Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase

Joining of DNA breaks- interplay between DNA ligases and poly (ADP-ribose) polymerases

The joining of DNA single- and double-strand breaks (SSB and DSB) is essential for maintaining genome stability and integrity. While this is ultimately accomplished in human cells by the DNA ligases encoded by the LIG1, LIG3 and LIG4 genes, these enzymes are recruited to DNA breaks through specific interactions with proteins involved in break sensing and recognition and/or break processing. In this review, we focus on the interplay between the DNA break-activated poly (ADP-ribose) polymerases, PARP1 and PARP2, poly (ADP-ribose) (PAR) and the DNA ligases in DNA replication and repair. The most extensively studied example of this interplay is the recruitment of DNA ligase IIIα (LigIIIα) and other repair proteins to SSBs through an interaction between XRCC1, a scaffold protein and partner protein of nuclear LigIIIα, and PAR synthesized by PARP1 and to a lesser extent PARP2. Recently, these proteins have been implicated in a back-up pathway for joining Okazaki fragments that appears to have a critical function even in cells with no defect in the major LigI-dependent pathway. Finally, we discuss the effects of FDA-approved PARP1/2 inhibitors on DNA replication and repair in cancer and non-malignant cells and the potential utility of DNA ligase inhibitors as cancer therapeutics.

Functional asymmetry in processivity clamp proteins

Symmetric homo-oligomeric proteins comprising multiple copies of identical subunits are abundant in all domains of life. To fulfill their biological function, these complexes undergo conformational changes, binding events, or posttranslational modifications, leading to loss of symmetry. Processivity clamp proteins that encircle DNA and play multiple roles in DNA replication and repair are archetypical homo-oligomeric symmetric protein complexes. The symmetrical nature of processivity clamps enables simultaneous interactions with multiple protein binding partners; such interactions result in asymmetric changes that facilitate the transition between clamp loading and DNA replication and between DNA replication and repair. The ring-shaped processivity clamps are opened and loaded onto DNA by clamp-loader complexes via asymmetric intermediates with one of the intermonomer interfaces disrupted, undergo spontaneous opening events, and bind heterogeneous partners. Eukaryotic clamp proteins are subject to ubiquitylation, SUMOylation, and acetylation, affecting their biological functions. There is increasing evidence of the functional asymmetry of the processivity clamp proteins from structural, biophysical, and computational studies. Here, we review the symmetry and asymmetry of processivity clamps and their roles in regulating the various functions of the clamps.

Structures of LIG1 uncover the mechanism of sugar discrimination against 5'-RNA-DNA junctions during ribonucleotide excision repair

Ribonucleotides in DNA cause several types of genome instability and can be removed by ribonucleotide excision repair (RER) that is finalized by DNA ligase 1 (LIG1). However, the mechanism by which LIG1 discriminates the RER intermediate containing a 5'-RNA-DNA lesion generated by RNase H2-mediated cleavage of ribonucleotides at atomic resolution remains unknown. Here, we determine X-ray structures of LIG1/5'-rG:C at the initial step of ligation where AMP is bound to the active site of the ligase and uncover a large conformational change downstream the nick resulting in a shift at Arg(R)871 residue in the Adenylation domain of the ligase. Furthermore, we demonstrate a diminished ligation of the nick DNA substrate with a 5'-ribonucleotide in comparison to an efficient end joining of the nick substrate with a 3'-ribonucleotide by LIG1. Finally, our results demonstrate that mutations at the active site residues of the ligase and LIG1 disease-associated variants significantly impact the ligation efficiency of RNA-DNA heteroduplexes harboring "wrong" sugar at 3'- or 5'-end of nick. Collectively, our findings provide a novel atomic insight into proficient sugar discrimination by LIG1 during the processing of the most abundant form of DNA damage in cells, genomic ribonucleotides, during the initial step of the RER pathway.

Proliferating Cell Nuclear Antigen in the Era of Oncolytic Virotherapy

Proliferating cell nuclear antigen (PCNA) is a well-documented accessory protein of DNA repair and replication. It belongs to the sliding clamp family of proteins that encircle DNA and acts as a mobile docking platform for interacting proteins to mount and perform their metabolic tasks. PCNA presence is ubiquitous to all cells, and when located in the nucleus it plays a role in DNA replication and repair, cell cycle control and apoptosis in proliferating cells. It also plays a crucial role in the infectivity of some viruses, such as herpes simplex viruses (HSVs). However, more recently it has been found in the cytoplasm of immune cells such as neutrophils and macrophages where it has been shown to be involved in the development of a pro-inflammatory state. PCNA is also expressed on the surface of certain cancer cells and can play a role in preventing immune cells from killing tumours, as well as being associated with cancer virulence. Given the growing interest in oncolytic viruses (OVs) as a novel cancer therapeutic, this review considers the role of PCNA in healthy, cancerous, and immune cells to gain an understanding of how PCNA targeted therapy and oncolytic virotherapy may interact in the future.

Structural and functional studies of PCNA from African swine fever virus

Proliferating cell nuclear antigen (PCNA) belongs to the DNA sliding clamp family. Via interacting with various partner proteins, PCNA plays critical roles in DNA replication, DNA repair, chromatin assembly, epigenetic inheritance, chromatin remodeling, and many other fundamental biological processes. Although PCNA and PCNA-interacting partner networks are conserved across species, PCNA of a given species is rarely functional in heterologous systems, emphasizing the importance of more representative PCNA studies. Here, we report two crystal structures of PCNA from African swine fever virus (ASFV), which is the only member of the Asfarviridae family. Compared to the eukaryotic and archaeal PCNAs and the sliding clamp structural homologs from other viruses, AsfvPCNA possesses unique sequences and/or conformations at several regions, such as the J-loop, interdomain-connecting loop (IDCL), P-loop, and C-tail, which are involved in partner recognition or modification of sliding clamps. In addition to double-stranded DNA binding, we also demonstrate that AsfvPCNA can modestly enhance the ligation activity of the AsfvLIG protein. The unique structural features of AsfvPCNA can serve as a potential target for the development of ASFV-specific inhibitors and help combat the deadly virus. IMPORTANCE Two high-resolution crystal structures of African swine fever virus proliferating cell nuclear antigen (AsfvPCNA) are presented here. Structural comparison revealed that AsfvPCNA is unique at several regions, such as the J-loop, the interdomain-connecting loop linker, and the P-loop, which may play important roles in ASFV-specific partner selection of AsfvPCNA. Unlike eukaryotic and archaeal PCNAs, AsfvPCNA possesses high double-stranded DNA-binding affinity. Besides DNA binding, AsfvPCNA can also modestly enhance the ligation activity of the AsfvLIG protein, which is essential for the replication and repair of ASFV genome. The unique structural features make AsfvPCNA a potential target for drug development, which will help combat the deadly virus.

Regulation of Human DNA Primase-Polymerase PrimPol

Transmission of genetic information depends on successful completion of DNA replication. Genomic DNA is subjected to damage on a daily basis. DNA lesions create obstacles for DNA polymerases and can lead to the replication blockage, formation of DNA breaks, cell cycle arrest, and apoptosis. Cells have evolutionary adapted to DNA damage by developing mechanisms allowing elimination of lesions prior to DNA replication (DNA repair) and helping to bypass lesions during DNA synthesis (DNA damage tolerance). The second group of mechanisms includes the restart of DNA synthesis at the sites of DNA damage by DNA primase-polymerase PrimPol. Human PrimPol was described in 2013. The properties and functions of this enzyme have been extensively studied in recent years, but very little is known about the regulation of PrimPol and association between the enzyme dysfunction and diseases. In this review, we described the mechanisms of human PrimPol regulation in the context of DNA replication, discussed in detail interactions of PrimPol with other proteins, and proposed possible pathways for the regulation of human PrimPol activity. The article also addresses the association of PrimPol dysfunction with human diseases.

Thermostable DNA ligases from hyperthermophiles in biotechnology

DNA ligase is an important enzyme ubiquitous in all three kingdoms of life that can ligate DNA strands, thus playing essential roles in DNA replication, repair and recombination in vivo. In vitro, DNA ligase is also used in biotechnological applications requiring in DNA manipulation, including molecular cloning, mutation detection, DNA assembly, DNA sequencing, and other aspects. Thermophilic and thermostable enzymes from hyperthermophiles that thrive in the high-temperature (above 80°C) environments have provided an important pool of useful enzymes as biotechnological reagents. Similar to other organisms, each hyperthermophile harbors at least one DNA ligase. In this review, we summarize recent progress on structural and biochemical properties of thermostable DNA ligases from hyperthermophiles, focusing on similarities and differences between DNA ligases from hyperthermophilic bacteria and archaea, and between these thermostable DNA ligases and non-thermostable homologs. Additionally, altered thermostable DNA ligases are discussed. Possessing improved fidelity or thermostability compared to the wild-type enzymes, they could be potential DNA ligases for biotechnology in the future. Importantly, we also describe current applications of thermostable DNA ligases from hyperthermophiles in biotechnology.

Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing

During lagging strand synthesis, DNA Ligase 1 (Lig1) cooperates with the sliding clamp PCNA to seal the nicks between Okazaki fragments generated by Pol δ and Flap endonuclease 1 (FEN1). We present several cryo-EM structures combined with functional assays, showing that human Lig1 recruits PCNA to nicked DNA using two PCNA-interacting motifs (PIPs) located at its disordered N-terminus (PIP_N-term) and DNA binding domain (PIP_DBD). Once Lig1 and PCNA assemble as two-stack rings encircling DNA, PIP_N-term is released from PCNA and only PIP_DBD is required for ligation to facilitate the substrate handoff from FEN1. Consistently, we observed that PCNA forms a defined complex with FEN1 and nicked DNA, and it recruits Lig1 to an unoccupied monomer creating a toolbelt that drives the transfer of DNA to Lig1. Collectively, our results provide a structural model on how PCNA regulates FEN1 and Lig1 during Okazaki fragments maturation.

DNA ligase and PCNA: Double-ring down to seal a break in DNA

In this issue of Structure, Sverzhinsky et al. (2022) report structures of archaeal DNA ligase bound to the proliferating cell nuclear antigen (PCNA) sliding clamp and a nicked DNA substrate. The structures provide snapshots of ligation intermediates, which reveal a dynamic nature of the complex and explain how PCNA stimulates the DNA ligase activity.