Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells.

ABSTRACT: Bottom-up and top-down approaches to synthetic biology each employ distinct methodologies with the common aim to harness living systems. Here, we realize a strategic merger of both approaches to convert light into proton gradients for the actuation of synthetic cellular systems. We genetically engineer E. coli to overexpress the light-driven inward-directed proton pump xenorhodopsin and encapsulate them in artificial cell-sized compartments. Exposing the compartments to light-dark cycles, we reversibly switch the pH by almost one pH unit and employ these pH gradients to trigger the attachment of DNA structures to the compartment periphery. For this purpose, a DNA triplex motif serves as a nanomechanical switch responding to the pH-trigger of the E. coli. When DNA origami plates are modified with the pH-sensitive triplex motif, the proton-pumping E. coli can trigger their attachment to giant unilamellar lipid vesicles (GUVs) upon illumination. A DNA cortex is formed upon DNA origami polymerization, which sculpts and deforms the GUVs. We foresee that the combination of bottom-up and top down approaches is an efficient way to engineer synthetic cells.

SUBMITTER: Jahnke K

PROVIDER: S-EPMC8233306 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Antenna proton sensitivity determines photosynthetic light harvesting strategy.

Project description:Photoprotective non-photochemical quenching (NPQ) represents an effective way to dissipate the light energy absorbed in excess by most phototrophs. It is often claimed that NPQ formation/relaxation kinetics are determined by xanthophyll composition. We, however, found that, for the alveolate alga Chromera velia, this is not the case. In the present paper, we investigated the reasons for the constitutive high rate of quenching displayed by the alga by comparing its light harvesting strategies with those of a model phototroph, the land plant Spinacia oleracea. Experimental results and in silico studies support the idea that fast quenching is due not to xanthophylls, but to intrinsic properties of the Chromera light harvesting complex (CLH) protein, related to amino acid composition and protein folding. The pKa for CLH quenching was shifted by 0.5 units to a higher pH compared with higher plant antennas (light harvesting complex II; LHCII). We conclude that, whilst higher plant LHCIIs are better suited for light harvesting, CLHs are 'natural quenchers' ready to switch into a dissipative state. We propose that organisms with antenna proteins intrinsically more sensitive to protons, such as C. velia, carry a relatively high concentration of violaxanthin to improve their light harvesting. In contrast, higher plants need less violaxanthin per chlorophyll because LHCII proteins are more efficient light harvesters and instead require co-factors such as zeaxanthin and PsbS to accelerate and enhance quenching.

| S-EPMC6093471 | biostudies-literature

Ultrafast delocalization of excitation in synthetic light-harvesting nanorings.

Project description:Rings of chlorophyll molecules harvest sunlight remarkably efficiently during photosynthesis in purple bacteria. The key to their efficiency lies in their highly delocalized excited states that allow for ultrafast energy migration. Here we show that a family of synthetic nanorings mimic the ultrafast energy transfer and delocalization observed in nature. π-Conjugated nanorings with diameters of up to 10 nm, consisting of up to 24 porphyrin units, are found to exhibit excitation delocalization within the first 200 fs of light absorption. Transitions from the first singlet excited state of the circular nanorings are dipole-forbidden as a result of symmetry constraints, but these selection rules can be lifted through static and dynamic distortions of the rings. The increase in the radiative emission rate in the larger nanorings correlates with an increase in static disorder expected from Monte Carlo simulations. For highly symmetric rings, the radiative rate is found to increase with increasing temperature. Although this type of thermally activated superradiance has been theoretically predicted in circular chromophore arrays, it has not previously been observed in any natural or synthetic systems. As expected, the activation energy for emission increases when a nanoring is fixed in a circular conformation by coordination to a radial template. These nanorings offer extended chromophores with high excitation delocalization that is remarkably stable against thermally induced disorder. Such findings open new opportunities for exploring coherence effects in nanometer molecular rings and for implementing these biomimetic light-harvesters in man-made devices.

| S-EPMC5424671 | biostudies-literature

Xanthorhodopsin: a proton pump with a light-harvesting carotenoid antenna.

Project description:Energy transfer from light-harvesting carotenoids to chlorophyll is common in photosynthesis, but such antenna pigments have not been observed in retinal-based ion pumps and photoreceptors. Here we describe xanthorhodopsin, a proton-pumping retinal protein/carotenoid complex in the eubacterium Salinibacter ruber. The wavelength dependence of the rate of pumping and difference absorption spectra measured under a variety of conditions indicate that this protein contains two chromophores, retinal and the carotenoid salinixanthin, in a molar ratio of about 1:1. The two chromophores interact strongly, and light energy absorbed by the carotenoid is transferred to the retinal with a quantum efficiency of approximately 40%. The antenna carotenoid extends the wavelength range of the collection of light for uphill transmembrane proton transport.

| S-EPMC3065861 | biostudies-literature

DNA as UV light-harvesting antenna.

Project description:The ordered structure of UV chromophores in DNA resembles photosynthetic light-harvesting complexes in which quantum coherence effects play a major role in highly efficient directional energy transfer. The possible role of coherent excitons in energy transport in DNA remains debated. Meanwhile, energy transport properties are greatly important for understanding the mechanisms of photochemical reactions in cellular DNA and for DNA-based artificial nanostructures. Here, we studied energy transfer in DNA complexes formed with silver nanoclusters and with intercalating dye (acridine orange). Steady-state fluorescence measurements with two DNA templates (15-mer DNA duplex and calf thymus DNA) showed that excitation energy can be transferred to the clusters from 21 and 28 nucleobases, respectively. This differed from the DNA-acridine orange complex for which energy transfer took place from four neighboring bases only. Fluorescence up-conversion measurements showed that the energy transfer took place within 100 fs. The efficient energy transport in the Ag-DNA complexes suggests an excitonic mechanism for the transfer, such that the excitation is delocalized over at least four and seven stacked bases, respectively, in one strand of the duplexes stabilizing the clusters. This result demonstrates that the exciton delocalization length in some DNA structures may not be limited to just two bases.

| S-EPMC6283424 | biostudies-literature

Programming Light-Harvesting Efficiency Using DNA Origami.

Project description:The remarkable performance and quantum efficiency of biological light-harvesting complexes has prompted a multidisciplinary interest in engineering biologically inspired antenna systems as a possible route to novel solar cell technologies. Key to the effectiveness of biological "nanomachines" in light capture and energy transport is their highly ordered nanoscale architecture of photoactive molecules. Recently, DNA origami has emerged as a powerful tool for organizing multiple chromophores with base-pair accuracy and full geometric freedom. Here, we present a programmable antenna array on a DNA origami platform that enables the implementation of rationally designed antenna structures. We systematically analyze the light-harvesting efficiency with respect to number of donors and interdye distances of a ring-like antenna using ensemble and single-molecule fluorescence spectroscopy and detailed Förster modeling. This comprehensive study demonstrates exquisite and reliable structural control over multichromophoric geometries and points to DNA origami as highly versatile platform for testing design concepts in artificial light-harvesting networks.

| S-EPMC5003508 | biostudies-literature

Identification of proton-active residues in a higher plant light-harvesting complex.

Project description:The thermal dissipation of absorbed light energy by the light-harvesting apparatus of higher plants is important in protecting the photosynthetic machinery from the effects of excess illumination. A major mechanism for such photoprotection, known as trans-thylakoid delta pH-dependent chlorophyll fluorescence quenching (qE), is induced by acidification of the lumen, is correlated with the interconversion of xanthophyll pigments, and is manifested as quenching of chloropyll fluorescence. The mechanistic basis for qE remains unknown. The reagent N, N'-dicyclohexylcarbodiimide (DCCD) specifically inhibits qE and covalently binds to two minor light-harvesting pigment-protein complexes (LHCII), LHCIIa and LHCIIc. It is shown that DCCD treatment of isolated LHCIIc complexes reverses acid-induced chlorophyll fluorescence quenching in an in vitro system. Fingerprinting of [14C]DCCD-labeled LHCIIc demonstrates that there are two DCCD-sensitive amino acid residues on this complex, and these are shown to be glutamate residues, each of which is located near the lumen. In view of the effects of DCCD on the pattern of proton release from photosystem II during photosynthesis, we propose a model for the mechanism of the induction of qE--that these residues from part of a proton pathway, the lumen pH being sensed via its effects on the rate of proton release. One possibility is that the resulting changes in the protonation state of these carboxyl side chains may modulate the structural and energetic organization of LHCII.

| S-EPMC19518 | biostudies-literature

Orthogonal Light-Activated DNA for Patterned Biocomputing within Synthetic Cells.

Project description:Cell-free gene expression is a vital research tool to study biological systems in defined minimal environments and has promising applications in biotechnology. Developing methods to control DNA templates for cell-free expression will be important for precise regulation of complex biological pathways and use with synthetic cells, particularly using remote, nondamaging stimuli such as visible light. Here, we have synthesized blue light-activatable DNA parts that tightly regulate cell-free RNA and protein synthesis. We found that this blue light-activated DNA could initiate expression orthogonally to our previously generated ultraviolet (UV) light-activated DNA, which we used to generate a dual-wavelength light-controlled cell-free AND-gate. By encapsulating these orthogonal light-activated DNAs into synthetic cells, we used two overlapping patterns of blue and UV light to provide precise spatiotemporal control over the logic gate. Our blue and UV orthogonal light-activated DNAs will open the door for precise control of cell-free systems in biology and medicine.

| S-EPMC10161232 | biostudies-literature

Energy transfer-enhanced photocatalytic reduction of protons within quantum dot light-harvesting-catalyst assemblies.

Project description:Excitonic energy transfer (EnT) is the mechanism by which natural photosynthetic systems funnel energy from hundreds of antenna pigments to a single reaction center, which allows multielectron redox reactions to proceed with high efficiencies in low-flux natural light. This paper describes the use of electrostatically assembled CdSe quantum dot (QD) aggregates as artificial light harvesting-reaction center units for the photocatalytic reduction of H+ to H2, where excitons are funneled through EnT from sensitizer QDs (sQDs) to catalyst QDs (cQDs). Upon increasing the sensitizer-to-catalyst ratio in the aggregates from 1:2 to 20:1, the number of excitons delivered to each cQD (via EnT) per excitation of the system increases by a factor of nine. At the optimized sensitizer-to-catalyst ratio of 4:1, the internal quantum efficiency (IQE) of the reaction system is 4.0 ± 0.3%, a factor of 13 greater than the IQE of a sample that is identical except that EnT is suppressed due to the relative core sizes of the sQDs and cQDs. A kinetic model supports the proposed exciton funneling mechanism for enhancement of the catalytic activity.

| S-EPMC6099859 | biostudies-other

Enhanced DNA repair by DNA photolyase bearing an artificial light-harvesting chromophore.

Project description:Photolyases are flavoenzymes responsible for the repair of carcinogenic DNA damage caused by ultraviolet radiation. They harbor the catalytic cofactor flavin adenine dinucleotide (FAD). The light-driven electron transfer from the excited state of the fully-reduced form of FAD to the DNA lesions causes rearrangement of the covalent bonds, leading to the restoration of intact nucleobases. In addition to the catalytic chromophore, some photolyases bear a secondary chromophore with better light absorption capability than FAD, acting as a light-harvesting chromophore that harvests photons in sunlight efficiently and transfers light energy to the catalytic center, as observed in natural photoreceptor proteins. Inspired by nature, we covalently and site-specifically attached a synthetic chromophore to the surface of photolyase using oligonucleotides containing a modified nucleoside and a cyclobutane-type DNA lesion, and successfully enhanced its enzymatic activity in the light-driven DNA repair. Peptide mapping in combination with theoretical calculations identified the amino acid residue that binds to the chromophore, working as an artificial light-harvesting chromophore. Our results broaden the strategies for protein engineering and provide a guideline for tuning of the light perception abilities and enzymatic activity of the photoreceptor proteins.

| S-EPMC7544235 | biostudies-literature

Supramolecular assembly of phenanthrene-DNA conjugates into light-harvesting nanospheres.

Project description:The self-assembly of highly functionalized phenanthrene-DNA conjugates into supramolecular nanostructures is presented. DNA oligomers modified with phenanthrene residues at the 3'-end and internal positions self-assemble into spherical nanostructures. The nanospheres exhibit light-harvesting properties. Upon irradiation of phenanthrene, the excitation energy is transferred along phenanthrene units, resulting in phenanthrene-pyrene exciplex formation.

| S-EPMC11367589 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data