Designer membraneless organelles sequester native factors for control of cell behavior

Subcellular compartmentalization of macromolecules increases flux and prevents inhibitory interactions to control biochemical reactions. Inspired by this functionality, we sought to build designer compartments that function as hubs to regulate the flow of information through cellular control systems. We report a synthetic membraneless organelle platform to control endogenous cellular activities through sequestration and insulation of native proteins. We engineer and express a disordered protein scaffold to assemble micron size condensates and recruit endogenous clients via genomic tagging with high-affinity dimerization motifs. By relocalizing up to ninety percent of a targeted enzymes to synthetic condensates, we efficiently control cellular behaviors, including proliferation, division, and cytoskeletal organization. Further, we demonstrate multiple strategies for controlled cargo release from condensates to switch cells between functional states. These synthetic organelles offer a powerful and generalizable approach to modularly control cell decision-making in a variety of model systems with broad applications for cellular engineering.

Controllable protein phase separation and modular recruitment to form responsive membraneless organelles

Many intrinsically disordered proteins self-assemble into liquid droplets that function as membraneless organelles. Because of their biological importance and ability to colocalize molecules at high concentrations, these protein compartments represent a compelling target for bio-inspired materials engineering. Here we manipulated the intrinsically disordered, arginine/glycine-rich RGG domain from the P granule protein LAF-1 to generate synthetic membraneless organelles with controllable phase separation and cargo recruitment. First, we demonstrate enzymatically triggered droplet assembly and disassembly, whereby miscibility and RGG domain valency are tuned by protease activity. Second, we control droplet composition by selectively recruiting cargo molecules via protein interaction motifs. We then demonstrate protease-triggered controlled release of cargo. Droplet assembly and cargo recruitment are robust, occurring in cytoplasmic extracts and in living mammalian cells. This versatile system, which generates dynamic membraneless organelles with programmable phase behavior and composition, has important applications for compartmentalizing collections of proteins in engineered cells and protocells.

Optochemical Control of Protein Localization and Activity within Cell-like Compartments

We report inducible dimerization strategies for controlling protein positioning, enzymatic activity, and organelle assembly inside synthetic cell-like compartments upon photostimulation. Using a photocaged TMP-Haloligand compound, we demonstrate small molecule and light-induced dimerization of DHFR and Haloenzyme to localize proteins to a compartment boundary and reconstitute tripartite sfGFP assembly. Using photocaged rapamycin and fragments of split TEV protease fused to FRB and FKBP, we establish optical triggering of protease activity inside cell-size compartments. We apply light-inducible protease activation to initiate assembly of membraneless organelles, demonstrating the applicability of these tools for characterizing cell biological processes in vitro. This modular toolkit, which affords spatial and temporal control of protein function in a minimal cell-like system, represents a critical step toward the reconstitution of a tunable synthetic cell, built from the bottom up.

Oxygen and carbon dioxide fluxes from barley shoots depend on nitrate assimilation

A custom oxygen analyzer in conjunction with an infrared carbon dioxide analyzer and humidity sensors permitted simultaneous measurements of oxygen, carbon dioxide, and water vapor fluxes from the shoots of intact barley plants (Hordeum vulgare L. cv Steptoe). The oxygen analyzer is based on a calciazirconium sensor and can resolve concentration differences to within 2 microliters per liter against the normal background of 210,000 microliters per liter. In wild-type plants receiving ammonium as their sole nitrogen source or in nitrate reductase-deficient mutants, photosynthetic and respiratory fluxes of oxygen equaled those of carbon dioxide. By contrast, wild-type plants exposed to nitrate had unequal oxygen and carbon dioxide fluxes: oxygen evolution at high light exceeded carbon dioxide consumption by 26% and carbon dioxide evolution in the dark exceeded oxygen consumption by 25%. These results indicate that a substantial portion of photosynthetic electron transport or respiration generates reductant for nitrate assimilation rather than for carbon fixation or mitochondrial electron transport.

Root excision decreases nutrient absorption and gas fluxes

The roots of barley plants (Hordeum vulgare L. cv Steptoe) were monitored before and after excision for net uptake of carbon dioxide, oxygen, ammonium, potassium, nitrate, and chloride and for their content of sucrose, glucose, fructose, and malic acid. All fluxes began to attenuate within 2 hours after excision. Net potassium uptake returned to control levels 6 hours after excision, but carbon dioxide, oxygen, ammonium, and nitrate fluxes continued to diminish for the remainder of the observation period. The addition of 0.1 molar glucose or 0.1 molar sucrose to excision medium had no significant effect on these changes in ion and gas fluxes. Net chloride uptake was negligible for all treatments. Sugar and malic acid content of the root declined after excision. Sucrose and glucose levels remained depressed for the entire observation period, whereas fructose and malic acid returned to control levels after 9 hours. These results indicate that excision has profound, adverse effects on root respiration and the absorption of mineral nitrogen.

Concerted evolution of human amylase genes

Cosmid clones containing 250 kilobases of genomic DNA from the human amylase gene cluster have been isolated. These clones contain seven distinct amylase genes which appear to comprise the complete multigene family. By sequence comparison with the cDNAs, we have identified two pancreatic amylase genes and three salivary amylase genes. Two truncated pseudogenes were also recovered. Intergenic distances of 17 to 22 kilobases separate the amylase gene copies. Within the past 10 million years, duplications, gene conversions, and unequal crossover events have resulted in a very high level of sequence similarity among human amylase gene copies. To identify sequence elements involved in tissue-specific expression and hormonal regulation, the promoter regions of the human amylase genes were sequenced and compared with those of the corresponding mouse genes. The promoters of the human and mouse pancreatic amylase genes are highly homologous between nucleotide -160 and the cap site. Two sequence elements thought to influence pancreas-specific expression of the rodent genes are present in the human genes. In contrast, similarity in the 5' flanking sequences of the salivary amylase genes is limited to several short sequence elements whose positions and orientations differ in the two species. Some of these sequence elements are also associated with other parotid-specific genes and may be involved in their tissue-specific expression. A glucocorticoid response element and a general enhancer element are closely associated in several of the amylase promoters.

Evolution of the amylase multigene family. YBR/Ki mice express a pancreatic amylase gene which is silent in other strains

The two isozymes of pancreatic amylase in mouse strain YBR/Ki are encoded by closely linked genes which are independently regulated. We have isolated these two pancreatic amylase genes, Amy-2.1 and Amy-2.2, from a cosmid library of YBR/Ki genomic DNA and compared the nucleotide sequences of coding regions with the amino acid sequences of the protein isozymes. Transcripts of both genes were also isolated from a pancreatic cDNA library and partially sequenced. The results demonstrate that Amy-2.1 encodes the A1 isozyme of YBR/Ki pancreatic amylase, while Amy- 2.2 encodes the insulin-dependent B1 isozyme. Similarities of restriction maps and nucleotide sequences suggest that Amy-2.1 is closely related to the active Amy-2a gene previously isolated from strain A/J (Schibler, U., Pittet, A.-C., Young, R. A., Hagenbüchle, O., Tosi, M., Gellman, S., and Wellauer, P. K. (1982) J. Mol. Biol. 155, 247-266). Expression of Amy-2.2 may be limited to strain YBR/Ki. The inactive Amy-X gene from A/J (Schibler, U., Pittet, A.-C., Young, R. A., Hagenbüchle, O., Tosi, M., Gellman, S., and Wellauer, P. K. (1982) J. Mol. Biol. 155, 247-266) is apparently a null allele of Amy-2.2. An additional amylase gene from YBR/Ki has been identified as a pancreatic amylase pseudogene which diverged between sixteen and thirty-two million years ago. The pancreatic amylase subfamily in strain YBR/Ki thus consists of two active genes and one pseudogene. The low rate of amylase production in YBR/Ki pancreas, relative to that of other inbred strains, can be accounted for by the lower number of gene copies in this strain. Comparison of pancreatic amylase genes from different inbred strains provides evidence for several duplication and deletion events during the recent evolution of this chromosome region.

Role of renal papillae in the regulation of sodium excretion during acute elevation of renal perfusion pressure in the rat

We studied the role of renal papillae in the mechanism of increased sodium excretion during acute increase in mean arterial pressure (MAP). Sodium excretion increased dramatically in normal rats after acute increase in MAP by epinephrine (E) infusion (0.4 micrograms/min/100g). Glomerular filtration rate (GFR), renal blood flow (RBF), and papillary plasma flow (PPF) remained unchanged after the E administration. To define the role of the medulla in the mechanism of pressure-induced natriuresis, experiments were performed in a group of rats 8 to 12 days after the development of papillary necrosis induced by bromoethylamine hydrobromide. Urinary sodium and fractional sodium excretions were 2.00 +/- 0.34 microEq/min and 2.37 +/- 0.53% (n = 7), respectively, in papillary necrosis rats infused with saline. Administration of E to papillary necrosis rats, however, failed to increase both urinary sodium (2.89 +/- 0.61 microEq/min) and fractional sodium (FENa, 2.82 +/- 0.63%, n = 6) excretions despite a marked increase in MAP (129 vs 150 mm Hg, p less than 0.01). The RBF increased slightly after E infusion (4.42 vs 3.24 ml/min/100 g, p less than 0.05), but the GFR was not different between the control (0.39 +/- 0.05 ml/min/100g, n = 7) and the E-treated rats (0.43 +/- 0.06, n = 6). Failure to increase sodium excretion during acute increase in MAP was not due to the decreased GFR, since control rats with bilateral partial nephrectomy were able to increase sodium excretion from 1.92 +/- 0.33 to 7.76 +/- 1.63 microEq/min (p less than 0.01) after E infusion. These findings, therefore, suggest that renal papillae play a major role in the mechanism of natriuresis during acute increase in MAP.

Renal phosphate excretion in spontaneously hypertensive and normotensive Wistar Kyoto rats

Renal tubular reabsorption of phosphate was studied in unanesthetized spontaneously hypertensive (SHR) and normotensive Wistar Kyoto rats (WKY). Three-hour-urinary phosphate excretions of 12-week-old-male SHR (53.0 +/- 13.1 micrograms/mg creatinine, N = 7) and 14-week-old female SHR (81.8 +/- 12.8, N = 8) were significantly lower than those of age sex-matched WKY (12 week, 435.8 +/- 73.2, N = 8, P less than 0.01; 14 week, 423.3 +/- 75.9, N = 8, P less than 0.01). Renal clearances were performed in 14-week-old female rats after an overnight fast. The serum phosphate concentration of SHR (4.61 +/- 0.25 mg/dl) was lower than that of WKY (5.44 +/- 0.14, P less than 0.02). Urinary phosphate excretion (U Pi V = 6.85 +/- 1.83 micrograms/min) and fractional phosphate excretion (FE Pi = 13.7 +/- 2.3%) of SHR were lower than those of WKY (U Pi V = 15.9 +/- 1.87 micrograms/min, P less than 0.01, FE Pi 22.8 +/- 2.6%, P less than 0.02). Acute hyperventilation could not account for the lower excretion of phosphate in SHR, since arterial pH and PCO2 were not different between WKY and SHR. The low renal phosphate clearance of SHR was noted at a very early age; the U Pi V of 5-week-old SHR was already lower than that of WKY. Maximum tubular phosphate reabsorption (TmPi) was studied in the 12-week-old SHR and WKY after acute thyroparathyroidectomy. TmPi of SHR (241 +/- 3.0 micrograms/ml GFR/100 g, N = 7) was greater than that of WKY (204 +/- 7.0, N = 8, P less than 0.01). However, the differences in 3-hr urinary phosphate excretion and clearances of phosphate were abolished between SHR and WKY after their blood pressures were lowered by chronic hydralazine treatment. The results indicate that hypertension is responsible for the lower renal phosphate clearances in SHR.

Stomatal Penetration of Wheat Seedlings by Stem and Leaf Rust: Effect of Light and Carbon Dioxide

Removal of atmospheric carbon dioxide enhanced penetration of seedling wheat by stem rust Puccinia graminis in light and dark but did not materially affect penetration by leaf rust P. recondita. A concentration of 5 percent CO(2) nearly suppressed penetration by P. graminis but not by P. recondita. Thus light may promote penetration by P. graminis through photosynthetic reduction of CO(2) within the leaf and P. recondita may penetrate independently of light because it is relatively insensitive to the effects of CO(2).