Biology subjects

Fridmann-Sirkis, Y.

Publications and source records attributed to Fridmann-Sirkis, Y..

4 recordsLinked to original sources

bioRxiv2023

Functional Ambidexterity of an Ancient Nucleic Acid-Binding Domain

Homochirality of biopolymers emerged early in the history of life on Earth, nearly 4 billion years ago. Whether the establishment of homochirality was the result of abiotic physical and chemical processes, or biological selection, remains unknown. However, given that significant events in protein evolution predate the last universal common ancestor, the history of homochirality may have been written into some of the oldest protein folds. To test this hypothesis, the evolutionary trajectory of the ancient and ubiquitous helix-hairpin-helix (HhH) protein family was analyzed for functional robustness to total chiral inversion of just one binding partner. Against expectations, functional ambidexterity was observed across the entire trajectory, from phase separation of HhH peptides with RNA to dsDNA binding of the duplicated (HhH)2-Fold. Moreover, dissociation kinetics, mutational analysis, and molecular dynamics simulations revealed significant overlap between the binding modes of a natural and a mirror-image protein to natural dsDNA. These data suggest that the veil between worlds with alternative chiral preferences may not be as impenetrable as is often assumed, and that the HhH protein family is an intriguing exception to the dogma of reciprocal chiral substrate specificity proposed by Milton and Kent (Milton et al. Science 1992).

biophysics↗

bioRxiv2022

Acanthamoeba polyphaga de novo transcriptome and its dynamics during Mimivirus infection

Acanthamoeba polyphaga mimivirus (Mimivirus) is a giant virus that infects Acanthamoeba species - opportunistic human pathogens. We applied long- and short-read sequencing to generate a de novo transcriptome of the host and followed the dynamics of both host and virus transcriptomes over the course of infection. The assembled transcriptome of the host included 22,604 transcripts and 13,043 genes, with N50 = 2,372 nucleotides. Functional enrichment analysis revealed major changes in the host transcriptome, namely, enrichment in downregulated genes associated with cytoskeleton homeostasis and DNA replication, repair, and nucleotide synthesis. These modulations, together with those implicated by other enriched processes, indicate cell cycle arrest, an event we demonstrated experimentally. We also observed upregulation of host genes associated with transcription, secretory pathways and, as reported here for the first time, peroxisomes and the ubiquitin-proteasome system. In Mimivirus, the early stages of infections were marked by upregulated genes related to DNA replication, transcription, translation, and nucleotide metabolism, and the later stages, by enrichment in genes associated with lipids metabolism, carbohydrates, and proteases. Some of the changes observed in the amoebal transcriptome likely point to Mimivirus infection causing the dismantling of the host cytoskeleton, the translocation of endoplasmic reticulum membranes to viral factory areas, and cell cycle arrest.

microbiology↗

bioRxiv2022

Intestinal Mucin Is a Chaperone of Multivalent Copper

Mucus protects the body by many mechanisms, but a role in managing toxic transition metals was not previously known. Here we report that secreted mucins, the major mucus glycoproteins coating the respiratory and intestinal epithelia, are specific copper-binding proteins. Most remarkably, the intestinal mucin, MUC2, has two juxtaposed copper binding sites, one that accommodates Cu2+ and the other Cu1+, which can be formed in situ by reduction with vitamin C. Copper is an essential trace metal because it is a cofactor for a variety of enzymes catalyzing electron transfer reactions, but copper damages macromolecules when unregulated. We observed that MUC2 protects against copper toxicity while permitting nutritional uptake into cells. These findings introduce mucins, produced in massive quantities to guard extensive mucosal surfaces, as extracellular copper chaperones and potentially important players in physiological copper homeostasis.

biochemistry↗

bioRxiv2020

Primordial emergence of a nucleic acid binding protein via phase separation and statistical ornithine to arginine conversion

De novo emergence, and emergence of the earliest proteins specifically, demands a transition from disordered polypeptides into structured proteins with well-defined functions. However, can peptides confer evolutionary relevant functions, let alone with minimal abiotic amino acid alphabets? How can such polypeptides evolve into mature proteins? Specifically, while nucleic acids binding is presumed a primordial function, it demands basic amino acids that do not readily form abiotically. To address these questions, we describe an experimentally-validated trajectory from a phase-separating polypeptide to a dsDNA-binding protein. The intermediates comprise sequence-duplicated, functional proteins made of only 10 amino acid types, with ornithine, which can form abiotically, as the only basic amino acid. Statistical, chemical modification of ornithine sidechains to arginine promoted structure and function. The function concomitantly evolved - from phase separation with RNA (coacervates) to avid and specific dsDNA binding - thereby demonstrating a smooth, gradual peptide-to-protein transition with respect to sequence, structure, and function.

biochemistry↗