Biology subjects

Jakobson, C. M.

Publications and source records attributed to Jakobson, C. M..

3 recordsLinked to original sources

bioRxiv2025

Protein structure shapes natural genetic variation and de novo adaptation

Protein structural context strongly influences the functional outcomes of mutations, but exploiting this intuition to interpret the consequences of natural variants has been limited by the paucity of structural information. Here, we show that simple molecular heuristics based on predicted protein structures-solvent accessibility and the local complexity of the protein fold-are strong predictors of protein-coding variation in genomes from yeast to plants to humans. Polymorphisms in structured and unstructured regions alike were subject to these constraints, revealing fine-grained selection across amino acid residues and secondary structures. The same analyses distinguished deleterious variants in datasets from existing deep mutational scans. Extending the metrics to de novo adaptation, we developed a massively parallel directed evolution platform that isolated hundreds of independent adapted lineages within days. Optimized experimental conditions revealed dozens of rapamycin-resistant alleles of the FPR1/FKBP gene in a single experiment-resistance mutations that matched predictions from our structural heuristics. Together, these data demonstrate the power of a biochemical perspective to contextualize the functional landscape of both existing and newly arising genetic variation.

evolutionary biology↗

bioRxiv2024

A genome-to-proteome atlas charts natural variants controlling proteome diversity and forecasts their fitness effects

Despite abundant genomic and phenotypic data across individuals and environments, the functional impact of most mutations on phenotype remains unclear. Here, we bridge this gap by linking genome to proteome in 800 meiotic progeny from an intercross between two closely related Saccharomyces cerevisiae isolates adapted to distinct niches. Modest genetic distance between the parents generated remarkable proteomic diversity that was amplified in the progeny and captured by 6,476 genotype-protein associations, over 1,600 of which we resolved to single variants. Proteomic adaptation emerged through the combined action of numerous cis- and trans-regulatory mutations, a regulatory architecture that was conserved across the species. Notably, trans-regulatory variants often arose in proteins not traditionally associated with gene regulation, such as enzymes. Moreover, the proteomic consequences of mutations predicted fitness under various stresses. Our study demonstrates that the collective action of natural genetic variants drives dramatic proteome diversification, with molecular consequences that forecast phenotypic outcomes. Highlights- Proteome diversity arises from natural genetic variants, with divergent proteomes in closely related parents and progeny. - Cis-regulatory elements had strong individual impacts, but coherent trans effects combined to dominate protein expression. - Directional selection and frequent transgression suggest much of the proteome is under selective pressure. - Many trans-regulators are enzymes or transporters, with fewer than 4% of pQTLs linking known interactors. - Genome-to-proteome connections predicted the fitness impact of mutations under various stresses, including a strong but hidden causal variant in IRA2/NF1.

systems biology↗

bioRxiv2017

Engineered shell proteins confer improved encapsulated pathway behavior in a bacterial microcompartment

Bacterial microcompartments are a class of proteinaceous organelles comprising a characteristic protein shell enclosing a set of enzymes. Compartmentalization can prevent escape of volatile or toxic intermediates, prevent off-pathway reactions, and create private cofactor pools. Encapsulation in synthetic microcompartment organelles will enhance the function of heterologous pathways, but to do so, it is critical to understand how to control diffusion in and out of the microcompartment organelle. To this end, we explored how small differences in the shell protein structure result in changes in the diffusion of metabolites through the shell. We found that the ethanolamine utilization (Eut) protein EutM properly incorporates into the 1,2-propanediol utilization (Pdu) microcompartment, altering native metabolite accumulation and the resulting growth on 1,2-propanediol as the sole carbon source. Further, we identified a single pore-lining residue mutation that confers the same phenotype as substitution of the full EutM protein, indicating that small molecule diffusion through the shell is the cause of growth enhancement. Finally, we show that the hydropathy index and charge of pore amino acids are important indicators to predict how pore mutations will affect growth on 1,2- propanediol, likely by controlling diffusion of one or more metabolites. This study highlights the success of two strategies to engineer microcompartment control over metabolite transport: altering the existing shell protein pore via mutation of the pore-lining residues, and generating chimeras using shell proteins with the desired pores.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC=\"FIGDIR/small/106716_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@1f69a12org.highwire.dtl.DTLVardef@fd5560org.highwire.dtl.DTLVardef@1f01d6aorg.highwire.dtl.DTLVardef@11b442c_HPS_FORMAT_FIGEXP M_FIG TOC Abstract Graphic C_FIG

synthetic biology↗