Biology subjects

Erber, L.

Publications and source records attributed to Erber, L..

4 recordsLinked to original sources

bioRxiv2026

Glyoxal induces DNA-Protein Crosslinking in Cells

Glyoxal (GO) is a small, highly reactive molecule that is produced naturally in cells during normal metabolism and can also come from processed foods and oxidative stress. Because of its high reactivity, glyoxal can modify DNA and proteins to form harmful products called advanced glycation end-products (AGEs), which have been linked to diseases such as diabetes, cancer, and aging. Although glyoxal is known to modify DNA and proteins, it is not well understood whether it can form DNA-protein crosslinks (DPCs), a type of DNA damage in which proteins become permanently attached to DNA. In this study, we investigated glyoxal induced DPC formation in HeLa cells using biochemical assays and mass spectrometry-based proteomics experiments. We observed that glyoxal exposure elevated cellular DPC formation in a concentration- and time-dependent manner. Cells with reduced SPRTN expression accumulated higher levels of DPCs, suggesting that SPRTN plays an important role in repairing glyoxal induced DNA damage. Proteomics experiments revealed 469 proteins exhibited elevated DNA association in glyoxal-treated samples, including histones and other proteins involved in chromatin organization, DNA replication, DNA repair, and gene expression. In-vitro experiments confirmed that glyoxal can directly crosslink DNA with histone proteins. Overall, this study provides the first evidence that glyoxal forms DNA-protein crosslinks in human cells. These findings provide a foundation for future studies on the chemical structure, biological effects and repair of glyoxal induced DNA-protein crosslinks and their possible role in human disease.

biochemistry↗

bioRxiv2025

Isotope Dilution nanoLC-MS/MS Quantitation of Methylglyoxal DNA-Protein Crosslinks: Formation and Repair in Human Cells

DNA-protein crosslinks (DPCs) represent a prevalent form of DNA damage that form when cellular proteins become covalently trapped to DNA strands upon exposure to various endogenous and exogenous agents. Methylglyoxal, is an endogenous metabolite that reacts with guanine and adenine bases in DNA and RNA, as well as cysteine, arginine and lysine residues in proteins, generating advanced glycation end-products (AGEs) including DPCs. These modifications have been linked to human disease, including cancer, liver disease, diabetes, and neurodegenerative disorders. Herein, we present a mass spectrometry method for quantifying MGO-induced DNA-protein crosslinks (DPCs) in human cells. We prepared an isotope 15N213C6-dG-MGO-Lys internal standard to develop a quantitative LC-MS/MS method for detecting and quantifying the formation and repair of dG-MGO-Lys DPCs in cells. Genomic DNA was extracted, subjected to sequential protease and nuclease digestion, purified by offline HPLC, and analyzed by LC-MS/MS. The methods standard curve showed a strong linear relationship across a concentration range of 10-1000 fmol (R2 = 0.9994). The method achieved limits of detection (LOD) and quantification (LOQ) of 10 and 20 fmol, respectively. Inhibition of proteasome and SPRTN activity revealed that SPRTN functions as a predominant proteolytic enzyme in MGO DPC repair. Overall, this analytical approach can offer valuable insights into the relevance of DPCs in diseases linked to elevated MGO levels.

cancer biology↗

bioRxiv2022

Mitochondrial genomes in Perkinsus decode conserved frameshifts in all genes

Mitochondrial genomes of apicomplexans, dino-flagellates and chrompodellids, that collectively make up the Myzozoa, are uncommonly reduced in coding capacity and display divergent gene configuration and expression mechanisms. They encode only three proteins -- COB, COX1, COX3 -- contain rRNAs fragmented to [~]100-200 base pair elements, and employ extensive recombination, RNA trans-splicing, and RNA-editing for genome maintenance and expression. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remain poorly characterized. Previous reports of Perkinsus cox1 and cob partial gene sequences have indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts in both genes. To determine ancestral myzozoan mitochondrial genome features, as well as any novel ones in Perkinsozoa, we sequenced and assembled four Perkinsus species mitochondrial genomes. These data show a simple ancestral genome with the common reduced coding capacity, but one already prone to rearrangement. Moreover, we identified 75 frameshifts across the four species that are present in all genes, that are highly conserved in gene location, and that occur as four distinct types. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of the frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. COX3 is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in COX3 and COB. All genes also lack cysteine codons implying a further constraint on these genomes with reduction to only 19 different amino acids. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA, suggesting these may be imported into the organelle as for tRNAs. Perkinsus demonstrates additional remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression.

molecular biology↗

bioRxiv2022

Deep Proteome Profiling Enabled Functional Annotation and Data-Independent Quantification of Proline Hydroxylation Targets

Proline hydroxylation (Hyp) regulates protein structure, stability and protein-protein interaction and is widely involved in diverse metabolic and physiological pathways in cells and diseases. To reveal functional features of the proline hydroxylation proteome, we integrated various data sources for deep proteome profiling of proline hydroxylation proteome in human and developed HypDB (https://www.HypDB.site), an annotated database and web server for proline hydroxylation proteome. HypDB provides site-specific evidence of modification based on extensive LC-MS analysis and literature mining with 15319 non-redundant Hyp sites and 8226 sites with high confidence on human proteins. Annotation analysis revealed significant enrichment of proline hydroxylation on key functional domains and tissue-specific distribution of Hyp abundance across 26 types of human organs and fluids and 6 cell lines. The network connectivity analysis further revealed a critical role of proline hydroxylation in mediating protein-protein interactions. Moreover, the spectral library generated by HypDB enabled data-independent analysis (DIA) of clinical tissues and the identification of novel Hyp biomarkers in lung cancer and kidney cancer. Taken together, our integrated analysis of human proteome with publicly accessible HypDB revealed functional diversity of Hyp substrates and provides a quantitative data source to characterize proline hydroxylation in pathways and diseases.

biochemistry↗