Biology subjects

Justman, Q. A.

Publications and source records attributed to Justman, Q. A..

5 recordsLinked to original sources

bioRxiv2025

Essentialome-Wide Multigenerational Imaging Reveals Mechanistic Origins of Cell Growth Laws

Escherichia coli is arguably the most thoroughly characterized organism, and yet [~]20% of its essential genes serve completely unknown functions,1,2 and many core quantitative physiological principles remain unexplained, including the famous nutrient growth law where cell volume seems to depend exponentially on growth rate. Here we develop a platform for massive, multi-generational Optical Pooled Screening (OPS)3-6, and apply it to link image-based phenotypes to genotypes for 133,000 CRISPRi knockdowns of essential genes, tracking tens of millions of lineages and analyzing 1.6 billion cells. Our multi-dimensional dynamic phenotypes correlate exceptionally well with known gene functions, allowing us to identify many unknown roles of essential genes. Quantifying the relation between growth and cell size in turn identifies three distinct variants of the bacterial growth laws, which we explain mechanistically by discovering a new role for (p)ppGpp and SpoT as a sensor of translation elongation. Finally, we propose and systematically test an exceedingly simple, passive mechanism for the nutrient growth law, based on triggering cell division through the accumulation of a protein that, unlike ribosomes, is not controlled by (p)ppGpp. The resulting hyperbolic growth law fits the data from our three variants even better than the previously proposed exponential relationship, and with fewer parameters.

systems biology↗

bioRxiv2025

Continuous accelerated rock weathering by marine bacteria with enhanced siderophore production

Silicate mineral weathering (dissolution) is a scalable strategy for capture and storage of CO2 but is too slow for industrial deployment. Bacteria can accelerate mineral dissolution by secreting siderophores, molecules that solubilize iron released from the mineral that would otherwise passivate the mineral surface. Here, we investigated how to deploy siderophore-producing bacteria at scale to continuously enhance dissolution of the mineral olivine. We demonstrated that natural genetic regulation precludes continuous siderophore production in mineral bioreactors. To overcome this limitation, we engineered the marine bacterium Alteromonas macleodii to enhance its production of siderophores, conferring a 2.6-fold increase in the rate of olivine dissolution. Life Cycle Analysis indicated that renewable feedstocks and minimal replenishment of modified cells are critical to achieve net CO2 removal at scale. With these guidelines, we constructed pilot-scale continuous mineral bioreactors that use unprocessed seawater and a renewable acetate feedstock. In reactors with engineered cells, we directly measured removal of 0.50 g CO2 per day from the air through alkalinity generation, while a control reactor without cells did not generate alkalinity in net. These platforms and bioprocess principles will inform the design of large-scale, sustainable, unit operations for alkaline mineral processing.

systems biology↗

bioRxiv2023

LanTERN: a fluorescent sensor that specifically binds lanthanides

Lanthanides, a series of fifteen f-block elements, are crucial in modern technology, and their purification by conventional chemical means comes at a significant environmental cost. Synthetic biology offers promising solutions. However, the lack of biochemical tools to measure lanthanide binding is a bottleneck to progress. Here, we introduce LanTERN, a lanthanide-responsive fluorescent protein rationally engineered from the lanmodulin-binding protein, LanM. LanTERN was designed based on GCaMP, a genetically encoded calcium indicator that couples the ion binding of four EF hand motifs to increased GFP fluorescence. We engineered seven mutations across the parent constructs four EF hand motifs to switch specificity from calcium to lanthanides. The resulting protein, LanTERN, directly converts the binding of 10 measured lanthanides to 14-fold or greater increased fluorescence. LanTERN development opens new avenues for creating improved lanthanide-binding proteins and bio-sensing systems.

synthetic biology↗

bioRxiv2020

Bet hedging buffers budding yeast against environmental instability

To grow and divide, cells must extract resources from dynamic and unpredictable environments. Organisms thus possess redundant metabolic pathways for distinct contexts. In budding yeast, ATP can be produced from carbon by mechanisms that prioritize either speed (fermentation) or yield (respiration). We find that in the absence of predictive cues, cells vary in their intrinsic ability to switch metabolic strategies from fermentation to respiration. We observe subpopulations of yeast cells which either rapidly adapt or enter a shock state characterized by deformation of many cellular structures, including mitochondria. This capacity to adapt is a bimodal and heritable state. We demonstrate that metabolic preparedness confers a fitness advantage during an environmental shift but is costly in a constant, high-glucose environment, and we observe natural variation in the frequency of prepared cells across wild yeast strains. These experiments suggest that bet-hedging has evolved in budding yeast.

cell biology↗

bioRxiv2019

Independent evolution of polymerization in the Actin ATPase clan regulates hexokinase activity

The actin protein fold is found in cytoskeletal polymers, chaperones, and various metabolic enzymes. Many actin-fold proteins, like the carbohydrate kinases, do not polymerize. We find that Glk1, a Saccharomyces cerevisiae glucokinase, forms two-stranded filaments with unique ultrastructure, distinct from that of cytoskeletal polymers. In cells, Glk1 polymerizes upon sugar addition and depolymerizes upon sugar withdrawal. Glk1 polymerization inhibits its enzymatic activity, thus the Glk1 monomer-polymer equilibrium sets a maximum rate of glucose phosphorylation regardless of Glk1 concentration. A mutation eliminating Glk1 polymerization alleviates concentration-dependent enzyme inhibition, causing glucokinase activity to become unconstrained. Polymerization-based regulation of Glk1 activity serves an important function in vivo: yeast containing non-polymerizing Glk1 are less fit when growing on sugars and more likely to die when refed glucose. Glucokinase polymerization arose within the ascomycete fungi and is conserved across a group of divergent (150-200 mya) yeast. We show that Glk1 polymerization arose independently from other actin-related filaments and allows yeast to rapidly modulate glucokinase activity as nutrient availability changes.\n\nOne-sentence summaryYeast glucokinase activity is limited by its polymerization, which is critical for cell viability during glucose refeeding.

biochemistry↗