Plasmodium DDI1 is an essential chromatin-associated protein with a role in DNA-protein crosslink repair

DDI1 proteins are conserved in eukaryotes and involved in a variety of cellular processes, including proteasomal degradation of specific proteins and DNA-protein crosslink repair. All DDI1 proteins contain ubiquitin-like (UBL) and retroviral aspartyl protease (RVP) domains, and some also contain ubiquitin-associated (UBA) domain, which mediate distinct activities of these proteins. We investigated the Plasmodium DDI1 to identify its roles during parasite development and potential as a therapeutic target. The DDI1 proteins of Plasmodium and other Apicomplexan parasites vary in domain architecture, share UBL and RVP domains, and the majority of proteins contain the UBA domain. Plasmodium DDI1 is expressed across all major life stages and is essential, as conditional depletion of DDI1 protein in P. berghei and P. falciparum drastically reduced the asexual stage parasite development. Infection of mice with DDI1 knock-down P. berghei parasites was self-limiting and protected from the subsequent infection with both homologous and heterologous parasites, indicating potential of DDI1 knock-down parasites as a whole organism vaccine. P. falciparum DDI1 (PfDDI1) is associated with chromatin and DNA-protein crosslinks, and PfDDI1 knock-down parasites showed increased DNA-protein crosslinks and susceptibility to DNA damaging chemicals, indicating an important role for DDI1 in repair of DNA-protein crosslinks. The knock-down of PfDDI1 increased susceptibility to retroviral protease inhibitors, epoxomicin and artemisinin, which suggests that simultaneous inhibition of DDI1 could potentiate antimalarial activity of these inhibitors or drugs. Hence, the essentiality, ability of DDI1 knock-down parasites to confer protective immunity and increased susceptibility to inhibitors support Plasmodium DDI1 as a dual-target therapeutic candidate.

PARylation prevents the proteasomal degradation of topoisomerase I DNA-protein crosslinks and induces their deubiquitylation

Poly(ADP)-ribosylation (PARylation) regulates chromatin structure and recruits DNA repair proteins. Using single-molecule fluorescence microscopy to track topoisomerase I (TOP1) in live cells, we found that sustained PARylation blocked the repair of TOP1 DNA-protein crosslinks (TOP1-DPCs) in a similar fashion as inhibition of the ubiquitin-proteasome system (UPS). PARylation of TOP1-DPC was readily revealed by inhibiting poly(ADP-ribose) glycohydrolase (PARG), indicating the otherwise transient and reversible PARylation of the DPCs. As the UPS is a key repair mechanism for TOP1-DPCs, we investigated the impact of TOP1-DPC PARylation on the proteasome and found that the proteasome is unable to associate with and digest PARylated TOP1-DPCs. In addition, PARylation recruits the deubiquitylating enzyme USP7 to reverse the ubiquitylation of PARylated TOP1-DPCs. Our work identifies PARG as repair factor for TOP1-DPCs by enabling the proteasomal digestion of TOP1-DPCs. It also suggests the potential regulatory role of PARylation for the repair of a broad range of DPCs.

Improved functional properties of meat analogs by laccase catalyzed protein and pectin crosslinks

The gap between the current supply and future demand of meat has increased the need to produce plant-based meat analogs. Methylcellulose (MC) is used in most commercial products. Consumers and manufacturers require the development of other novel binding systems, as MC is not chemical-free. We aimed to develop a novel chemical-free binding system for meat analogs. First, we found that laccase (LC) synergistically crosslinks proteins and sugar beet pectin (SBP). To investigate the ability of these SBP-protein crosslinks, textured vegetable protein (TVP) was used. The presence of LC and SBP improved the moldability and binding ability of patties, regardless of the type, shape, and size of TVPs. The hardness of LC-treated patties with SBP reached 32.2 N, which was 1.7- and 7.9-fold higher than that of patties with MC and transglutaminase-treated patties. Additionally, the cooking loss and water/oil-holding capacity of LC-treated patties with SBP improved by up to 8.9–9.4% and 5.8–11.3%, compared with patties with MC. Moreover, after gastrointestinal digestion, free amino nitrogen released from LC-treated patties with SBP was 2.3-fold higher than that released from patties with MC. This is the first study to report protein-SBP crosslinks by LC as chemical-free novel binding systems for meat analogs.

Apurinic/Apyrimidinic Endonuclease 1 and Tyrosyl-DNA Phosphodiesterase 1 Prevent Suicidal Covalent DNA-Protein Crosslink at Apurinic/Apyrimidinic Site

Bifunctional 8-oxoguanine-DNA glycosylase (OGG1), a crucial DNA-repair enzyme, removes from DNA 8-oxo-7,8-dihydroguanine (8-oxoG) with following cleavage of the arising apurinic/apyrimidinic (AP) site. The major enzyme in eukaryotic cells that catalyzes the cleavage of AP sites is AP endonuclease 1 (APE1). Alternatively, AP sites can be cleaved by tyrosyl-DNA phosphodiesterase 1 (TDP1) to initiate APE1-independent repair, thus expanding the ability of the base excision repair (BER) process. Poly(ADP-ribose) polymerase 1 (PARP1) is a regulatory protein of DNA repair. PARP2 is also activated in response to DNA damage and can be regarded as the BER participant. Here we analyze PARP1 and PARP2 interactions with DNA intermediates of the initial stages of the BER process (8-oxoG and AP-site containing DNA) and their interplay with the proteins recognizing and processing these DNA structures focusing on OGG1. OGG1 as well as PARP1 and PARP2 form covalent complex with AP site-containing DNA without borohydride reduction. AP site incision by APE1 or TDP1 removal of protein adducts but not proteins’ PARylation prevent DNA-protein crosslinks.

DNA–protein crosslink proteases in genome stability

Proteins covalently attached to DNA, also known as DNA–protein crosslinks (DPCs), are common and bulky DNA lesions that interfere with DNA replication, repair, transcription and recombination. Research in the past several years indicates that cells possess dedicated enzymes, known as DPC proteases, which digest the protein component of a DPC. Interestingly, DPC proteases also play a role in proteolysis beside DPC repair, such as in degrading excess histones during DNA replication or controlling DNA replication checkpoints. Here, we discuss the importance of DPC proteases in DNA replication, genome stability and their direct link to human diseases and cancer therapy.