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Post-Translational Modifications of PCNA: Guiding for the Best DNA Damage Tolerance Choice. J Fungi (Basel) 2022; 8:jof8060621. [PMID: 35736104 PMCID: PMC9225081 DOI: 10.3390/jof8060621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
The sliding clamp PCNA is a multifunctional homotrimer mainly linked to DNA replication. During this process, cells must ensure an accurate and complete genome replication when constantly challenged by the presence of DNA lesions. Post-translational modifications of PCNA play a crucial role in channeling DNA damage tolerance (DDT) and repair mechanisms to bypass unrepaired lesions and promote optimal fork replication restart. PCNA ubiquitination processes trigger the following two main DDT sub-pathways: Rad6/Rad18-dependent PCNA monoubiquitination and Ubc13-Mms2/Rad5-mediated PCNA polyubiquitination, promoting error-prone translation synthesis (TLS) or error-free template switch (TS) pathways, respectively. However, the fork protection mechanism leading to TS during fork reversal is still poorly understood. In contrast, PCNA sumoylation impedes the homologous recombination (HR)-mediated salvage recombination (SR) repair pathway. Focusing on Saccharomyces cerevisiae budding yeast, we summarized PCNA related-DDT and repair mechanisms that coordinately sustain genome stability and cell survival. In addition, we compared PCNA sequences from various fungal pathogens, considering recent advances in structural features. Importantly, the identification of PCNA epitopes may lead to potential fungal targets for antifungal drug development.
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Toth R, Halmai M, Gyorfy Z, Balint E, Unk I. The inner side of yeast PCNA contributes to genome stability by mediating interactions with Rad18 and the replicative DNA polymerase δ. Sci Rep 2022; 12:5163. [PMID: 35338218 PMCID: PMC8956578 DOI: 10.1038/s41598-022-09208-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/14/2022] [Indexed: 11/09/2022] Open
Abstract
PCNA is a central orchestrator of cellular processes linked to DNA metabolism. It is a binding platform for a plethora of proteins and coordinates and regulates the activity of several pathways. The outer side of PCNA comprises most of the known interacting and regulatory surfaces, whereas the residues at the inner side constitute the sliding surface facing the DNA double helix. Here, by investigating the L154A mutation found at the inner side, we show that the inner surface mediates protein interactions essential for genome stability. It forms part of the binding site of Rad18, a key regulator of DNA damage tolerance, and is required for PCNA sumoylation which prevents unscheduled recombination during replication. In addition, the L154 residue is necessary for stable complex formation between PCNA and the replicative DNA polymerase δ. Hence, its absence increases the mutation burden of yeast cells due to faulty replication. In summary, the essential role of the L154 of PCNA in guarding and maintaining stable replication and promoting DNA damage tolerance reveals a new connection between these processes and assigns a new coordinating function to the central channel of PCNA.
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Affiliation(s)
- Robert Toth
- The Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, 6726, Hungary
| | - Miklos Halmai
- The Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, 6726, Hungary
| | - Zsuzsanna Gyorfy
- The Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, 6726, Hungary
| | - Eva Balint
- The Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, 6726, Hungary
| | - Ildiko Unk
- The Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged, 6726, Hungary.
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Toth R, Balogh D, Pinter L, Jaksa G, Szeplaki B, Graf A, Gyorfy Z, Enyedi MZ, Kiss E, Haracska L, Unk I. The Rad5 Helicase and RING Domains Contribute to Genome Stability through their Independent Catalytic Activities. J Mol Biol 2022; 434:167437. [PMID: 34990655 DOI: 10.1016/j.jmb.2021.167437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/08/2021] [Accepted: 12/28/2021] [Indexed: 11/27/2022]
Abstract
Genomic stability is compromised by DNA damage that obstructs replication. Rad5 plays a prominent role in DNA damage bypass processes that evolved to ensure the continuation of stalled replication. Like its human orthologs, the HLTF and SHPRH tumor suppressors, yeast Rad5 has a RING domain that supports ubiquitin ligase activity promoting PCNA polyubiquitylation and a helicase domain that in the case of HLTF and Rad5 was shown to exhibit an ATPase-linked replication fork reversal activity. The RING domain is embedded in the helicase domain, confusing their separate investigation and the understanding of the exact role of Rad5 in DNA damage bypass. Particularly, it is still debated whether the helicase domain plays a catalytic or a non-enzymatic role during error-free damage bypass and whether it facilitates a function separately from the RING domain. In this study, through in vivo and in vitro characterization of domain-specific mutants, we delineate the contributions of the two domains to Rad5 function. Yeast genetic experiments and whole-genome sequencing complemented with biochemical assays demonstrate that the ubiquitin ligase and the ATPase-linked activities of Rad5 exhibit independent catalytic activities in facilitating separate pathways during error-free lesion bypass. Our results also provide important insights into the mutagenic role of Rad5 and indicate its tripartite contribution to DNA damage tolerance.
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Affiliation(s)
- Robert Toth
- DNA Repair Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary; University of Szeged, Doctoral School of Biology, Hungary
| | - David Balogh
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary
| | | | | | | | - Alexandra Graf
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary
| | - Zsuzsanna Gyorfy
- DNA Repair Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary
| | - Marton Zs Enyedi
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary; Delta Bio 2000 Ltd., Szeged H-6726, Hungary
| | - Erno Kiss
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary
| | - Ildiko Unk
- DNA Repair Research Group, Institute of Genetics, Biological Research Centre, Szeged, Eotvos Loránd Research Network, Szeged H-6726, Hungary.
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