Engineering a Rhodopsin-Based Photo-Electrosynthetic System in Bacteria for CO2 Fixation

Extracellular-proton-transfer driving high energy-conserving methanogenesis in anaerobic digestion

Anaerobic digestion (AD) is a promising technology to realize the conversion from organic matters to methane, which is highly mediated by syntrophic microbial community via mutualistic interactions. However, small energy available in methanogenic conversion usually limits the metabolic activity. To adapt such energy-limited environment, efficient energy conservation is critical to support active physiological functions of anaerobic consortia for methanogenic metabolism. In this study, the contribution of extracellular proton transfer (EPT) enhancement to achieving energy-conserving methanogenesis in AD was explored. Proton-conductive medium (PCM) was applied to construct efficient proton transport pathway, and a large number of protons from extracellular water were found available to upregulate methanogenesis in AD, as indicated by the increase in the content of 2H (D) in methane molecules (over 40.7%), among which CO2-reduction-to-CH4 was effectively enhanced. The increases of adenosine triphosphate (ATP) concentration (+54.1%) and gene expression activities related to ATPase (+100.0%) and proton pump (+580.1%) revealed that enhanced EPT by PCM promoted transmembrane proton motive force generation to facilitate ATP synthesis. Based on genome-centric metatranscriptomic analyses, MAG14, MAG63 and MAG61 with high energy conservation activity displayed most pronounced positive response to the EPT enhancement. In these core MAGs, the metabolic pathway reconstruction and the key genes activity identification further proved that EPT enhancement-driven efficient ATP synthesis stimulated the cross-feeding of carbon and proton/electron to facilitate microbial mutualism, thereby resulting in the high energy-conserving methanogenesis. Overall, our work provides new insights into how EPT enhancement drives high energy-conserving methanogenesis, expanding our understanding of the ecological role of EPT in AD.

Engineering bionanoreactor in bacteria for efficient hydrogen production

Hydrogen production through water splitting is a vital strategy for renewable and sustainable clean energy. In this study, we developed an approach integrating nanomaterial engineering and synthetic biology to establish a bionanoreactor system for efficient hydrogen production. The periplasmic space (20 to 30 nm) of an electroactive bacterium, Shewanella oneidensis MR-1, was engineered to serve as a bionanoreactor to enhance the interaction between electrons and protons, catalyzed by hydrogenases for hydrogen generation. To optimize electron transfer, we used the microbially reduced graphene oxide (rGO) to coat the electrode, which improved the electron transfer from the electrode to the cells. Native MtrCAB protein complex on S. oneidensis and self-assembled iron sulfide (FeS) nanoparticles acted in tandem to facilitate electron transfer from an electrode to the periplasm. To enhance proton transport, S. oneidensis MR-1 was engineered to express Gloeobacter rhodopsin (GR) and the light-harvesting antenna canthaxanthin. This led to efficient proton pumping when exposed to light, resulting in a 35.6% increase in the rate of hydrogen production. The overexpression of native [FeFe]-hydrogenase further improved the hydrogen production rate by 56.8%. The bionanoreactor engineered in S. oneidensis MR-1 achieved a hydrogen yield of 80.4 μmol/mg protein/day with a Faraday efficiency of 80% at a potential of -0.75 V. This periplasmic bionanoreactor combines the strengths of both nanomaterial and biological components, providing an efficient approach for microbial electrosynthesis.

Rhodopsin-based light-harvesting system for sustainable synthetic biology

Rhodopsins, a diverse class of light-sensitive proteins found in various life domains, have attracted considerable interest for their potential applications in sustainable synthetic biology. These proteins exhibit remarkable photochemical properties, undergoing conformational changes upon light absorption that drive a variety of biological processes. Exploiting rhodopsin's natural properties could pave the way for creating sustainable and energy-efficient technologies. Rhodopsin-based light-harvesting systems offer innovative solutions to a few key challenges in sustainable engineering, from bioproduction to renewable energy conversion. In this opinion article, we explore the recent advancements and future possibilities of employing rhodopsins for sustainable engineering, underscoring the transformative potential of these biomolecules.

Picosecond quantum-classical dynamics reveals that the coexistence of light-induced microbial and animal chromophore rotary motion modulates the isomerization quantum yield of heliorhodopsin

Rhodopsins are light-responsive proteins forming two vast and evolutionary distinct superfamilies whose functions are invariably triggered by the photoisomerization of a single retinal chromophore. In 2018 a third widespread superfamily of rhodopsins called heliorhodopsins was discovered using functional metagenomics. Heliorhodopsins, with their markedly different structural features with respect to the animal and microbial superfamilies, offer an opportunity to study how evolution has manipulated the chromophore photoisomerization to achieve adaptation. One question is related to the mechanism of such a reaction and how it differs from that of animal and microbial rhodopsins. To address this question, we use hundreds of quantum-classical trajectories to simulate the spectroscopically documented picosecond light-induced dynamics of a heliorhodopsin from the archaea thermoplasmatales archaeon (TaHeR). We show that, consistently with the observations, the trajectories reveal two excited state decay channels. However, inconsistently with previous hypotheses, only one channel is associated with the -C13C14- rotation of microbial rhodopsins while the second channel is characterized by the -C11C12- rotation typical of animal rhodopsins. The fact that such -C11C12- rotation is aborted upon decay and ground state relaxation, explains why illumination of TaHeR only produces the 13-cis isomer with a low quantum efficiency. We argue that the documented lack of regioselectivity in double-bond excited state twisting motion is the result of an "adaptation" that could be completely lost via specific residue substitutions modulating the steric hindrance experienced along the isomerization motion.

Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production

The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.

Engineering artificial photosynthesis based on rhodopsin for CO2 fixation

Microbial rhodopsin, a significant contributor to sustaining life through light harvesting, holds untapped potential for carbon fixation. Here, we construct an artificial photosynthesis system which combines the proton-pumping ability of rhodopsin with an extracellular electron uptake mechanism, establishing a pathway to drive photoelectrosynthetic CO2 fixation by Ralstonia eutropha (also known as Cupriavidus necator) H16, a facultatively chemolithoautotrophic soil bacterium. R. eutropha is engineered to heterologously express an extracellular electron transfer pathway of Shewanella oneidensis MR-1 and Gloeobacter rhodopsin (GR). Employing GR and the outer-membrane conduit MtrCAB from S. oneidensis, extracellular electrons and GR-driven proton motive force are integrated into R. eutropha's native electron transport chain (ETC). Inspired by natural photosynthesis, the photoelectrochemical system splits water to supply electrons to R. eutropha via the Mtr outer-membrane route. The light-activated proton pump - GR, supported by canthaxanthin as an antenna, powers ATP synthesis and reverses the ETC to regenerate NADH/NADPH, facilitating R. eutropha's biomass synthesis from CO2. Overexpression of a carbonic anhydrase further enhances CO2 fixation. This artificial photosynthesis system has the potential to advance the development of efficient photosynthesis, redefining our understanding of the ecological role of microbial rhodopsins in nature.

Self-Powered Biohybrid Systems Based on Organic Materials for Sustainable Biosynthesis

Sustainable energy conversion and effective biosynthesis for value-added chemicals have attracted considerable attention, but most biosynthesis systems cannot work independently without external power. In this work, a self-powered biohybrid system based on organic materials is designed and constructed successfully by integrating electroactive microorganisms with electrochemical devices. Among them, the hybrid living materials based on S. oneidensis/poly[3-(3'-N,N,N-triethylamino-1'-propyloxy)-4-methyl-2,5-thiophene chloride] (PMNT) biofilms for microbial fuel cells played a crucial role in electrocatalytic biocurrent generation by using biowaste as the only energy source. Without any external power supplies, the self-powered biohybrid systems could generate, convert, and store electrical energy for effective photosynthetic regulation and sustained chemical production. This work provides a new strategy to combine comprehensive renewable energy production with chemical manufacturing without an external power source in the future.

Toward Interdisciplinary Synergies in Molecular Communications: Perspectives from Synthetic Biology, Nanotechnology, Communications Engineering and Philosophy of Science

Within many chemical and biological systems, both synthetic and natural, communication via chemical messengers is widely viewed as a key feature. Often known as molecular communication, such communication has been a concern in the fields of synthetic biologists, nanotechnologists, communications engineers, and philosophers of science. However, interactions between these fields are currently limited. Nevertheless, the fact that the same basic phenomenon is studied by all of these fields raises the question of whether there are unexploited interdisciplinary synergies. In this paper, we summarize the perspectives of each field on molecular communications, highlight potential synergies, discuss ongoing challenges to exploit these synergies, and present future perspectives for interdisciplinary efforts in this area.

Revealing CO2-Fixing SAR11 Bacteria in the Ocean by Raman-Based Single-Cell Metabolic Profiling and Genomics

The majority of marine microbes remain uncultured, which hinders the identification and mining of CO2-fixing genes, pathways, and chassis from the oceans. Here, we investigated CO2-fixing microbes in seawater from the euphotic zone of the Yellow Sea of China by detecting and tracking their 13C-bicarbonate (13C-HCO3-) intake via single-cell Raman spectra (SCRS) analysis. The target cells were then isolated by Raman-activated Gravity-driven Encapsulation (RAGE), and their genomes were amplified and sequenced at one-cell resolution. The single-cell metabolism, phenotype and genome are consistent. We identified a not-yet-cultured Pelagibacter spp., which actively assimilates 13C-HCO3-, and also possesses most of the genes encoding enzymes of the Calvin-Benson cycle for CO2 fixation, a complete gene set for a rhodopsin-based light-harvesting system, and the full genes necessary for carotenoid synthesis. The four proteorhodopsin (PR) genes identified in the Pelagibacter spp. were confirmed by heterologous expression in E. coli. These results suggest that hitherto uncultured Pelagibacter spp. uses light-powered metabolism to contribute to global carbon cycling.