Bacterial microcompartments are a class of proteinaceous organelles comprising characteristic protein shell enclosing set enzymes. Compartmentalization can prevent escape volatile or toxic intermediates, off-pathway reactions, and create private cofactor pools. Encapsulation in synthetic microcompartment will enhance the function heterologous pathways, but to do so, it is critical understand how control diffusion out organelle. To this end, we explored small differences structure result...

Nature uses protein compartmentalization to great effect for control over enzymatic pathways, and the strategy has promise synthetic biology. In particular, encapsulation in nanometer-sized containers create nanoreactors potential elicit interesting, unexplored effects resulting from deviations well-understood bulk processes. Self-assembled shells are especially desirable their uniform structures ease of perturbation through genetic mutation. Here, we use MS2 capsid, a well-defined porous 27...

The spatial organization of metabolism is common to all domains life. Enteric and other bacteria use subcellular organelles known as bacterial microcompartments spatially organize the pathogenicity-relevant carbon sources, such 1,2-propanediol. are thought sequester a private cofactor pool, minimize effects toxic intermediates, enhance flux through encapsulated metabolic pathways. We develop mathematical model function 1,2-propanediol utilization microcompartment Salmonella enterica it...

Abstract Self-assembling proteins are critical to biological systems and industrial technologies, but predicting how mutations affect self-assembly remains a significant challenge. Here, we report technique, termed SyMAPS (Systematic Mutation Assembled Particle Selection), that can be used characterize the assembly competency of all single amino acid variants self-assembling viral structural protein. studies on MS2 bacteriophage coat protein revealed high-resolution fitness landscape...

Virus-like particles are used to encapsulate drugs, imaging agents, enzymes, and other biologically active molecules in order enhance their function. However, the size of most virus-like is inflexible, precluding design appropriately sized containers for different applications. Here, we describe a chromatographic selection particle assembly. Using this selection, identified single amino acid substitution coat protein bacteriophage MS2 that mediates uniform switch geometry from T = 3 1...

Organizing heterologous biosyntheses inside bacterial cells can alleviate common problems owing to toxicity, poor kinetic performance, and cofactor imbalances. A subcellular organelle known as a microcompartment, such the 1,2-propanediol utilization microcompartment of Salmonella, is promising chassis for this strategy. Here we demonstrate de novo design N-terminal signal sequences used direct cargo these organelles. We expand native repertoire using rational library-based approaches show...

ABSTRACT The essential stress-responsive chaperone Hsp90 impacts development and adaptation from microbes to humans. Yet despite evidence of its role in evolution, pathogenesis, oncogenic transformation, the molecular mechanisms by which alters consequences mutations remain vigorously debated. Here we exploit power nucleotide-resolution genetic mapping Saccharomyces cerevisiae uncover more than 1,000 natural variant-to-phenotype associations governed this chaperone. Strikingly, frequently...

Bacterial microcompartments (MCPs) show great promise for the organization of engineered metabolic pathways within bacterial cytoplasm. This subcellular organelle is composed a protein shell 100–200 nm diameter that natively encapsulates multi-enzyme pathways. The high energy cost synthesizing thousands subunits required each MCP demands precise regulation formation both native and systems. Here, we study propanediol utilization (Pdu) MCP, which growth on 1,2-propanediol induces expression...

In fluctuating environments, switching between different growth strategies, such as those affecting cell size and proliferation, can be advantageous to an organism. Trade-offs arise, however. Mechanisms that aberrantly increase or proliferation-such mutations chemicals interfere with regulatory pathways-can also shorten lifespan. Here we report a natural example of how the interplay lifespan epigenetically controlled. We find highly conserved RNA-modifying enzyme, pseudouridine synthase...

Abstract Natural biochemical systems are ubiquitously organized both in space and time. Engineering the spatial organization of biochemistry has emerged as a key theme synthetic biology, with numerous technologies promising improved biosynthetic pathway performance. One strategy, however, may produce disparate results for different pathways. We use spatially resolved kinetic model to explore this fundamental design choice biology. predict that two example pathways have distinct optimal...

Abstract Quantitative genetics aims to map genotype phenotype, often with the goal of understanding how organisms evolved. However, it remains unclear whether genetic variants identified are exemplary evolution. Here we analyzed progeny two wild Saccharomyces cerevisiae isolates identify 195 loci underlying complex metabolic traits, resolving 107 single polymorphisms diverse molecular mechanisms. More than 20% causal exhibited patterns emergence inconsistent neutrality. Moreover, contrary...

Summary Despite abundant genomic and phenotypic data across individuals 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 distinct niches. Modest genetic distance parents generated remarkable proteomic diversity that was amplified captured 6,476 genotype-protein associations, over 1,600 which...

Abstract Bacterial microcompartments are a class of proteinaceous organelles comprising characteristic protein shell enclosing set enzymes. Compartmentalization can prevent escape volatile or toxic intermediates, off-pathway reactions, and create private cofactor pools. Encapsulation in synthetic microcompartment will enhance the function heterologous pathways, but to do so, it is critical understand how control diffusion out organelle. To this end, we explored small differences structure...

Abstract The spatial organization of metabolism is common to all domains life. Enteric and other bacteria use subcellular organelles known as bacterial microcompartments spatially organize the pathogenicity-relevant carbon sources, such 1,2-propanediol. are thought sequester a private cofactor pool, minimize effects toxic intermediates, enhance flux through encapsulated metabolic pathways. We develop mathematical model function 1,2-propanediol utilization microcompartment Salmonella enterica...