Biology subjects

Hartig, J.

Publications and source records attributed to Hartig, J..

3 recordsLinked to original sources

bioRxiv2026

Probabilistic mouse-human brain correspondence by multimodal optimal transport

The mouse is the principal model for brain mechanism and disease, allowing experiments that cannot be performed in humans. However, findings often translate poorly because homologous regions differ in relative size and some human territories have no clear mouse counterpart. Here we present OTTER, which learns mouse-human brain correspondence as a probabilistic, parcel-resolution coupling using multimodal fused Gromov-Wasserstein optimal transport, integrating functional and structural connectivity with spatial position and curated homologies. OTTER recovers established homologues on a transcriptomic benchmark and preserves broad cross-species organisation along the cortical areal hierarchy. Applying the coupling to human functional connectivity reveals a graded decline in mouse-based reconstruction across evolutionarily expanded association cortex, with the lowest values in lateral prefrontal territory. Finally, the bidirectional map generates testable human predictions from mouse experiments and ranks mouse circuits corresponding to human clinical targets.

neuroscience↗

bioRxiv2025

Small molecule-controlled gene expression: Design of drug-like high affinity small molecule modulators of a custom-made riboswitch

Riboswitches are regulatory RNA structures that modulate gene expression in response to a small molecule. Until now, efforts to design ligand analogs were motivated by their potential antibiotic activity. However, riboswitches are ideally suited as tools for gene therapy, enabling precise control of gene ex-pression without the need of potentially immunogenic regulatory proteins. Developing synthetic RNA switches starting from natural riboswitches will require engineering both, the ligand and the RNA sequence in order to achieve full orthogonality i.e., sensitivity to the designed small molecule modulator, but not to the natural ligand. We present the structure-based design of a drug-like small molecule ligand of the thiamine pyrophosphate (TPP) aptamer, BI-5232. BI-5232 is structurally highly diverse from the natural ligand TPP but rivals its binding affinity (KD = 1.0 nM). Importantly, in our design the pyrophosphate of TPP was replaced by an uncharged heterocycle that interacts with the PP helix in an unprecedented way, as revealed by Molecular Dynamics simulations. Subsequently, we altered the aptamer sequence to drastically reduce its affinity to TPP while retaining binding properties for our designed ligand. Based on the developed orthogonal small molecule/RNA aptamer interaction we finally constructed orthogonal ribozyme-based ON- and OFF-switches of gene expression in human cell lines. Such systems are valuable additions to the synthetic toolbox for conditionally controlling gene expression with potential applications in next-generation gene therapies.

synthetic biology↗

bioRxiv2024

Indel-driven evolution of the canavanine tRNA-editing deacetylase enzyme CtdA

AbstractProteins are heteropolymers composed of twenty standard amino acids. However, over 500 non-proteogenic amino acids exist in nature that can get misincorporated into proteins. Canavanine is an antimetabolite of L-arginine, with which it shares high chemical similarity. It can be utilized by bacteria such as Pseudomonas canavaninivorans in the legume rhizome as a sole source of carbon and nitrogen. However, canavanine is also incorporated in proteins of this bacterium as its arginyl-tRNA synthetase loads tRNAArg with both canavanine and arginine. The recently discovered canavanyl-tRNAArg deacetylase (CtdA) removes canavanine from misloaded tRNAArg and thereby prevents its incorporation in proteins. CtdA is the first enzyme known to edit tRNA mischarged with a non-proteinogenic amino acid. We have elucidated its crystal structure to 1.5 [A] resolution and studied its active site using site-directed mutagenesis. We found that CtdA is a small monomeric enzyme that presents a central, deep cavity that predictably constitutes the canavanine binding site and a positively charged surface area that likely coordinates the CCA-3 tRNA attachment sequence. The stand-alone, trans-editing CtdA is distantly related to the B3/B4 cis-editing domains of the large multi-subunit enzyme Phenylalanine tRNA synthetase (PheRS). Our comparative study reveals that CdtA and B3/B4 domains from bacterial and archeal/eukaryotic origin are three subclasses of a same conserved 3D-fold that differ in type-specific indels, which distinctly shape the substrate binding cleft of these proteins. We propose a unifying nomenclature of secondary structure elements for this 3D-fold. In CtdA, residues E191, Y104, N105 and E118 prove to be relevant for catalysis, of which N105 is conserved in bacterial B3/B4 domains. No other shared residues of catalytic relevance could be identified across enzymes of this class, so that a shared mechanism of catalysis appears unlikely in these editing enzymes.

biochemistry↗