Structural basis for bacterial energy extraction from atmospheric hydrogen

High-resolution cryo-EM using a common LaB6 120-keV electron microscope equipped with a sub-200-keV direct electron detector

High-resolution cryo-electron microscopy (cryo-EM) requires costly 200- to 300-keV cryo-transmission electron microscopes (cryo-TEMs) with field emission gun (FEG) sources, stable columns, constant-powered lenses, autoloader, and direct electron detectors (DED). Recent advances in 100-keV imaging with the emergence of sub-200-keV optimized DED technology promises the development of more affordable cryo-TEMs. So far, 100-keV imaging has required microscopes with FEG sources. We here explored whether a standard 120-keV TEMs with thermionic lanthanum hexaboride (LaB6) source can be upgraded with a sub-200-keV DED for high-resolution cryo-EM. Using this imaging configuration, we successfully obtained a 2.65 Å reconstruction for apoferritin, 4.33 Å for 64-kDa hemoglobin, and 4.4 Å for an asymmetric 153kDa membrane protein GPCR. All results were achieved using standard automated data collection with SerialEM, demonstrating the feasibility to collect large cryo-EM datasets with a side-entry cryo-holder. These results showcase a widely accessible solution to obtaining interpretable cryo-EM structures at low cost and contribute to the "democratization" of cryo-EM.

Microbiome associated to an H2-emitting zone in the São Francisco basin Brazil

BACKGROUND

Dihydrogen (H₂) natural gas is a clean and renewable energy source of significant interest in the transition to sustainable energy. Unlike conventional petroleum-based fuels, H₂ releases only water vapor upon combustion, making it a promising alternative for reducing carbon footprints in the future. However, the microbial impact on H₂ dynamics in H2-emitting zones remains unclear, as does the origin of H2 - whether it is produced at greater depths or within shallow soil layers. In the São Francisco Basin, soil hydrogen concentrations of approximately 200 ppm were identified in barren ground depressions. In this study, we investigated the microbiome associated with this area using the 16S rRNA gene sequencing, with a focus on metabolic processes related to H₂ consumption and production. Soil samples were collected from two monitored (< 1 m) depths - 10 cm and 1 m - in the emission zone, which is predominantly covered with pasture vegetation, and from an adjacent area with medium and small trees.

RESULTS

Our findings suggest that the H2-emitting zone significantly influences the composition and function of the microbiome, with Bacillus emerging as the dominant genus. In contrast to typical Cerrado soil, we observed a higher prevalence of Actinobacteriota (∼ 40%) and Firmicutes (∼ 20%). Additionally, we identified an abundance of sporulating bacteria and taxonomic groups previously described as H2-oxidizing bacteria.

CONCLUSIONS

The H2-emitting zone in the São Francisco Basin presents a unique opportunity to deepen our understanding of the impact of H₂ on microbial communities. This study is the first to characterize a natural H2-associated bacterial community in Cerrado soil using a culture-independent approach.

Structure of a fully assembled γδ T cell antigen receptor

T cells in jawed vertebrates comprise two lineages, αβ T cells and γδ T cells, defined by the antigen receptors they express-that is, αβ and γδ T cell receptors (TCRs), respectively. The two lineages have different immunological roles, requiring that γδ TCRs recognize more structurally diverse ligands1. Nevertheless, the receptors use shared CD3 subunits to initiate signalling. Whereas the structural organization of αβ TCRs is understood2,3, the architecture of γδ TCRs is unknown. Here, we used cryogenic electron microscopy to determine the structure of a fully assembled, MR1-reactive, human Vγ8Vδ3 TCR-CD3δγε2ζ2 complex bound by anti-CD3ε antibody Fab fragments4,5. The arrangement of CD3 subunits in γδ and αβ TCRs is conserved and, although the transmembrane α-helices of the TCR-γδ and -αβ subunits differ markedly in sequence, packing of the eight transmembrane-helix bundles is similar. However, in contrast to the apparently rigid αβ TCR2,3,6, the γδ TCR exhibits considerable conformational heterogeneity owing to the ligand-binding TCR-γδ subunits being tethered to the CD3 subunits by their transmembrane regions only. Reducing this conformational heterogeneity by transfer of the Vγ8Vδ3 TCR variable domains to an αβ TCR enhanced receptor signalling, suggesting that γδ TCR organization reflects a compromise between efficient signalling and the ability to engage structurally diverse ligands. Our findings reveal the marked structural plasticity of the TCR on evolutionary timescales, and recast it as a highly versatile receptor capable of initiating signalling as either a rigid or flexible structure.

Structure of Aquifex aeolicus lumazine synthase by cryo-electron microscopy to 1.42 Å resolution

Single-particle cryo-electron microscopy (cryo-EM) has become an essential structural determination technique with recent hardware developments making it possible to reach atomic resolution, at which individual atoms, including hydrogen atoms, can be resolved. In this study, we used the enzyme involved in the penultimate step of riboflavin biosynthesis as a test specimen to benchmark a recently installed microscope and determine if other protein complexes could reach a resolution of 1.5 Å or better, which so far has only been achieved for the iron carrier ferritin. Using state-of-the-art microscope and detector hardware as well as the latest software techniques to overcome microscope and sample limitations, a 1.42 Å map of Aquifex aeolicus lumazine synthase (AaLS) was obtained from a 48 h microscope session. In addition to water molecules and ligands involved in the function of AaLS, we can observe positive density for ∼50% of the hydrogen atoms. A small improvement in the resolution was achieved by Ewald sphere correction which was expected to limit the resolution to ∼1.5 Å for a molecule of this diameter. Our study confirms that other protein complexes can be solved to near-atomic resolution. Future improvements in specimen preparation and protein complex stabilization may allow more flexible macromolecules to reach this level of resolution and should become a priority of study in the field.

The missing pieces in the catalytic cycle of [FeFe] hydrogenases

Hydrogen could provide a suitable means for storing energy from intermittent renewable sources for later use on demand. However, many challenges remain regarding the activity, specificity, stability and sustainability of current hydrogen production and consumption methods. The lack of efficient catalysts based on abundant and sustainable elements lies at the heart of this problem. Nature's solution led to the evolution of hydrogenase enzymes capable of reversible hydrogen conversion at high rates using iron- and nickel-based active sites. Through a detailed understanding of these enzymes, we can learn how to mimic them to engineer a new generation of highly active synthetic catalysts. Incredible progress has been made in our understanding of biological hydrogen activation over the last few years. In particular, detailed studies of the [FeFe] hydrogenase class have provided substantial insight into a sophisticated, optimised, molecular catalyst, the active site H-cluster. In this short perspective, we will summarise recent findings and highlight the missing pieces needed to complete the puzzle.

Marine sponge microbe provides insights into evolution and virulence of the tubercle bacillus

Reconstructing the evolutionary origins of Mycobacterium tuberculosis, the causative agent of human tuberculosis, has helped identify bacterial factors that have led to the tubercle bacillus becoming such a formidable human pathogen. Here we report the discovery and detailed characterization of an exceedingly slow growing mycobacterium that is closely related to M. tuberculosis for which we have proposed the species name Mycobacterium spongiae sp. nov., (strain ID: FSD4b-SM). The bacterium was isolated from a marine sponge, taken from the waters of the Great Barrier Reef in Queensland, Australia. Comparative genomics revealed that, after the opportunistic human pathogen Mycobacterium decipiens, M. spongiae is the most closely related species to the M. tuberculosis complex reported to date, with 80% shared average nucleotide identity and extensive conservation of key M. tuberculosis virulence factors, including intact ESX secretion systems and associated effectors. Proteomic and lipidomic analyses showed that these conserved systems are functional in FSD4b-SM, but that it also produces cell wall lipids not previously reported in mycobacteria. We investigated the virulence potential of FSD4b-SM in mice and found that, while the bacteria persist in lungs for 56 days after intranasal infection, no overt pathology was detected. The similarities with M. tuberculosis, together with its lack of virulence, motivated us to investigate the potential of FSD4b-SM as a vaccine strain and as a genetic donor of the ESX-1 genetic locus to improve BCG immunogenicity. However, neither of these approaches resulted in superior protection against M. tuberculosis challenge compared to BCG vaccination alone. The discovery of M. spongiae adds to our understanding of the emergence of the M. tuberculosis complex and it will be another useful resource to refine our understanding of the factors that shaped the evolution and pathogenesis of M. tuberculosis.

Unveiling the Low-Lying Spin States of [Fe3S4] Clusters via the Extended Broken-Symmetry Method

Photosynthetic water splitting, when synergized with hydrogen production catalyzed by hydrogenases, emerges as a promising avenue for clean and renewable energy. However, theoretical calculations have faced challenges in elucidating the low-lying spin states of iron-sulfur clusters, which are integral components of hydrogenases. To address this challenge, we employ the Extended Broken-Symmetry method for the computation of the cubane-[Fe3S4] cluster within the [FeNi] hydrogenase enzyme. This approach rectifies the error caused by spin contamination, allowing us to obtain the magnetic exchange coupling constant and the energy level of the low-lying state. We find that the Extended Broken-Symmetry method provides more accurate results for differences in bond length and the magnetic coupling constant. This accuracy assists in reconstructing the low-spin ground state force and determining the geometric structure of the ground state. By utilizing the Extended Broken-Symmetry method, we further highlight the significance of the geometric arrangement of metal centers in the cluster's properties and gain deeper insights into the magnetic properties of transition metal iron-sulfur clusters at the reaction centers of hydrogenases. This research illuminates the untapped potential of hydrogenases and their promising role in the future of photosynthesis and sustainable energy production.

Outer-sphere effects on the O2 sensitivity, catalytic bias and catalytic reversibility of hydrogenases

The comparison of homologous metalloenzymes, in which the same inorganic active site is surrounded by a variable protein matrix, has demonstrated that residues that are remote from the active site may have a great influence on catalytic properties. In this review, we summarise recent findings on the diverse molecular mechanisms by which the protein matrix may define the oxygen tolerance, catalytic directionality and catalytic reversibility of hydrogenases, enzymes that catalyse the oxidation and evolution of H2. These mechanisms involve residues in the second coordination sphere of the active site metal ion, more distant residues affecting protein flexibility through their side chains, residues lining the gas channel and even accessory subunits. Such long-distance effects, which contribute to making enzymes efficient, robust and different from one another, are a source of wonder for biochemists and a challenge for synthetic bioinorganic chemists.

Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures

Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.

Hydrogen sulfide donors across time: From origins to cutting-edge applications

This review aims to analyze the developmental trajectory of hydrogen sulfide (H2S) donors over the past three decades and explore the historical background, research hotspots, and emerging trends in related fields from a temporal perspective. A total of 5092 literature articles on H2S donors were retrieved from the Web of Science Core Collection (WoSCC), encompassing 1303 journals, 20638 authors, 10992 institutions, and 459 countries and regions. Utilizing CiteSpace as a bibliometric tool, historical features, evolving active topics, and emerging trends in the field of H2S donors were identified. Over the past 30 years, the field of H2S donors has remained in a prominent stage. This article discusses both inorganic and organic types of H2S donors, including NaHS and Na2S, GYY4137, AP39, and AP123, as well as briefly outlines research and applications of H2S donors in nanotechnology, advanced materials, composite materials, nanostructures, and optical properties. Mechanistically, the review outlines how H2S donors regulate cellular signal transduction, anti-inflammatory responses, neuroprotection, and other pathways within the organism by modulating protein S-sulfhydration, antioxidant effects, and interactions with metal proteins. In terms of applications, the review summarizes the extensive use of H2S donors in biomedical research, encompassing cardiovascular, neurological, anti-inflammatory, and anti-cancer characteristics, as well as their potential applications in the treatment of metabolic diseases. Finally, challenges and limitations faced by H2S donor research are discussed, and potential future research directions are proposed.

Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration

Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.

Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis

SUMMARY

Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.

Protein target highlights in CASP15: Analysis of models by structure providers

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.

CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction

For ligand binding prediction, it is crucial for molecular docking programs to integrate template-based modeling with a precise scoring function. Here, we proposed the CoDock-Ligand docking method that combines template-based modeling and the GNINA scoring function, a Convolutional Neural Network-based scoring function, for the ligand binding prediction in CASP15. Among the 21 targets, we obtained successful predictions in top 5 submissions for 14 targets and partially successful predictions for 4 targets. In particular, for the most complicated target, H1114, which contains 56 metal cofactors and small molecules, our docking method successfully predicted the binding of most ligands. Analysis of the failed systems showed that the predicted receptor protein presented conformational changes in the backbone and side chains of the binding site residues, which may cause large structural deviations in the ligand binding prediction. In summary, our hybrid docking scheme was efficiently adapted to the ligand binding prediction challenges in CASP15.

Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition

High-affinity H2-oxidizing bacteria (HA-HOB) thriving in soil are responsible for the most important sink of atmospheric H2. Their activity increases with soil organic carbon content, but the incidence of different carbohydrate fractions on the process has received little attention. Here we tested the hypothesis that carbon amendments impact HA-HOB activity and diversity differentially depending on their recalcitrance and their concentration. Carbon sources (sucrose, starch, cellulose) and application doses (0, 0.1, 1, 3, 5% Ceq soildw-1) were manipulated in soil microcosms. Only 0.1% Ceq soildw-1 cellulose treatment stimulated the HA-HOB activity. Sucrose amendments induced the most significant changes, with an abatement of 50% activity at 1% Ceq soildw-1. This was accompanied with a loss of bacterial and fungal alpha diversity and a reduction of high-affinity group 1 h/5 [NiFe]-hydrogenase gene (hhyL) abundance. A quantitative classification framework was elaborated to assign carbon preference traits to 16S rRNA gene, ITS and hhyL genotypes. The response was uneven at the taxonomic level, making carbon preference a difficult trait to predict. Overall, the results suggest that HA-HOB activity is more susceptible to be stimulated by low doses of recalcitrant carbon, while labile carbon-rich environment is an unfavorable niche for HA-HOB, inducing catabolic repression of hydrogenase.

Developing high-affinity, oxygen-insensitive [NiFe]-hydrogenases as biocatalysts for energy conversion

The splitting of hydrogen (H2) is an energy-yielding process, which is important for both biological systems and as a means of providing green energy. In biology, this reaction is mediated by enzymes called hydrogenases, which utilise complex nickel and iron cofactors to split H2 and transfer the resulting electrons to an electron-acceptor. These [NiFe]-hydrogenases have received considerable attention as catalysts in fuel cells, which utilise H2 to produce electrical current. [NiFe]-hydrogenases are a promising alternative to the platinum-based catalysts that currently predominate in fuel cells due to the abundance of nickel and iron, and the resistance of some family members to inhibition by gases, including carbon monoxide, which rapidly poison platinum-based catalysts. However, the majority of characterised [NiFe]-hydrogenases are inhibited by oxygen (O2), limiting their activity and stability. We recently reported the isolation and characterisation of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis, which is insensitive to inhibition by O2 and has an extremely high affinity, making it capable of oxidising H2 in air to below atmospheric concentrations. These properties make Huc a promising candidate for the development of enzyme-based fuel cells (EBFCs), which utilise H2 at low concentrations and in impure gas mixtures. In this review, we aim to provide context for the use of Huc for this purpose by discussing the advantages of [NiFe]-hydrogenases as catalysts and their deployment in fuel cells. We also address the challenges associated with using [NiFe]-hydrogenases for this purpose, and how these might be overcome to develop EBFCs that can be deployed at scale.

The Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: Insights from CASP15

In CASP15, 87 predictors submitted around 11,000 models on 41 assembly targets. The community demonstrated exceptional performance in overall fold and interface contact prediction, achieving an impressive success rate of 90% (compared to 31% in CASP14). This remarkable accomplishment is largely due to the incorporation of DeepMind's AF2-Multimer approach into custom-built prediction pipelines. To evaluate the added value of participating methods, we compared the community models to the baseline AF2-Multimer predictor. In over 1/3 of cases the community models were superior to the baseline predictor. The main reasons for this improved performance were the use of custom-built multiple sequence alignments, optimized AF2-Multimer sampling, and the manual assembly of AF2-Multimer-built subcomplexes. The best three groups, in order, are Zheng, Venclovas and Wallner. Zheng and Venclovas reached a 73.2% success rate over all (41) cases, while Wallner attained 69.4% success rate over 36 cases. Nonetheless, challenges remain in predicting structures with weak evolutionary signals, such as nanobody-antigen, antibody-antigen, and viral complexes. Expectedly, modeling large complexes remains also challenging due to their high memory compute demands. In addition to the assembly category, we assessed the accuracy of modeling interdomain interfaces in the tertiary structure prediction targets. Models on seven targets featuring 17 unique interfaces were analyzed. Best predictors achieved the 76.5% success rate, with the UM-TBM group being the leader. In the interdomain category, we observed that the predictors faced challenges, as in the case of the assembly category, when the evolutionary signal for a given domain pair was weak or the structure was large. Overall, CASP15 witnessed unprecedented improvement in interface modeling, reflecting the AI revolution seen in CASP14.

A Chimeric NiFe Hydrogenase Heterodimer to Assess the Role of the Electron Transfer Chain in Tuning the Enzyme's Catalytic Bias and Oxygen Tolerance

The observation that some homologous enzymes have the same active site but very different catalytic properties demonstrates the importance of long-range effects in enzyme catalysis, but these effects are often difficult to rationalize. The NiFe hydrogenases 1 and 2 (Hyd 1 and Hyd 2) from E. coli both consist of a large catalytic subunit that embeds the same dinuclear active site and a small electron-transfer subunit with a chain of three FeS clusters. Hyd 1 is mostly active in H2 oxidation and resistant to inhibitors, whereas Hyd 2 also catalyzes H2 production and is strongly inhibited by O2 and CO. Based on structural and site-directed mutagenesis data, it is currently believed that the catalytic bias and tolerance to O2 of Hyd 1 are defined by the distal and proximal FeS clusters, respectively. To test these hypotheses, we produced and characterized a hybrid enzyme made of the catalytic subunit of Hyd 1 and the electron transfer subunit of Hyd 2. We conclude that catalytic bias and sensitivity to CO are set by the catalytic subunit rather than by the electron transfer chain. We confirm the importance of the proximal cluster in making the enzyme Hyd 1 resist long-term exposure to O2, but we show that other structural determinants, in both subunits, contribute to O2 tolerance. A similar strategy based on the design of chimeric heterodimers could be used in the future to elucidate various structure-function relationships in hydrogenases and other multimeric metalloenzymes and to engineer useful hydrogenases that combine the desirable properties of distinct, homologous enzymes.

Synthesis of phosphine derivatives of [Fe2(CO)6(μ-sdt)] (sdt = SCH2SCH2S) and investigation of their proton reduction capabilities

The reactions of [Fe2(CO)6(μ-sdt)] (1) (sdt = SCH2SCH2S) with phosphine ligands have been investigated. Treatment of 1 with dppm (bis(diphenylphosphino)methane) or dcpm (bis(dicyclohexylphosphino)methane) affords the diphosphine-bridged products [Fe2(CO)4(μ-sdt)(μ-dppm)] (2) and [Fe2(CO)4(μ-sdt)(μ-dcpm)] (3), respectively. The complex [Fe2(CO)4(μ-sdt)(κ2-dppv)] (4) with a chelating diphosphine was obtained by reacting 1 with dppv (cis-1,2-bis(diphenylphosphino)ethene). Reaction of 1 with dppe (1,2-bis(diphenylphosphino)ethane) produces [{Fe2(CO)4(μ-sdt)}2(μ-κ1-dppe)] (5) in which the diphosphine forms an intermolecular bridge between two diiron cluster fragments. Three products were obtained when dppf (1,1'-bis(diphenylphosphino)ferrocene) was introduced to complex 1; they were [Fe2(CO)5(μ-sdt)(κ1-dppfO)] (6), the previously known [{Fe2(CO)5(μ-sdt)}2(μ-κ1-κ1-dppf)] (7), and [Fe2(CO)4(μ-sdt)(μ-dppf)] (8), with complex 8 being produced in highest yield. Single crystal X-ray diffraction analysis was performed on compounds 2, 3 and 8. All structures reveal the adoption of an anti-arrangement of the dithiolate bridges, while the diphosphines occupy dibasal positions. Infra-red spectroscopy indicates that the mono-substituted complexes 5, 6, and 7 are inert to protonation by HBF4.Et2O, but complexes 2, 3, 4 and [Fe2(CO)5(μ-sdt)(κ1-PPh3)] (9) show shifts of their ν(C-O) resonances that indicate that protons bind to the metal cores of the clusters. Addition of the one-electron oxidant [Cp2Fe]PF6 does not lead to any discernable shift in the IR resonances. The redox chemistry of the complexes was investigated by cyclic voltammetry, and the abilities of complexes to catalyze electrochemical proton reduction were examined.

CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps

CASP assessments primarily rely on comparing predicted coordinates with experimental reference structures. However, errors in the reference structures can potentially reduce the accuracy of the assessment. This issue is particularly prominent in cryoEM-determined structures, and therefore, in the assessment of CASP15 cryoEM targets, we directly utilized density maps to evaluate the predictions. A method for ranking the quality of protein chain predictions based on rigid fitting to experimental density was found to correlate well with the CASP assessment scores. Overall, the evaluation against the density map indicated that the models are of high accuracy although local assessment of predicted side chains in a 1.52 Å resolution map showed that side-chains are sometimes poorly positioned. The top 136 predictions associated with 9 protein target reference structures were selected for refinement, in addition to the top 40 predictions for 11 RNA targets. To this end, we have developed an automated hierarchical refinement pipeline in cryoEM maps. For both proteins and RNA, the refinement of CASP15 predictions resulted in structures that are close to the reference target structure, including some regions with better fit to the density. This refinement was successful despite large conformational changes and secondary structure element movements often being required, suggesting that predictions from CASP-assessed methods could serve as a good starting point for building atomic models in cryoEM maps for both proteins and RNA. Loop modeling continued to pose a challenge for predictors with even short loops failing to be accurately modeled or refined at times. The lack of consensus amongst models suggests that modeling holds the potential for identifying more flexible regions within the structure.

Biotechnological perspective for wireless energy: H2-based power extraction from air

Despite its extreme scarcity, atmospheric H2 serves as an energy source for some prokaryotes. Recently, Grinter, Kropp, et al. reported the structural, biochemical, electrochemical, and spectroscopic elucidation of an underlying H2 catalyst, a [NiFe]-hydrogenase, which, owing to its extremely high affinity, facilitates the extraction of energy from ambient air.

Novel concepts and engineering strategies for heterologous expression of efficient hydrogenases in photosynthetic microorganisms

Hydrogen is considered one of the key enablers of the transition towards a sustainable and net-zero carbon economy. When produced from renewable sources, hydrogen can be used as a clean and carbon-free energy carrier, as well as improve the sustainability of a wide range of industrial processes. Photobiological hydrogen production is considered one of the most promising technologies, avoiding the need for renewable electricity and rare earth metal elements, the demands for which are greatly increasing due to the current simultaneous electrification and decarbonization goals. Photobiological hydrogen production employs photosynthetic microorganisms to harvest solar energy and split water into molecular oxygen and hydrogen gas, unlocking the long-pursued target of solar energy storage. However, photobiological hydrogen production has to-date been constrained by several limitations. This review aims to discuss the current state-of-the art regarding hydrogenase-driven photobiological hydrogen production. Emphasis is placed on engineering strategies for the expression of improved, non-native, hydrogenases or photosynthesis re-engineering, as well as their combination as one of the most promising pathways to develop viable large-scale hydrogen green cell factories. Herein we provide an overview of the current knowledge and technological gaps curbing the development of photobiological hydrogenase-driven hydrogen production, as well as summarizing the recent advances and future prospects regarding the expression of non-native hydrogenases in cyanobacteria and green algae with an emphasis on [FeFe] hydrogenases.