bims-enlima Biomed News
on Engineered living materials
Issue of 2025–04–20
twenty-six papers selected by
Rahul Kumar, Tallinna Tehnikaülikool
  1. Hydrogels with prestressed tensegrity structures.
  2. Mechanically robust non-swelling cold water fish gelatin hydrogels for 3D bioprinting.
  3. Preclinical Assessment of Living Therapeutic Materials: State-of-Art and Challenges.
  4. Cocrystals combining order and correlated disorder via colloidal crystal engineering with DNA.
  5. Ultrasound Cavitation Enables Rapid, Initiator-Free Fabrication of Tough Anti-Freezing Hydrogels.
  6. Engineering intercellular communication using M13 phagemid and CRISPR-based gene regulation for multicellular computing in Escherichia coli.
  7. Convergence of DNA nanotechnology and polymer chemistry to 'synthesize' nanopolymers with branching architectures: a computational perspective.
  8. Advancing Yeast Metabolism for a Sustainable Single Carbon Bioeconomy.
  9. Engineered depalmitoylases enable selective manipulation of protein localization and function.
  10. Metabolic Regulation and Engineering Strategies of Carbon and Nitrogen Metabolism in Escherichia coli.
  11. Expanding catalytic versatility of modular polyketide synthases for alcohol biosynthesis.
  12. Print, melt, repeat: 3D-printing formula yields sturdy objects time after time.
  13. Plug-and-play engineering of modular polyketide synthases.
  14. The impact of fungal developmental structures on mechanical properties of mycelial materials.
  15. Optochemical control over mRNA translation by photocaged phosphorodiamidate morpholino oligonucleotides in vivo.
  16. Production of borneol, camphor, and bornyl acetate using engineered Saccharomyces cerevisiae.
  17. Assessing the feasibility of CRISPRa approaches to enhance protein-based biomaterial expression in bacterial systems for more efficient production.
  18. Mechanical control of the alternative splicing factor PTBP1 regulates extracellular matrix stiffness induced proliferation and cell spreading.
  19. Engineering Magnetotactic Bacteria as Medical Microrobots.
  20. Hydrophilic/Omniphobic Droplet Arrays for High-throughput and Quantitative Enzymology.
  21. Induced proximity to PML protects TDP-43 from aggregation via SUMO-ubiquitin networks.
  22. Functionally Tunable Star-Shaped Multivalent crRNAs for Photocontrol CRISPR/Cas Editing.
  23. Engineered interaction elements enable enhanced multi-enzyme assembly and cascade biocatalysis for indigo synthesis.
  24. Stretchable composites with high oxide loading.
  25. Conformationally Locked Peptide-DNA Nanostructures for CRISPR-Amplified Activity-Based Sensing.
  26. A hydrophobic photouncaging reaction to profile the lipid droplet interactome in tissues.
  1. Nat Commun. 2025 Apr 16. 16(1): 3637
    Hydrogels with prestressed tensegrity structures.
    Bin Xue, Xu Han, Haoqi Zhu, Qingtai Li, Yu Zhang, Ming Bai, Ying Li, Yiran Li, Meng Qin, Tasuku Nakajima, Wei Wang, Jian Ping Gong, Yi Cao.
      Tensegrity structures are isolated rigid compression components held in place by a continuous network of tensile components, and are central to natural systems such as the extracellular matrix and the cell cytoskeleton. These structures enable the nonreciprocal mechanical properties essential for dynamic biological functions. Here, we introduce a synthetic approach to engineer hydrogels with tensegrity architectures, drawing inspiration from the mechanochemical principles underlying biological systems. By employing in-situ enzyme-induced amino acid crystal growth within preformed polymeric networks, we achieve a hierarchical integration of micro crystal sticks randomly interlocked in the prestressed polymer matrice. This design mirrors natural tensegrity structures, balancing mechanical forces to maintain high stiffness (tensile moduli up to 30 MPa), fracture toughness (2600 J m⁻²), and water content (exceeding 80%). The resultant hydrogels exhibit bimodulus behavior due to their tensegrity structure, featuring a tensile-to-compressive modulus ratio of 13. This biomimetic approach provides a strategy for creating robust, adaptive materials for applications in tissue engineering and beyond.
    DOI:  https://doi.org/10.1038/s41467-025-58956-3
  2. Mater Today Bio. 2025 Jun;32 101701
    Mechanically robust non-swelling cold water fish gelatin hydrogels for 3D bioprinting.
    Tobias Hammer, Ke Yang, Tobias Spirig, Barbara Meier-Schiesser, Markus Rottmar, Katharina Maniura-Weber, René M Rossi, Kongchang Wei.
      Three-dimensional (3D) bioprinting of hydrogels allows embedded cells to be patterned and hosted in an extracellular matrix (ECM)-mimicking environment. This method shows great promise for the engineering of complex tissues on account of the facile spatial control over materials and cells within the printed constructs. Hydrogels, which represent extensively explored and employed biomaterials for 3D bioprinting, are characterized by both their high water content and swelling behavior. Post-printing swelling inevitably alters the geometrical and mechanical properties of printed features, thus causing a deviation from the original design and affecting both cellular function and tissue structure. Despite substantial effort being dedicated to the development of non-swelling hydrogels, their application in 3D encapsulation and bioprinting of living cells is yet to be realized, owing to limitations imposed by their often tedious material syntheses and complex network structures. Herein, we describe a new type of non-swelling hydrogel based fully on cold water fish gelatin (cfGel-Hydrogel) consisting of only a single network formed via thiol-ene "click" chemistry. We show that such cfGel-Hydrogels enable 3D patterning of living cells in a shape-retaining and mechanically robust matrix. These cfGel-Hydrogels show negligible swelling (<2 %) under physiologically relevant conditions (simulated by 37 °C PBS buffer), while also being able to withstand large cyclic deformations (80 % compressive strain) by dissipating around 40 % of the imposed loading energy. Human dermal fibroblast (HDF)-laden cfGel-Hydrogels could be fabricated via extrusion-based 3D printing, allowing for the in vitro culturing of cells in shape-retaining constructs, thus offering new opportunities for hydrogel-based applications in tissue engineering and regenerative medicine.
    DOI:  https://doi.org/10.1016/j.mtbio.2025.101701
  3. ACS Biomater Sci Eng. 2025 Apr 15.
    Preclinical Assessment of Living Therapeutic Materials: State-of-Art and Challenges.
    Krupansh Desai, Joëlle Mekontso, Ketaki Deshpande, Sara Trujillo.
      Living Therapeutic Materials represent a promising technology to tackle therapeutic problems that classical materials cannot address. Despite the advancements on new functions of these devices, new applications, and new fabrication methods, the preclinical evaluation of Living Therapeutic Materials is still very limited and new challenges appear when incorporating the living devices in contact with the host. This is a critical bottleneck in the path to translation to the clinic. Therefore, we have compiled the literature on Living Therapeutic Materials, with a focus on microorganism-based living therapeutic materials, and summarized the investigations carried out to assess their biocompatibility, safety, and efficacy. We have split the investigations in three parts: in vitro, ex vivo, and in vivo assessments, where we describe common practices and remaining challenges.
    Keywords:  Living Therapeutic Materials; biocompatibility; drug delivery; preclinical assessment
    DOI:  https://doi.org/10.1021/acsbiomaterials.5c00247
  4. Sci Adv. 2025 Apr 18. 11(16): eadu4919
    Cocrystals combining order and correlated disorder via colloidal crystal engineering with DNA.
    Yuanwei Li, Wenjie Zhou, Yuan Zhou, Ho Fung Cheng, Byeongdu Lee, Xiaobing Hu, Eric W Roth, Vinayak P Dravid, Sharon C Glotzer, Chad A Mirkin.
      Colloidal cocrystallization enables the formation of multicomponent materials with unique physicochemical properties, yet the role of nanoparticle (NP) shape and specific ligand interactions to cocrystallize anisotropic and isotropic NPs, with order and correlated disorder, remains underexplored. Here, geometry-inspired strategies along with programmable DNA interactions are combined to achieve structural control of colloidal cocrystal assemblies. Coassembling polyhedral and spherical NPs with complementary DNA yields two classes of cocrystals: one where both components order, and another where polyhedral NPs form a periodic lattice, while spherical NPs remain disordered but spatially correlated with polyhedral edges and corners. The size ratio of the building blocks can be used to control the ordering of spherical NPs-smaller octahedral-to-sphere size ratios favor fully ordered cocrystals. Molecular dynamics simulations further elucidate the role of NP shapes and dimensions in the structural outcome of the cocrystal. This work provides a framework for deliberately targeting and accessing crystals with exotic multicomponent structures.
    DOI:  https://doi.org/10.1126/sciadv.adu4919
  5. Adv Sci (Weinh). 2025 Apr 17. e2416844
    Ultrasound Cavitation Enables Rapid, Initiator-Free Fabrication of Tough Anti-Freezing Hydrogels.
    Yixun Cheng, Stephen Lee, Yihang Xiao, Shou Ohmura, Louis-Jacques Bourdages, Justin Puma, Zixin He, Zhen Yang, Jeremy Brown, Jean Provost, Jianyu Li.
      Hydrogels are often synthesized with thermal or photo-initiated gelation, leaving alternative energy sources less explored. While ultrasound has been used for polymer synthesis and mechanochemistry, its application through cavitation for hydrogel synthesis as a constructive force is rare, and the underlying sonochemical mechanisms are poorly understood. Here, the application and mechanism of ultrasound cavitation for rapid, initiator-free, and oxygen-tolerant fabrication of tough anti-freezing hydrogels is reported. By incorporating polyol solvents and interpenetrating polymers into the gelling solution, radical generation is amplified and network formation is enhanced. Using tough polyacrylamide-alginate hydrogels as a model system, rapid gelation (as fast as 2 minutes) and high fracture toughness (up to 600 J m- 2) is demonstrated. By varying ultrasound intensity, crosslinker-to-monomer ratio, and glycerol concentration, the synthesis-structure-property relation is established for the resulting sonogels and the underlying mechanism is uncovered using combined molecular, optical, and mechanical testing techniques. The coupling of gelation and convection under ultrasound results in sonogels with unique structural and mechanical properties. Additionally, the fabrication of hydrogel constructs is demonstrated using both non-focused and high-intensity focused ultrasound. This work establishes a foundation for ultrasound-driven sono-fabrication and highlights new avenues in soft materials, advanced manufacturing, bioadhesives, and tissue engineering.
    Keywords:  hydrogels; mechanical properties; radical polymerization; sonochemistry; ultrasound
    DOI:  https://doi.org/10.1002/advs.202416844
  6. Nat Commun. 2025 Apr 15. 16(1): 3569
    Engineering intercellular communication using M13 phagemid and CRISPR-based gene regulation for multicellular computing in Escherichia coli.
    Hadiastri Kusumawardhani, Florian Zoppi, Roberto Avendaño, Yolanda Schaerli.
      Engineering multicellular consortia, where information processing is distributed across specialized cell types, offers a promising strategy for implementing sophisticated biocomputing systems. However, a major challenge remains in establishing orthogonal intercellular communication, or "wires," within synthetic bacterial consortia. In this study, we address this bottleneck by integrating phagemid-mediated intercellular communication with CRISPR-based gene regulation for multicellular computing in synthetic E. coli consortia. We achieve intercellular communication with high sensitivity by regulating the transfer of single guide RNAs (sgRNAs) encoded on M13 phagemids from sender to receiver cells. Once inside the receiver cells, the transferred sgRNAs mediate gene regulation via CRISPR interference. Leveraging this approach, we successfully constructed one-, two-, and four-input logic gates. Our work expands the toolkit for intercellular communication and paves the way for complex information processing in synthetic microbial consortia, with diverse potential applications, including biocomputing, biosensing, and biomanufacturing.
    DOI:  https://doi.org/10.1038/s41467-025-58760-z
  7. Soft Matter. 2025 Apr 17.
    Convergence of DNA nanotechnology and polymer chemistry to 'synthesize' nanopolymers with branching architectures: a computational perspective.
    Tianyun Cai, Qianlin Cai, Jiaping Lin, Liangshun Zhang.
      Polymer-like superstructures termed nanopolymers from the self-assembly of atom-like nanoparticles are an emerging class of structured metamaterials with enhanced functionalities, but the controllable 'synthesis' of nanopolymers with non-linear architecture and spatially defined dimensions remains a challenge. Inspired by synthetic concepts of branched polymers, we propose a hierarchical polymerization-like protocol for the programmable coassembly of DNA-based multicomponent mixtures into non-linear nanopolymers with well-defined branching architecture and predictable spatial dimensions. By employing computational simulations, it is theoretically demonstrated that the synergy of sequence-designed DNA motifs and the proposed protocol enables the precise control over the assembly kinetics of atom-like nanoparticles and the branching architectures of nanopolymers, in agreement with the predictions of the generalized polymerization kinetics model. Furthermore, it is demonstrated that the fundamental correlations between the spatial dimension and branching architecture of nanopolymers satisfy the scaling law acquired in polymer science. These findings will facilitate the programmable coassembly of DNA supramolecules into structured metamaterials with architectural complexity observed in nature.
    DOI:  https://doi.org/10.1039/d5sm00243e
  8. FEMS Yeast Res. 2025 Apr 17. pii: foaf020. [Epub ahead of print]
    Advancing Yeast Metabolism for a Sustainable Single Carbon Bioeconomy.
    Miriam Kuzman, Özge Ata, Diethard Mattanovich.
      Single carbon (C1) molecules are considered as valuable substrates for biotechnology, as they serve as intermediates of carbon dioxide recycling, and enable bio-based production of a plethora of substances of our daily use without relying on agricultural plant production. Yeasts are valuable chassis organisms for biotech production, and they are able to use C1 substrates either natively or as synthetic engineered strains. This review highlights native yeast pathways for methanol and formate assimilation, their engineering, and the realization of heterologous C1 pathways including CO2, in different yeast species. Key features determining the choice among C1 substrates are discussed, including their chemical nature and specifics of their assimilation, their availability, purity and concentration as raw materials, as well as features of the products to be made from them.
    Keywords:  bioeconomy; carbon dioxide; formate; methanol; sustainability
    DOI:  https://doi.org/10.1093/femsyr/foaf020
  9. Nat Commun. 2025 Apr 13. 16(1): 3514
    Engineered depalmitoylases enable selective manipulation of protein localization and function.
    Srinidhi Jayaraman, Audrey Kochiss, Thy-Lan Alcalay, Pedro J Del Rivero Morfin, Manu Ben-Johny.
      S-Palmitoylation is a reversible post-translational modification that tunes the localization, stability, and function of an impressive array of proteins including ion channels, G-proteins, and synaptic proteins. Indeed, altered protein palmitoylation is linked to various human diseases including cancers, neurodevelopmental and neurodegenerative diseases. As such, strategies to selectively manipulate protein palmitoylation with enhanced temporal and subcellular precision are sought after to both delineate physiological functions and as potential therapeutics. Here, we develop chemogenetically and optogenetically inducible engineered depalmitoylases to manipulate the palmitoylation status of target proteins. We demonstrate that this strategy is programmable allowing selective depalmitoylation in specific organelles, triggered by cell-signaling events, and of individual protein complexes. Application of this methodology revealed bidirectional tuning of neuronal excitability by distinct depalmitoylases. Overall, this strategy represents a versatile and powerful method for manipulating protein palmitoylation in live cells, providing insights into their regulation in distinct physiological contexts.
    DOI:  https://doi.org/10.1038/s41467-025-58908-x
  10. ACS Synth Biol. 2025 Apr 17.
    Metabolic Regulation and Engineering Strategies of Carbon and Nitrogen Metabolism in Escherichia coli.
    Jijiao Zhang, Huan Fang, Guangqing Du, Dawei Zhang.
      The intricacies of carbon and nitrogen metabolism in Escherichia coli indeed present both challenges and opportunities for metabolic engineering aimed at optimizing microbial production processes. Carbon is the primary energy source and building block for biomolecules at the cellular level, while nitrogen is vital for synthesizing amino acids, nucleotides, and other nitrogen-containing compounds. This review provides a comprehensive summary of the metabolic regulation of central metabolism and outlines engineering strategies for carbon and nitrogen metabolism in E. coli. This perspective enhances our understanding of the molecular mechanisms involved and enables the development of rational metabolic engineering strategies. One key aspect of metabolic engineering consists of understanding the regulatory networks that govern these processes. Both carbon and nitrogen metabolisms are tightly regulated to ensure cellular homeostasis. By elucidating the interconnected nature of carbon and nitrogen metabolism, this review serves not just to better inform the academic community but also to stimulate advancements in biotechnological applications. Metabolic engineering in E. coli, targeting these complex networks, holds immense promise for the sustainable production of chemicals, biofuels, and pharmaceuticals.
    Keywords:  carbon metabolism; metabolic engineering; metabolic regulation; nitrogen metabolism
    DOI:  https://doi.org/10.1021/acssynbio.5c00039
  11. Nat Chem Biol. 2025 Apr 18.
    Expanding catalytic versatility of modular polyketide synthases for alcohol biosynthesis.
    Shunyu Yao, Shengling Xie, Run-Zhou Liu, Zilei Huang, Lihan Zhang.
      Modular polyketide synthases biosynthesize structurally diverse natural products by a set of catalytic domains that operate in an assembly line fashion. Although extensive research has focused on the rational reprogramming of modular polyketide synthases, little has been attempted to introduce noncanonical catalytic reactions on the assembly line. Here, we demonstrate the insertion of a thioester reductase domain, which can generate a terminal alcohol group instead of the canonical carboxylic acid, onto the assembly line polyketide synthases. We show that the didomain insertion of the acyl carrier protein and thioester reductase pair is generally effective for engineering of various polyketide synthase pathways. As a proof of concept, stereoselective and stereodivergent bioproduction of non-natural diols, namely, 1,3-butanediols and 2-methyl-1,3-butanediols, is achieved by harnessing the modularity of polyketide synthases. Our study expands the catalytic versatility of modular polyketide synthases and paves the way toward biosynthesis of designer alcohols.
    DOI:  https://doi.org/10.1038/s41589-025-01883-7
  12. Nature. 2025 Apr;640(8060): 861
    Print, melt, repeat: 3D-printing formula yields sturdy objects time after time.
      
    Keywords:  Materials science
    DOI:  https://doi.org/10.1038/d41586-025-01110-2
  13. Nat Chem Biol. 2025 Apr 18.
    Plug-and-play engineering of modular polyketide synthases.
    Zilei Huang, Shengling Xie, Run-Zhou Liu, Changjun Xiang, Shunyu Yao, Lihan Zhang.
      Modular polyketide synthases (PKSs) are multidomain, assembly line enzymes that biosynthesize complex antibiotics such as erythromycin and rapamycin. The modular characteristic of PKSs makes them an ideal platform for the custom production of designer polyketides by combinatorial biosynthesis. However, engineered hybrid PKS pathways often exhibit severe loss of enzyme activity, and a general principle for PKS reprogramming has not been established. Here we present a widely applicable strategy for designing hybrid PKSs. We reveal that two conserved motifs are robust cut sites to connect modules from different PKS pathways and demonstrate the custom production of polyketides with different starter units, extender units and variable reducing states. Furthermore, we expand the applicability of these cut sites to construct hybrid pathways involving cis-AT PKS, trans-AT PKS and even nonribosomal peptide synthetase. Collectively, our findings enable plug-and-play reprogramming of modular PKSs and facilitate the application of assembly line enzymes toward the bioproduction of designer molecules.
    DOI:  https://doi.org/10.1038/s41589-025-01878-4
  14. bioRxiv. 2025 Apr 01. pii: 2025.04.01.644731. [Epub ahead of print]
    The impact of fungal developmental structures on mechanical properties of mycelial materials.
    Kelsey Gray, Harley Edwards, Alexander G Doan, Walker Huso, JungHun Lee, Wanwei Pan, Nelanne Bolima, Isha Gautam, Tuo Wang, Ranjan Srivastava, Marc Zupan, Mark R Marten, Steven Harris.
      This study explores how suppressing asexual development in Aspergillus nidulans enhances the mechanical properties of mycelial materials. Using four aconidial mutants ( Δ brlA , Δ flbA , Δ fluG , and fadA G42R ) that lack asexual development and a control strain (A28) that undergoes typical asexual development, we found that the absence of asexual development significantly improves mechanical strength. All mutants exhibited higher ultimate tensile strength (UTS) than the control, with Δ fluG and Δ brlA (fluffy nonsporulating, FNS phenotype) showing the highest UTS. Additionally, fadA G42R and Δ flbA (fluffy autolytic dominant, FAD phenotype) demonstrated significantly higher strain at failure (SF), linked to increased autolysis and lower dry cell mass compared to the control and FNS mutants. Solid-state NMR analysis revealed that autolysis in FAD mutants disrupts galactofuranose-related metabolic processes, altering cell wall composition and contributing to higher elasticity. These findings suggest that suppressing asexual development enhances mycelial material strength, while autolysis mechanisms influence elasticity. This research highlights the potential for genetic manipulation in fungi to engineer advanced mycelial-based materials with tailored mechanical properties.
    DOI:  https://doi.org/10.1101/2025.04.01.644731
  15. Nat Commun. 2025 Apr 16. 16(1): 3614
    Optochemical control over mRNA translation by photocaged phosphorodiamidate morpholino oligonucleotides in vivo.
    Katsiaryna Tarbashevich, Atanu Ghosh, Arnab Das, Debajyoti Kuilya, Swrajit Nath Sharma, Surajit Sinha, Erez Raz.
      We developed an efficient, robust, and broadly applicable system for light-induced protein translation to control the production of proteins of interest and study their function. The method is based on the displacement of a single type of antisense morpholino from RNA by the uncaged guanidinium-linked morpholino (GMO)-phosphorodiamidate morpholino oligonucleotide (PMO) chimera upon UV irradiation. The GMO-PMO chimera designed here is cell-permeable and the GMO part can be produced employing a mercury-free approach compatible with the synthesis on solid support. We demonstrate the function of this optochemical approach in live embryos by inducing, at desired times and locations, the expression of proteins that label specific cells, ablate tissue regions, and affect embryonic development. Together, our results demonstrate that the cell-permeable GMO-PMO chimera offers a strategy for controlling the function of mRNAs of interest. This method allows for the production of proteins at specific times and positions within live organisms, facilitating numerous applications in biomedical research and therapy.
    DOI:  https://doi.org/10.1038/s41467-025-58207-5
  16. Metab Eng Commun. 2025 Jun;20 e00259
    Production of borneol, camphor, and bornyl acetate using engineered Saccharomyces cerevisiae.
    Masahiro Tominaga, Kazuma Kawakami, Hiro Ogawa, Tomomi Nakamura, Akihiko Kondo, Jun Ishii.
      Microbial production of bicyclic monoterpenes is of great interest because their production primarily utilizes non-sustainable resources. Here, we report an engineered Saccharomyces cerevisiae yeast that produces bicyclic monoterpenes, including borneol, camphor, and bornyl acetate. The engineered yeast expresses a bornyl pyrophosphatase synthase from Salvia officinalis fused with mutated farnesyl pyrophosphate synthase from S. cerevisiae and two mevalonate pathway enzymes (an acetoacetyl-CoA thiolase/hydroxymethylglutaryl-CoA [HMG-CoA] reductase and an HMG-CoA synthase) from Enterococcus faecalis. The yeast produced up to 23.0 mg/L of borneol in shake-flask fermentation. By additionally expressing borneol dehydrogenase from Pseudomonas sp. TCU-HL1 or bornyl acetyltransferase from Wurfbainia villosa, the engineered yeast produced 23.5 mg/L of camphor and 21.1 mg/L of bornyl acetate, respectively. This is the first report of heterologous production of camphor and bornyl acetate.
    Keywords:  Borneol; Bornyl acetate; Camphor; Monoterpene; Yeast
    DOI:  https://doi.org/10.1016/j.mec.2025.e00259
  17. Mater Today Bio. 2025 Jun;32 101720
    Assessing the feasibility of CRISPRa approaches to enhance protein-based biomaterial expression in bacterial systems for more efficient production.
    Pablo Rodríguez-Alonso, Viktoriya Chaskovska, Desiré Venegas-Bustos, Alba Herraiz, Matilde Alonso, Jose Carlos Rodríguez-Cabello.
      Recombinant protein production is crucial for biomedical and industrial applications; however, achieving high yields for complex protein-like biomaterials such as elastin-like recombinamers (ELRs) remains challenging. ELRs, protein-based polymers derived from tropoelastin, emulate the mechanical and bioactive properties of natural tissues, making them valuable for numerous uses. Despite their promise, implementing a sophisticated molecular system for ELR production in Escherichia coli involves overcoming multiple hurdles, including metabolic bottlenecks and low yields. In this study, we employed a CRISPR activation (CRISPRa) system to enhance ELR expression in E. coli. Although further optimization is required to reach industrial-scale outputs, our findings establish a proof of concept for taking advantage of CRISPRa to boost recombinamers yields. Such improvements represent a crucial step toward scalable production, facilitating the commercial adoption of ELRs and, in general, recombinamers not only in biomedical applications but also in broader industries that stand to benefit from these versatile biomaterials.
    DOI:  https://doi.org/10.1016/j.mtbio.2025.101720
  18. iScience. 2025 Apr 18. 28(4): 112273
    Mechanical control of the alternative splicing factor PTBP1 regulates extracellular matrix stiffness induced proliferation and cell spreading.
    Pei-Li Tseng, Weiwei Sun, Ahmed Salem, Mubarak Alaklobie, Sarah C Macfarlane, Annica K B Gad, Mark O Collins, Kai S Erdmann.
      Cells sense mechanical cues and convert them into biochemical responses to regulate biological processes such as embryonic development, aging, cellular homeostasis, and disease progression. In this study, we introduce a large-scale, systematic approach to identify proteins with mechanosensitive nuclear localization, highlighting their potential roles in mechanotransduction. Among the proteins identified, we focus here on the splicing factor PTBP1. We demonstrate that its nuclear abundance is regulated by mechanical cues such as cell density, size, and extracellular matrix (ECM) stiffness and that PTBP1 medicates the mechanosensitive alternative splicing of the endocytic adapter protein Numb. Furthermore, we show that PTBP1 and Numb alternative splicing is critical for ECM stiffness-induced epithelial cell spreading and proliferation as well as for mesenchymal stem cell differentiation into osteoblasts on a stiff matrix. Our results underscore the emerging role of alternative splicing in mechanotransduction and provide novel mechanistic insights into how matrix stiffness modulates cellular mechanoresponses.
    Keywords:  Cell biology; Functional aspects of cell biology; Organizational aspects of cell biology
    DOI:  https://doi.org/10.1016/j.isci.2025.112273
  19. Adv Mater. 2025 Apr 17. e2416966
    Engineering Magnetotactic Bacteria as Medical Microrobots.
    Jiaqi Wang, Yi Xing, Michael Ngatio, Paulina Bies, Lu Lucy Xu, Liuxi Xing, Ahmed Zarea, Ashley V Makela, Christopher H Contag, Jinxing Li.
      Nature's ability to create complex and functionalized organisms has long inspired engineers and scientists to develop increasingly advanced machines. Magnetotactic bacteria (MTB), a group of Gram-negative prokaryotes that biomineralize iron and thrive in aquatic environments, have garnered significant attention from the bioengineering community. These bacteria possess chains of magnetic nanocrystals known as magnetosomes, which allow them to align with Earth's geomagnetic field and navigate through aquatic environments via magnetotaxis, enabling localization to areas rich in nutrients and optimal oxygen concentration. Their built-in magnetic components, along with their intrinsic and/or modified biological functions, make them one of the most promising platforms for future medical microrobots. Leveraging an externally applied magnetic field, the motion of MTBs can be precisely controlled, rendering them suitable for use as a new type of biohybrid microrobotics with great promise in medicine for bioimaging, drug delivery, cancer therapy, antimicrobial treatment, and detoxification. This mini-review provides an up-to-date overview of recent advancements in MTB microrobots, delineates the interaction between MTB microrobots and magnetic fields, elucidates propulsion mechanisms and motion control, and reports state-of-the-art strategies for modifying and functionalizing MTB for medical applications.
    Keywords:  bioimaging; cancer therapy; drug delivery; magnetotactic bacteria; microrobotics
    DOI:  https://doi.org/10.1002/adma.202416966
  20. Anal Chem. 2025 Apr 16.
    Hydrophilic/Omniphobic Droplet Arrays for High-throughput and Quantitative Enzymology.
    Byungjin Lee, Fanny Sunden, Michael Miller, Bumshik Pak, Anke Krebber, Stefan Lutz, PollyMorrell Fordyce.
      Engineered enzymes with enhanced or novel functions are specific catalysts with wide-ranging applications in industry and medicine. Here, we introduce droplet array microfluidic enzyme kinetics (DA-MEK), a high-throughput enzyme screening platform that combines water-in-air droplet microarrays formed on patterned superhydrophilic/omniphobic surfaces with cell-free protein synthesis to enable cost-effective expression and quantitative kinetic characterization of enzyme variants. By printing DNA templates encoding enzyme variants onto hydrophilic spots, stamping slides to add cell-free expression mix, and imaging the resulting arrays, we demonstrate reproducible expression of enzyme variants across hundreds of microwells per slide, with line of sight toward replicating this across larger libraries. By specifically patterning slides with antibodies, we further demonstrate parallel immobilization, purification, and iterative characterization of the expressed variants. Subsequent stamping of fluorogenic substrates and time-lapse imaging allows determination of Michaelis-Menten parameters for each variant, with measured catalytic efficiencies spanning 5 orders of magnitude and agreeing well with values obtained via traditional microtiter plate assays. DA-MEK consumes orders of magnitude less reagents than plate-based assays, while providing accurate and detailed kinetic information for both beneficial and deleterious mutations. In future work, we anticipate that DA-MEK will provide a powerful and versatile platform to accelerate enzyme engineering and enable screening of large variant libraries under diverse conditions.
    DOI:  https://doi.org/10.1021/acs.analchem.5c00333
  21. Nat Chem Biol. 2025 Apr 17.
    Induced proximity to PML protects TDP-43 from aggregation via SUMO-ubiquitin networks.
    Kristina Wagner, Jan Keiten-Schmitz, Bikash Adhikari, Upayan Patra, Koraljka Husnjak, François McNicoll, Dorothee Dormann, Michaela Müller-McNicoll, Georg Tascher, Elmar Wolf, Stefan Müller.
      The established role of cytosolic and nuclear inclusions of TDP-43 in the pathogenesis of neurodegenerative disorders has multiplied efforts to understand mechanisms that control TDP-43 aggregation and has spurred searches for approaches limiting this process. Formation and clearance of TDP-43 aggregates are controlled by an intricate interplay of cellular proteostasis systems that involve post-translational modifications and frequently rely on spatial control. We demonstrate that attachment of the ubiquitin-like SUMO2 modifier compartmentalizes TDP-43 in promyelocytic leukemia protein (PML) nuclear bodies and limits the aggregation of TDP-43 in response to proteotoxic stress. Exploiting this pathway through proximity-inducing recruitment of TDP-43 to PML triggers a SUMOylation-ubiquitylation cascade protecting TDP-43 from stress-induced insolubility. The protective function of PML is mediated by ubiquitylation in conjunction with the p97 disaggregase. Altogether, we demonstrate that SUMO-ubiquitin networks protect cells from insoluble TDP-43 inclusions and propose the functionalization of PML as a potential future therapeutic avenue countering aggregation.
    DOI:  https://doi.org/10.1038/s41589-025-01886-4
  22. Angew Chem Int Ed Engl. 2025 Apr 14. e202506527
    Functionally Tunable Star-Shaped Multivalent crRNAs for Photocontrol CRISPR/Cas Editing.
    Wen-Da Chen, Li Liu, Liang Cheng.
      Clustered regularly interspaced shortpalindromic repeats/CRISPR-associated (CRISPR/Cas)-based genome editing has significantly advanced genetic engineering due to its precision, simplicity, and versatility.  However, achieving precise spatial and temporal control remains challenging, restricting therapeutic and research applications.  Herein, we introduce a novel class of star-shaped, multivalent crRNAs engineered for precise spatiotemporal control of CRISPR/Cas9 and Cas12a editing systems.  These crRNAs are synthesized via single-site chemical modification and can be efficiently purified.  By integrating distinct photo-responsive chemical linkages, we achieved selective activation of crRNA activity upon irradiation with specific wavelengths, enabling orthogonal regulation of multiple genetic targets simultaneously.  This method demonstrated robust OFF-ON switching capabilities in vitro, characterized by minimal leakage and rapid activation.  Importantly, the approach also proved highly effective for temporally controlled gene editing in mammalian cells in vivo, achieving considerable editing efficiency following brief photoactivation.  Due to its target sequence-independent, single-site modification design, this strategy may serve as a universal solution for diverse CRISPR/Cas systems, eliminating cumbersome optimization processes.  Future advancements incorporating long-wavelength responsive and reversible linkers promise further enhancement of tissue penetration and control, significantly broadening the applicability and impact of this approach in biological research and therapeutic interventions.
    Keywords:  CRISPR/Cas editing; multivalent crRNA; orthogonal control; photo-activation; spatiotemporal regulation
    DOI:  https://doi.org/10.1002/anie.202506527
  23. Bioresour Technol. 2025 Apr 15. pii: S0960-8524(25)00506-1. [Epub ahead of print]429 132540
    Engineered interaction elements enable enhanced multi-enzyme assembly and cascade biocatalysis for indigo synthesis.
    Shumin Xu, Gao Song, Xianghui Qi, Guoshi Kan, J A A Sampath Jayaweer, Yingfeng An.
      Efficient interacting peptides or protein scaffolds can be used to achieve multi-enzymatic cascade reactions to trigger substrate channeling effect, prevent intermediate diffusion, and control the flux of metabolites. However, the limited availability of existing interactive elements hinders the broad application of the multi-enzyme assembly strategy. Here, a peptide-peptide pair (PB1C/PB2N) and a protein-peptide pair (importin/PB2C) were fused to the target protein to induce protein assembly for the first time. The newly developed interactive elements, when combined with the existing RIDD/RIAD pair, can more efficiently achieve multi-enzymatic cascade reactions. The indigo synthesis pathway was optimized through cascade biocatalysis based on these interactive elements. As a result, compared with the co-expression of multiple enzymes, the interaction element-based cascade biocatalysis increased the yield of indigo by twofold. Our results demonstrate the potential of PB1C/PB2N and importin/PB2C scaffold systems as tools for enzyme assembly to control metabolic flux and increase the efficiency of biosynthetic pathways.
    Keywords:  Biocatalysis; Cascade reaction; Metabolic engineering; Scaffold multienzyme system; Synthetic biology
    DOI:  https://doi.org/10.1016/j.biortech.2025.132540
  24. Nat Commun. 2025 Apr 15. 16(1): 3562
    Stretchable composites with high oxide loading.
    Yinglin Zhi, Yan Shao, Rui Xia, Weikun Lin, Daohang Cai, Fuxing Zhao, Jiufeng Dong, Qingxian Li, Zihao Wang, Lixuan Li, Long Gu, Peng Tian, Zhen He, Jinlong Wang, Guiling Ning, Baowen Li, Canhui Yang, Hong Wang, Shuhong Yu, Yanhao Yu.
      Oxide/elastomer composites combine the functional attributes of metal oxides with the mechanical deformability of elastomers, but face the challenge of balancing oxide loading and stretchability as ceramic fillers decrease the entropic elasticity of polymer networks. Here, we report an interfacial composite design that enables high oxide fraction and large stretchability by minimizing the contact area yet maximizing the binding strength between the oxide and elastomer. The elongation at break for an interfacial composite with 80 vol% of oxides reaches 500%, whereas that of a regular bulk composite with the same oxide fraction is 20%. These composites are synthesized based on a Marangoni co-assembly process with tuned interfacial tension and reaction at the water-oil interface. The assembly chemistry is nearly independent of oxides' sizes, compositions, geometries, and functions, making this interfacial structure broadly applicable to optical, electric, magnetic, and thermal-conducting oxides. Compared to bulk composites, the interfacial composites deliver larger magnetic actuation, lower thermal resistance, and higher conformability with nonplanar surfaces, providing rich implications for designing intelligent and electronic systems.
    DOI:  https://doi.org/10.1038/s41467-025-58844-w
  25. Angew Chem Int Ed Engl. 2025 Apr 13. e202500649
    Conformationally Locked Peptide-DNA Nanostructures for CRISPR-Amplified Activity-Based Sensing.
    Dylan Snider, Mackenzie Coffin, Brian Armijo, Ryan Khetan, Mark Duchow, Anna Capasso, Devleena Samanta.
      We introduce a new class of chemical probes for activity-based sensing of proteases, termed Cleavable, Locked Initiator Probes (CLIPs). CLIPs contain a protease-cleavable peptide linked between two programmable DNA strands - an "initiator" DNA and a shorter "blocking" DNA. These DNA sequences are designed to hybridize, creating a "locked" hairpin-like structure. Upon proteolytic cleavage, the initiator strand is released, triggering the activation of CRISPR-Cas12a enzymes and producing an amplified fluorescence response. CLIPs generate more than 20-fold turn-on signals at room temperature (25°C), significantly outperforming commercial probes by yielding ~40-fold lower limits of detection (LOD) at 100-fold lower concentrations. Their versatility enables the detection of various disease-relevant proteases - including the SARS-CoV-2 main protease, caspase-3, matrix metalloproteinase-7, and cathepsin B - simply by altering the peptide sequence. Importantly, CLIPs detect cathepsin B in four different colorectal cancer cell lines, highlighting their clinical potential. Taken together, the sensitivity (LOD: ~88 pM), selectivity, and rapid assay time (down to 35 minutes), combined with the ability to operate in complex biological media with minimal sample preparation, position CLIPs as powerful chemical tools for activity-based sensing of functional enzymes.
    Keywords:  Activity-based sensing; DNA; Nanostructures; detection; protease
    DOI:  https://doi.org/10.1002/anie.202500649
  26. Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2420861122
    A hydrophobic photouncaging reaction to profile the lipid droplet interactome in tissues.
    Di Shen, Qun Zhao, Huaiyue Zhang, Ci Wu, Hao Jin, Kun Guo, Rui Sun, Hengke Guo, Qi Zhao, Huan Feng, Xuepeng Dong, Zhenming Gao, Lihua Zhang, Yu Liu.
      Most bioorthogonal photouncaging reactions preferentially occur in polar environments to accommodate biological applications in the aqueous cellular milieu. However, they are not precisely designed to chemically adapt to the diverse microenvironments of the cell. Herein, we report a hydrophobic photouncaging reaction with tailored photolytic kinetics toward solvent polarity. Structural modulations of the aminobenzoquinone-based photocage reveal the impact of cyclic ring size, steric substituent, and electronic substituent on the individual uncaging kinetics (kH2O and kdioxane) and polarity preference (kdioxane/kH2O). Rational incorporation of optimized moieties leads to up to 20.2-fold nonpolar kinetic selectivity (kdioxane/kH2O). Further photochemical spectroscopic characterizations and theoretical calculations together uncover the mechanism underlying the polarity-dependent uncaging kinetics. The uncaged ortho-quinone methide product bears covalent reactivity toward diverse nucleophiles of a protein revealed by tandem mass spectrometry. Finally, we demonstrate the application of such lipophilic photouncaging chemistry toward selective labeling and profiling of proteins in proximity to lipid droplets inside human fatty liver tissues. Together, this work studies the solvent polarity effects of a photouncaging reaction and chemically adapts it toward suborganelle-targeted protein proximity labeling and profiling.
    Keywords:  lipid droplets; photocage; photouncaging; proximity labeling; quinone methide
    DOI:  https://doi.org/10.1073/pnas.2420861122
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