (NLSs) is involved in the regulation of nucleocytoplasmic transport. The nuclear isoform of human dUTPase, an enzyme that is essential for genomic integrity, has been shown to be phosphorylated on a serine residue (Ser11) in the vicinity of its nuclear localization signal; however, the effect...

A thermophilic strain producing an extracellular esterase/lipase was isolated from a hot spring in Tăşnad, Romania, and was identified phenotypically and by 16S rDNA sequencing as Anoxybacillus flavithermus (GenBank ID: JQ267733). The gene encoding the putative carboxyl esterase (GenBank ID: JX494348) was cloned by direct PCR amplification from gen...

Luminescent nanocrystals or quantum dots (QDs) have great potential for bioanalysis as well as optoelectronics. Here we report an effective and inexpensive fabrication method of silicon carbide quantum dots (SiC QDs), with diameter below 8 nm, based on electroless wet chemical etching. Our samples show strong violet-blue emission in the 410–450 nm...

Percentage of fluorescent cells upon transfection with normal (T pl.) or uracil-substituted plasmids (U pl.). (A) Drosophila S2 cells, (B) HeLa cells. The number of observed fluorescent cells is also presented within the bars together with the total number of scored cells (shown in brackets). (PDF)

Genomic position of UAS-IR constructs in dUTPase RNAi stocks. (PDF)

dUTPase transgene rescues the dUTPase RNAi phenotype. Table shows the results of the rescue crosses. UAS-IR/SM6b; UAS-dUTPase-FLAG/TM3 males were crossed to Act-Gal4/CyO females (Figure S4). Two UAS-IR (21883 and 21884) and two transgenic rescue lines (DMDUT20 and DMDUT29) were combined. Number of progenies of the relevant F1 categories is shown. G...

Scheme of crossing for silencing of dUTPase in Drosophila larvae and pupae and for rescue of dUTPase RNAi. Crossing schemes are shown on panel A and C: Act-Gal4 means Gal4 gene coupled with actin 5C promoter that result in ubiquitous and constitutive expression of yeast transcription factor, Gal4 in transgenic D. melanogaster driving transcription...

Summary of pupal developmental processes. Red arrow shows the stage P5 (around 12–14 h after puparium formation) until lethality due to dUTPase silencing appear. (PDF)

Wild type structures of pharate adults 3 days after puparium formation. Wild type pupa was dissected at stage P11 where adult organs have already developed (A). Dissected Malpighian tubules (arrows on B) and Yellow Body (asterices on B) of wild type pupa these organs have never identified within dUTPase silenced pupae. (PDF)

Uracil–DNA repair is perturbed in Drosophila. Microarray data available on FlyBase were used. Table shows mRNA level for genes involved in different DNA repair pathways, elements of uracil–DNA repair are highlighted on grey background. ↓ indicates mRNA level decrease, ↑ mRNA level increase, ≈ no stage-specific change. Note that the overall base exc...

Supplementary information. Includes Supplementary Materials and Methods and Supplementary References. (DOC)

Genomic uracil content of embryo is under detection limit. Uracil content of Drosophila embryonic genome compared to that of DNA plasmid purified from wild-type E. coli. Both of the samples showed a value under the detection limit. (PDF)

Ung-ARP assay. UNG-ARP assay shows presence of uracil–DNA in Drosophila larvae. For negative and positive controls, genomic DNA samples from XL1 Blue and CJ236 ung-1, dut-1 E.coli strains were used respectively. CJ236 ung-1, dut-1 E.coli strain produces DNA with high uracil content (approx. 5500 uracil/million bases [8], [10]). (PDF)

Larval traits in dissected silenced pupae 3 days after puparium formation. Three days after puparium formation, dissected tissues of silenced pupae still preserve larval traits: testis is oval (A), foregut and gastric caeca show larval characteristics (B, D, asterices), Malpighian tubules (B, arrows) are thin characteristic for larval ones, and bra...

Developmental arrest caused by dUTPase silencing in Drosophila pupae. Wild type (upper panels) and dUTPase silenced (bottom panels) pupae were compared in stages P4, P5–6, P6–7, and P9. Every panel shows four views of the same pupa: dorsal (upper two) and ventral (bottom two) with and without its puparium. Specific differences appear at or before P...

Scheme of crossing for silencing of dUTPase in the dorsal compartment of Drosophila wing imaginal discs. Crossing scheme is shown on panel (A): virgin females of the MS1096 Gal4 enhancer trap line expressing Gal4 preferentially in the dorsal compartment of the wing and carrying UAS-Dicer2 in homozygous form on the second chromosome (Bloomington sto...

Base-excision repair and control of nucleotide pools safe-guard against permanent uracil accumulation in DNA relying on two key enzymes: uracil-DNA glycosylase and dUTPase. Lack of the major uracil-DNA glycosylase UNG gene from the fruit fly genome and dUTPase from fruit fly larvae prompted the hypotheses that i) uracil may accumulate in Drosophila...

Staphylococcus aureus superantigen-carrying pathogenicity islands (SaPIs) play a determinant role in spreading virulence genes among bacterial populations that constitute a major health hazard. Repressor (Stl) proteins are responsible for the transcriptional regulation of pathogenicity island genes. Recently, a derepressing interaction between the...

MS/MS spectrum of m/z 485.33 (2+) confirming peptide sequence SEHATAPTR. # stands for water loss. (TIF)

MS/MS spectrum of m/z 607.96 (2+) confirming peptide sequence EETPAISPSKR. # stands for water loss. (TIF)