Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science

Integrative Transcriptome and Proteome Analysis of the Tube Foot and Adhesive Secretions of the Sea Urchin Paracentrotus lividus

Echinoderms, such as the rock-boring sea urchin Paracentrotus lividus, attach temporarily to surfaces during locomotion using their tube feet. They can attach firmly to any substrate and release from it within seconds through the secretion of unknown molecules. The composition of the adhesive, as well as the releasing secretion, remains largely unknown. This study re-analyzed a differential proteome dataset from Lebesgue et al. by mapping mass spectrometry-derived peptides to a P. lividusde novo transcriptome generated in this study. This resulted in a drastic increase in mapped proteins in comparison to the previous publication. The data were subsequently combined with a differential RNAseq approach to identify potential adhesion candidate genes. A gene expression analysis of 59 transcripts using whole mount in situ hybridization led to the identification of 16 transcripts potentially involved in bioadhesion. In the future these data could be useful for the production of synthetic reversible adhesives for industrial and medical purposes.

Three-dimensional structure of Megabalanus rosa Cement Protein 20 revealed by multi-dimensional NMR and molecular dynamics simulations

Barnacles employ a protein-based cement to firmly attach to immersed substrates. The cement proteins (CPs) have previously been identified and sequenced. However, the molecular mechanisms of adhesion are not well understood, in particular, because the three-dimensional molecular structure of CPs remained unknown to date. Here, we conducted multi-dimensional nuclear magnetic resonance (NMR) studies and molecular dynamics (MD) simulations of recombinant Megabalanus rosa Cement Protein 20 (rMrCP20). Our NMR results show that rMrCP20 contains three main folded domain regions intervened by two dynamic loops, resulting in multiple protein conformations that exist in equilibrium. We found that 12 out of 32 Cys in the sequence engage in disulfide bonds that stabilize the β-sheet domains owing to their placement at the extremities of β-strands. Another feature unveiled by NMR is the location of basic residues in turn regions that are exposed to the solvent, playing an important role for intermolecular contact with negatively charged surfaces. MD simulations highlight a highly stable and conserved β-motif (β7-β8), which may function as nuclei for amyloid-like nanofibrils previously observed in the cured adhesive cement. To the best of our knowledge, this is the first report describing the tertiary structure of an extracellular biological adhesive protein at the molecular level. This article is part of the theme issue 'Transdisciplinary approaches to the study of adhesion and adhesives in biological systems'.

Using Large Datasets to Understand Nanotechnology

Advances in sequencing technologies have made studying biological processes with genomics, transcriptomics, and proteomics commonplace. As a result, this suite of increasingly integrated techniques is well positioned to study drug delivery, a process that is influenced by many biomolecules working in concert. Omics-based approaches can be used to study the vast nanomaterial chemical space as well as the biological factors that affect the safety, toxicity, and efficacy of nanotechnologies. The generation and analysis of large datasets, methods to interpret them, and dataset applications to nanomaterials to date, are demonstrated here. Finally, new approaches for how sequencing-generated datasets can answer fundamental questions in nanotechnology based drug delivery are proposed.

Expansion and loss events characterized the occurrence of MIF-like genes in bivalves

Macrophage migration inhibitory factor (MIF) dynamically connects innate and adaptive immune systems in vertebrate animals, allowing highly orchestrated systemic responses to various insults. The occurrence of MIF-like genes in non-vertebrate organisms suggests its origin from an ancestral metazoan gene, whose function is still a matter of debate. In the present work, by analyzing available genomic and transcriptomic data from bivalve mollusks, we identified 137 MIF-like sequences, which were classified into three types, based on phylogeny and conservation of key residues: MIF, D-DT, and the lineage-specific type MDL. Comparative genomics revealed syntenic conservation of homologous genes at the family level, the loss of D-DT in the Ostreidae family as well as the expansion of MIF-like genes in the Mytilidae family, possibly underpinning the neofunctionalization of duplicated gene copies. In M. galloprovincialis, MIF and one D-DT were mostly expressed in haemocytes and mantle rim of untreated animals, while D-DT paralogs often showed very limited expression, suggesting an accessory role or their persistence as relict genes.

Role of dendritic cells in the host response to biomaterials and their signaling pathways

Strategies to enhance, inhibit, or qualitatively modulate immune responses are important for diverse biomedical applications such as vaccine adjuvant, drug delivery, immunotherapy, cell transplant, tissue engineering, and regenerative medicine. However, the clinical efficiency of these biomaterial systems is affected by the limited understanding of their interaction with complex host microenvironments, for example, excessive foreign body reaction and immunotoxicity. Biomaterials and biomedical devices implanted in the body may induce a highly complicated and orchestrated series of host responses. As macrophages are among the first cells to infiltrate and respond to implanted biomaterials, the macrophage-mediated host response to biomaterials has been well studied. Dendritic cells (DCs) are the most potent antigen-presenting cells that activate naive T cells and bridge innate and adaptive immunity. The potential interaction of DCs with biomaterials appears to be critical for exerting the function of biomaterials and has become an important, developing area of investigation. Herein, we summarize the effects of the physicochemical properties of biomaterials on the immune function of DCs together with their receptors and signaling pathways. This review might provide a complete understanding of the interaction of DCs with biomaterials and serve as a reference for the design and selection of biomaterials with particular effects on targeted cells. STATEMENT OF SIGNIFICANCE: Biomaterials implanted in the body are increasingly applied in clinical practice. The performance of these implanted biomaterials is largely dependent on their interaction with the host immune system. As antigen-presenting cells, dendritic cells (DCs) directly interact with biomaterials through pattern recognition receptors (PRRs) recognizing "biomaterial-associated molecular patterns" and generate a battery of immune responses. In this review, the physicochemical properties of biomaterials that regulate the immune function of DCs together with their receptors and signaling pathways of biomaterial-DC interactions are summarized and discussed. We believe that knowledge of the interplay of DC and biomaterials may spur clinical translation by guiding the design and selection of biomaterials with particular effects on targeted cell for tissue engineering, vaccine delivery, and cancer therapy.

Multifunctional and biodegradable self-propelled protein motors

A diversity of self-propelled chemical motors, based on Marangoni propulsive forces, has been developed in recent years. However, most motors are non-functional due to poor performance, a lack of control, and the use of toxic materials. To overcome these limitations, we have developed multifunctional and biodegradable self-propelled motors from squid-derived proteins and an anesthetic metabolite. The protein motors surpass previous reports in performance output and efficiency by several orders of magnitude, and they offer control of their propulsion modes, speed, mobility lifetime, and directionality by regulating the protein nanostructure via local and external stimuli, resulting in programmable and complex locomotion. We demonstrate diverse functionalities of these motors in environmental remediation, microrobot powering, and cargo delivery applications. These versatile and degradable protein motors enable design, control, and actuation strategies in microrobotics as modular propulsion sources for autonomous minimally invasive medical operations in biological environments with air-liquid interfaces.

Recombinant mussel protein Pvfp-5β: A potential tissue bioadhesive

During their lifecycle, many marine organisms rely on natural adhesives to attach to wet surfaces for movement and self-defense in aqueous tidal environments. Adhesive proteins from mussels are biocompatible and elicit only minimal immune responses in humans. Therefore these proteins have received increased attention for their potential applications in medicine, biomaterials, and biotechnology. The Asian green mussel Perna viridis secretes several byssal plaque proteins, molecules that help anchoring the mussel to surfaces. Among these proteins, protein-5β (Pvfp-5β) initiates interactions with the substrate, displacing interfacial water molecules before binding to the surface. Here, we established the first recombinant expression in Escherichia coli of Pvfp-5β. We characterized recombinant Pvfp-5β, finding that despite displaying a CD spectrum consistent with features of a random coil, the protein is correctly folded as indicated by MS and NMR analyses. Pvfp-5β folds as a β-sheet-rich protein as expected for an epidermal growth factor-like module. We examined the effects of Pvfp-5β on cell viability and adhesion capacity in NIH-3T3 and HeLa cell lines, revealing that Pvfp-5β has no cytotoxic effects at the protein concentrations used and provides good cell-adhesion strength on both glass and plastic plates. Our findings suggest that the adhesive properties of recombinant Pvfp-5β make it an efficient surface-coating material, potentially suitable for biomedical applications including regeneration of damaged tissues.

Functional Protein-Based Bioinspired Nanomaterials: From Coupled Proteins, Synthetic Approaches, Nanostructures to Applications

Protein-based bioinspired nanomaterials (PBNs) combines the advantage of the size, shape, and surface chemistry of nanomaterials, the morphology and functions of natural materials, and the physical and chemical properties of various proteins. Recently, there are many exciting developments on biomimetic nanomaterials using proteins for different applications including, tissue engineering, drug delivery, diagnosis and therapy, smart materials and structures, and water collection and separation. Protein-based biomaterials with high biocompatibility and biodegradability could be modified to obtain the healing effects of natural organisms after injury by mimicking the extracellular matrix. For cancer and other diseases that are difficult to cure now, new therapeutic methods involving different kinds of biomaterials are studied. The nanomaterials with surface modification, which can achieve high drug loading, can be used as drug carriers to enhance target and trigger deliveries. For environment protection and the sustainability of the world, protein-based nanomaterials are also applied for water treatment. A wide range of contaminants from natural water source, such as organic dyes, oil substances, and multiple heavy ions, could be absorbed by protein-based nanomaterials. This review summarizes the formation and application of functional PBNs, and the details of their nanostructures, the proteins involved, and the synthetic approaches are addressed.

Nucleic Acid-Based Functional Nanomaterials as Advanced Cancer Therapeutics

Nucleic acid-based functional nanomaterials (NAFN) have been widely used as emerging drug delivery nanocarriers for cancer therapeutics. Considerable works have demonstrated that NAFN can effectively load and protect therapeutic agents, and particularly enable targeting delivery to the tumor site and stimuli-responsive release. These outstanding performances are due to NAFN's unique properties including inherent biological functions and sequence programmability as well as biocompatibility and biodegradability. In this Review, the recent progress on NAFN as advanced cancer therapeutics is highlighted. Three main cancer therapy approaches are categorized including chemo-, immuno-, and gene-therapy. Examples are presented to show how NAFN are rationally and exquisitely designed to address problems in cancer therapy. The challenges and future development of NAFN are also discussed toward future more practical biomedical applications.

Shear-Induced β-Crystallite Unfolding in Condensed Phase Nanodroplets Promotes Fiber Formation in a Biological Adhesive

Natural materials provide an increasingly important role model for the development and processing of next-generation polymers. The velvet worm Euperipatoides rowelli hunts using a projectile, mechanoresponsive adhesive slime that rapidly and reversibly transitions into stiff glassy polymer fibers following shearing and drying. However, the molecular mechanism underlying this mechanoresponsive behavior is still unclear. Previous work showed the slime to be an emulsion of nanoscale charge-stabilized condensed droplets comprised primarily of large phosphorylated proteins, which under mechanical shear coalesce and self-organize into nano- and microfibrils that can be drawn into macroscopic fibers. Here, we utilize wide-angle X-ray diffraction and vibrational spectroscopy coupled with in situ shear deformation to explore the contribution of protein conformation and mechanical forces to the fiber formation process. Although previously believed to be unstructured, our findings indicate that the main phosphorylated protein component possesses a significant β-crystalline structure in the storage phase and that shear-induced partial unfolding of the protein is a key first step in the rapid self-organization of nanodroplets into fibers. The insights gained here have relevance for sustainable production of advanced polymeric materials.

High-throughput identification of heavy metal binding proteins from the byssus of chinese green mussel (Perna viridis) by combination of transcriptome and proteome sequencing

The Byssus, which is derived from the foot gland of mussels, has been proved to bind heavy metals effectively, but few studies have focused on the molecular mechanisms behind the accumulation of heavy metals by the byssus. In this study, we integrated high-throughput transcriptome and proteome sequencing to construct a comprehensive protein database for the byssus of Chinese green mussel (Perna viridis), aiming at providing novel insights into the molecular mechanisms by which the byssus binds to heavy metals. Illumina transcriptome sequencing generated a total of 55,670,668 reads. After filtration, we obtained 53,047,718 clean reads and subjected them to de novo assembly using Trinity software. Finally, we annotated 73,264 unigenes and predicted a total of 34,298 protein coding sequences. Moreover, byssal samples were analyzed by proteome sequencing, with the translated protein database from the foot transcriptome as the reference for further prediction of byssal proteins. We eventually determined 187 protein sequences in the byssus, of which 181 proteins are reported for the first time. Interestingly, we observed that many of these byssal proteins are rich in histidine or cysteine residues, which may contribute to the byssal accumulation of heavy metals. Finally, we picked one representative protein, Pvfp-5-1, for recombinant protein synthesis and experimental verification of its efficient binding to cadmium (Cd2+) ions.

A compendium of current developments on polysaccharide and protein-based microneedles

Microneedles (MNs), i.e. minimally invasive three-dimensional microstructures that penetrate the stratum corneum inducing relatively little or no pain, have been studied as appealing therapeutic vehicles for transdermal drug delivery. Over the last years, the fabrication of MNs using biopolymers, such as polysaccharides and proteins, has sparked the imagination of scientists due to their recognized biocompatibility, biodegradability, ease of fabrication and sustainable character. Owing to their wide range of functional groups, polysaccharides and proteins enable the design and preparation of materials with tunable properties and functionalities. Therefore, these biopolymer-based MNs take a revolutionary step offering great potential not only in drug administration, but also in sensing and response to physiological stimuli. In this review, a critical and comprehensive overview of the polysaccharides and proteins employed in the design and engineering of MNs will be given. The strategies adopted for their preparation, their advantages and disadvantages will be also detailed. In addition, the potential and challenges of using these matrices to deliver drugs, vaccines and other molecules will be discussed. Finally, this appraisal ends with a perspective on the possibilities and challenges in research and development of polysaccharide and protein MNs, envisioning the future advances and clinical translation of these platforms as the next generation of drug delivery systems.

A diecast mineralization process forms the tough mantis shrimp dactyl club

Biomineralization, the process by which mineralized tissues grow and harden via biogenic mineral deposition, is a relatively lengthy process in many mineral-producing organisms, resulting in challenges to study the growth and biomineralization of complex hard mineralized tissues. Arthropods are ideal model organisms to study biomineralization because they regularly molt their exoskeletons and grow new ones in a relatively fast timescale, providing opportunities to track mineralization of entire tissues. Here, we monitored the biomineralization of the mantis shrimp dactyl club-a model bioapatite-based mineralized structure with exceptional mechanical properties-immediately after ecdysis until the formation of the fully functional club and unveil an unusual development mechanism. A flexible membrane initially folded within the club cavity expands to form the new club's envelope. Mineralization proceeds inwards by mineral deposition from this membrane, which contains proteins regulating mineralization. Building a transcriptome of the club tissue and probing it with proteomic data, we identified and sequenced Club Mineralization Protein 1 (CMP-1), an abundant mildly phosphorylated protein from the flexible membrane suggested to be involved in calcium phosphate mineralization of the club, as indicated by in vitro studies using recombinant CMP-1. This work provides a comprehensive picture of the development of a complex hard tissue, from the secretion of its organic macromolecular template to the formation of the fully functional club.

Squid-Inspired Tandem Repeat Proteins: Functional Fibers and Films

Production of repetitive polypeptides that comprise one or more tandem copies of a single unit with distinct amorphous and ordered regions have been an interest for the last couple of decades. Their molecular structure provides a rich architecture that can micro-phase-separate to form periodic nanostructures (e.g., lamellar and cylindrical repeating phases) with enhanced physicochemical properties via directed or natural evolution that often exceed those of conventional synthetic polymers. Here, we review programmable design, structure, and properties of functional fibers and films from squid-inspired tandem repeat proteins, with applications in soft photonics and advanced textiles among others.

Catecholic Compounds in Ctenophore Colloblast and Nerve Net Proteins Suggest a Structural Role for DOPA-Like Molecules in an Early-Diverging Animal Lineage

Ctenophores, or comb jellies, are among the earliest-diverging extant animal lineages. Several recent phylogenomic studies suggest that they may even be the sister group to all other animals. This unexpected finding remains difficult to contextualize, particularly given ctenophores' unique and sometimes poorly understood physiology. Colloblasts, a ctenophore-specific cell type found on the surface of these animals' tentacles, are emblematic of this difficulty. The exterior of the colloblast is dotted with granules that burst and release an adhesive on contact with prey, ensnaring it for consumption. To date, little is known about the fast-acting underwater adhesive that these cells secrete or its biochemistry. We present evidence that proteins in the colloblasts of the ctenophore Pleurobrachia bachei incorporate catecholic compounds similar to the amino acid l-3,4-dihydroxyphenylalanine. These compounds are associated with adhesive-containing granules on the surface of colloblasts, suggesting that they may play a role in prey capture, akin to dihydroxyphenylalanine-based adhesives in mussel byssus. We also present unexpected evidence of similar catecholic compounds in association with the subepithelial nerve net. There, catecholic compounds are present in spatial patterns similar to those of l-3,4-dihydroxyphenylalanine and its derivatives in cnidarian nerves, where they are associated with membranes and possess unknown functionality. This "structural" use of catecholic molecules in ctenophores represents the earliest-diverging animal lineage in which this trait has been observed, though it remains unclear whether structural catechols are deeply rooted in animals or whether they have arisen multiple times.

Controlling Supramolecular Chiral Nanostructures by Self-Assembly of a Biomimetic β-Sheet-Rich Amyloidogenic Peptide

Squid sucker ring teeth (SRT) have emerged as a promising protein-only, thermoplastic biopolymer with an increasing number of biomedical and engineering applications demonstrated in recent years. SRT is a supra-molecular network whereby a flexible, amorphous matrix is mechanically reinforced by nanoconfined β-sheets. The building blocks for the SRT network are a family of suckerin proteins that share a common block copolymer architecture consisting of amorphous domains intervened by smaller, β-sheet forming modules. Recent studies have identified the peptide A1H1 (peptide sequence AATAVSHTTHHA) as one of the most abundant β-sheet forming domains within the suckerin protein family. However, we still have little understanding of the assembly mechanisms by which the A1H1 peptide may assemble into its functional load-bearing domains. In this study, we conduct a detailed self-assembly study of A1H1 and show that the peptide undergoes β-strands-driven elongation into amyloid-like fibrils with a rich polymorphism. The nanostructure of the fibrils was elucidated by small and wide-angle X-ray scattering (SAXS and WAXS) and atomic force microscopy (AFM). The presence of His-rich and Ala-rich segments results in an amphiphilic behavior and drives its assembly into fibrillar supramolecular chiral aggregates with helical ribbon configuration in solution, with the His-rich region exposed to the solvent molecules. Upon increase in concentration, the fibrils undergo gel formation, while preserving the same mesoscopic features. This complex phase behavior suggests that the repeat peptide modules of suckerins may be manipulated beyond their native biological environment to produce a wider variety of self-assembled amyloid-like nanostructures.

Phase transitions as intermediate steps in the formation of molecularly engineered protein fibers

A central concept in molecular bioscience is how structure formation at different length scales is achieved. Here we use spider silk protein as a model to design new recombinant proteins that assemble into fibers. We made proteins with a three-block architecture with folded globular domains at each terminus of a truncated repetitive silk sequence. Aqueous solutions of these engineered proteins undergo liquid-liquid phase separation as an essential pre-assembly step before fibers can form by drawing in air. We show that two different forms of phase separation occur depending on solution conditions, but only one form leads to fiber assembly. Structural variants with one-block or two-block architectures do not lead to fibers. Fibers show strong adhesion to surfaces and self-fusing properties when placed into contact with each other. Our results show a link between protein architecture and phase separation behavior suggesting a general approach for understanding protein assembly from dilute solutions into functional structures.

Adhesive gland transcriptomics uncovers a diversity of genes involved in glue formation in marine tube-building polychaetes

Tube-building sabellariid polychaetes are hermatypic organisms capable of forming vast reefs in highly turbulent marine habitats. Sabellariid worms assemble their tube by gluing together siliceous and calcareous clastic particles using a polyelectrolytic biocement. Here, we performed transcriptomic analyses to investigate the genes that are differentially expressed in the parathorax region, which contains the adhesive gland and tissues, from the rest of the body. We found a large number of candidate genes to be involved in the composition and formation of biocement in two species: Sabellaria alveolata and Phragmatopoma caudata. Our results indicate that the glue is likely to be composed by a large diversity of cement-related proteins, including Poly(S), GY-rich, H-repeat and miscellaneous categories. However, sequences divergence and differences in expression profiles between S. alveolata and P. caudata of cement-related proteins may reflect adaptation to the type of substratum used to build their tube, and/or to their habitat (temperate vs tropical, amplitude of pH, salinity …). Related to the L-DOPA metabolic pathways and linked with the genes that were differentially expressed in the parathorax region, we found that tyrosinase and peroxidase gene families may have undergone independent expansion in the two Sabellariidae species investigated. Our data also reinforce the importance of protein modifications in cement formation. Altogether these new genomic resources help to identify novel transcripts encoding for cement-related proteins, but also important enzymes putatively involved in the chemistry of the adhesion process, such as kinases, and may correspond to new targets to develop biomimetic approaches.

STATEMENTS OF SIGNIFICANCE

The diversity of bioadhesives elaborated by marine invertebrates is a tremendous source of inspiration to develop biomimetic approaches for biomedical and technical applications. Recent studies on the adhesion system of mussel, barnacle and sea star had highlighted the usefulness of high-throughput RNA sequencing in accelerating the development of biomimetic adhesives. Adhesion in sandcastle worms, which involves catechol and phosphate chemistries, polyelectrolyte complexes, supramolecular architectures, and a coacervation process, is a useful model to develop multipurpose wet adhesives. Using transcriptomic tools, we have explored the diversity of genes encoding for structural and catalytic proteins involved in cement formation of two sandcastle worm species, Sabellaria alveolata and Phragmatopoma caudata. The important genomic resource generated should help to design novel "blue" adhesives.

Byssus Structure and Protein Composition in the Highly Invasive Fouling Mussel Limnoperna fortunei

Biofouling mediated by byssus adhesion in invasive bivalves has become a global environmental problem in aquatic ecosystems, resulting in negative ecological and economic consequences. Previous studies suggested that mechanisms responsible for byssus adhesion largely vary among bivalves, but it is poorly understood in freshwater species. Understanding of byssus structure and protein composition is the prerequisite for revealing these mechanisms. Here, we used multiple methods, including scanning electron microscope, liquid chromatography–tandem mass spectrometry, transcriptome sequencing, real-time quantitative PCR, inductively coupled plasma mass spectrometry, to investigate structure, and protein composition of byssus in the highly invasive freshwater mussel Limnoperna fortunei. The results indicated that the structure characteristics of adhesive plaque, proximal and distal threads were conducive to byssus adhesion, contributing to the high biofouling capacity of this species. The 3,4-dihydroxyphenyl-α-alanine (Dopa) is a major post-transnationally modification in L. fortunei byssus. We identified 16 representative foot proteins with typical repetitive motifs and conserved domains by integrating transcriptomic and proteomic approaches. In these proteins, Lfbp-1, Lffp-2, and Lfbp-3 were specially located in foot tissue and highly expressed in the rapid byssus formation period, suggesting the involvement of these foot proteins in byssus production and adhesion. Multiple metal irons, including Ca²⁺, Mg²⁺, Zn²⁺, Al³⁺, and Fe³⁺, were abundant in both foot tissue and byssal thread. The heavy metals in these irons may be directly accumulated by L. fortunei from surrounding environments. Nevertheless, some metal ions (e.g., Ca²⁺) corresponded well with amino acid preferences of L. fortunei foot proteins, suggesting functional roles of these metal ions by interacting with foot proteins in byssus adhesion. Overall, this study provides structural and molecular bases of adhesive mechanisms of byssus in L. fortunei, and findings here are expected to develop strategies against biofouling by freshwater organisms.

A cohort of new adhesive proteins identified from transcriptomic analysis of mussel foot glands

The adaptive attachment of marine mussels to a wide range of substrates in a high-energy, saline environment has been explored for decades and is a significant driver of bioinspired wet adhesion research. Mussel attachment relies on a fibrous holdfast known as the byssus, which is made by a specialized appendage called the foot. Multiple adhesive and structural proteins are rapidly synthesized, secreted and moulded by the foot into holdfast threads. About 10 well-characterized proteins, namely the mussel foot proteins (Mfps), the preCols and the thread matrix proteins, are reported as representing the bulk of these structures. To explore how robust this proposition is, we sequenced the transcriptome of the glandular tissues that produce and secrete the various holdfast components using next-generation sequencing methods. Surprisingly, we found around 15 highly expressed genes that have not previously been characterized, but bear key similarities to the previously defined mussel foot proteins, suggesting additional contribution to byssal function. We verified the validity of these transcripts by polymerase chain reaction, cloning and Sanger sequencing as well as confirming their presence as proteins in the byssus. These newly identified proteins greatly expand the palette of mussel holdfast biochemistry and provide new targets for investigation into bioinspired wet adhesion.

Mechanical Properties of Tandem-Repeat Proteins Are Governed by Network Defects

Topological defects in highly repetitive structural proteins strongly affect their mechanical properties. However, there are no universal rules for structure-property prediction in structural proteins due to high diversity in their repetitive modules. Here, we studied the mechanical properties of tandem-repeat proteins inspired by squid ring teeth proteins using rheology and tensile experiments as well as spectroscopic and X-ray techniques. We also developed a network model based on entropic elasticity to predict structure-property relationships for these proteins. We demonstrated that shear modulus, elastic modulus, and toughness scale inversely with the number of repeats in these proteins. Through optimization of structural repeats, we obtained highly efficient protein network topologies with 42 MJ/m³ ultimate toughness that are capable of withstanding deformations up to 350% when hydrated. Investigation of topological network defects in structural proteins will improve the prediction of mechanical properties for designing novel protein-based materials.

Supramolecular propensity of suckerin proteins is driven by β-sheets and aromatic interactions as revealed by solution NMR

The solution structure of a suckerin protein obtained by NMR illustrates β-sheet conformation with stabilising aromatic interactions in dynamic domains.

Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins

Bivalve molluscs are descendants of an early-Cambrian lineage superbly adapted to benthic filter feeding. Adaptations in form and behavior are well recognized, but the underlying molecular mechanisms are largely unknown. Here, we investigate the genome, various transcriptomes, and proteomes of the scallop Chlamys farreri, a semi-sessile bivalve with well-developed adductor muscle, sophisticated eyes, and remarkable neurotoxin resistance. The scallop's large striated muscle is energy-dynamic but not fully differentiated from smooth muscle. Its eyes are supported by highly diverse, intronless opsins expanded by retroposition for broadened spectral sensitivity. Rapid byssal secretion is enabled by a specialized foot and multiple proteins including expanded tyrosinases. The scallop uses hepatopancreas to accumulate neurotoxins and kidney to transform to high-toxicity forms through expanded sulfotransferases, probably as deterrence against predation, while it achieves neurotoxin resistance through point mutations in sodium channels. These findings suggest that expansion and mutation of those genes may have profound effects on scallop's phenotype and adaptation.

Squid Suckerin Biomimetic Peptides Form Amyloid-like Crystals with Robust Mechanical Properties

We present the self-assembly of fibers formed from a peptide sequence (A1H1) derived from suckerin proteins of squid sucker ring teeth (SRT). SRT are protein-only biopolymers with an unconventional set of physicochemical and mechanical properties including high elastic modulus coupled with thermoplastic behavior. We have identified a conserved peptide building block from suckerins that possess the ability to assemble into materials with similar mechanical properties as the native SRT. A1H1 displays amphiphilic characteristics and self-assembles from the bottom-up into mm-scale fibers initiated by the addition of a polar aprotic solvent. A1H1 fibers are thermally resistant up to 239 °C, coupled with an elastic modulus of ∼7.7 GPa, which can be explained by the tight packing of β-sheet-enriched crystalline building blocks as identified by wide-angle X-ray scattering (WAXS), with intersheet and interstrand distances of 5.37 and 4.38 Å, respectively. A compact packing of the peptides at their Ala-rich terminals within the fibers was confirmed from molecular dynamics simulations, and we propose a hierarchical model of fiber assembly of the mature peptide fiber.

Functional and Biomimetic Materials for Engineering of the Three-Dimensional Cell Microenvironment

The cell microenvironment has emerged as a key determinant of cell behavior and function in development, physiology, and pathophysiology. The extracellular matrix (ECM) within the cell microenvironment serves not only as a structural foundation for cells but also as a source of three-dimensional (3D) biochemical and biophysical cues that trigger and regulate cell behaviors. Increasing evidence suggests that the 3D character of the microenvironment is required for development of many critical cell responses observed in vivo, fueling a surge in the development of functional and biomimetic materials for engineering the 3D cell microenvironment. Progress in the design of such materials has improved control of cell behaviors in 3D and advanced the fields of tissue regeneration, in vitro tissue models, large-scale cell differentiation, immunotherapy, and gene therapy. However, the field is still in its infancy, and discoveries about the nature of cell-microenvironment interactions continue to overturn much early progress in the field. Key challenges continue to be dissecting the roles of chemistry, structure, mechanics, and electrophysiology in the cell microenvironment, and understanding and harnessing the roles of periodicity and drift in these factors. This review encapsulates where recent advances appear to leave the ever-shifting state of the art, and it highlights areas in which substantial potential and uncertainty remain.

Synchrotron imaging and Markov Chain Monte Carlo reveal tooth mineralization patterns

The progressive character of tooth formation records aspects of mammalian life history, diet, seasonal behavior and climate. Tooth mineralization occurs in two stages: secretion and maturation, which overlap to some degree. Despite decades of study, the spatial and temporal pattern of elemental incorporation during enamel mineralization remains poorly characterized. Here we use synchrotron X-ray microtomography and Markov Chain Monte Carlo sampling to estimate mineralization patterns from an ontogenetic series of sheep molars (n = 45 M1s, 18 M2s). We adopt a Bayesian approach that posits a general pattern of maturation estimated from individual- and population-level mineral density variation over time. This approach converts static images of mineral density into a dynamic model of mineralization, and demonstrates that enamel secretion and maturation waves advance at nonlinear rates with distinct geometries. While enamel secretion is ordered, maturation geometry varies within a population and appears to be driven by diffusive processes. Our model yields concrete expectations for the integration of physiological and environmental signals, which is of particular significance for paleoseasonality research. This study also provides an avenue for characterizing mineralization patterns in other taxa. Our synchrotron imaging data and model are available for application to multiple disciplines, including health, material science, and paleontological research.

Recent advances in the synthesis of functional materials by engineered and recombinant living cells

At the interface of materials science and synthetic biology, several concepts were recently developed for the production of functional materials by living cells. Selected recent strategies for this are highlighted here with a focus on bioactive, electronic and fluorescent materials.

Squid suckerin microneedle arrays for tunable drug release

Microneedles are increasingly used in transdermal delivery of therapeutic agents due to the elimination of first-pass metabolism, simplicity of operation, and lack of pain, which collectively lead to improved patient compliance. However, microneedles are still met by challenges with regard to the choice of biocompatible materials and the control of drug release profiles. Herein, we tackle these limitations by producing microneedles from a biocompatible robust biopolymer, namely squid sucker ring teeth (SRT) proteins (suckerins), using a soft lithography method. Taking advantage of the modular sequence design of suckerins leading to their self-assembly into β-sheet enriched structures, suckerin microneedles display an accurate replication of their templates with robust mechanical properties, endowing them with a high skin penetration capability. Critically, the β-sheet content in the microneedles can be modulated by varying the solvent conditions, which allows tuning of the mechanical response, and in turn the drug release rates by more than one order of magnitude. In vitro skin permeation studies of suckerin microneedles using human cadaver skin samples suggest a fast onset and enhanced skin permeation of drugs compared to flat patches. The skin permeation can also be tailored 10-fold by applying hydrogen bond disruptor solutions. As a proof-of-concept, the anti-bacterial drug kanamycin is encapsulated within the microneedles, leading to efficient anti-bacterial activity and offering an additional benefit to further minimize the risk of infections caused by microneedle-based drug delivery systems. Lastly, suckerin microneedles are found to be biocompatible in cell culture studies, opening the door to further clinical applications.

The purplish bifurcate mussel Mytilisepta virgata gene expression atlas reveals a remarkable tissue functional specialization

BACKGROUND

Mytilisepta virgata is a marine mussel commonly found along the coasts of Japan. Although this species has been the subject of occasional studies concerning its ecological role, growth and reproduction, it has been so far almost completely neglected from a genetic and molecular point of view. In the present study we present a high quality de novo assembled transcriptome of the Japanese purplish mussel, which represents the first publicly available collection of expressed sequences for this species.

RESULTS

The assembled transcriptome comprises almost 50,000 contigs, with a N50 statistics of ~1 kilobase and a high estimated completeness based on the rate of BUSCOs identified, standing as one of the most exhaustive sequence resources available for mytiloid bivalves to date. Overall this data, accompanied by gene expression profiles from gills, digestive gland, mantle rim, foot and posterior adductor muscle, presents an accurate snapshot of the great functional specialization of these five tissues in adult mussels.

CONCLUSIONS

We highlight that one of the most striking features of the M. virgata transcriptome is the high abundance and diversification of lectin-like transcripts, which pertain to different gene families and appear to be expressed in particular in the digestive gland and in the gills. Therefore, these two tissues might be selected as preferential targets for the isolation of molecules with interesting carbohydrate-binding properties. In addition, by molecular phylogenomics, we provide solid evidence in support of the classification of M. virgata within the Brachidontinae subfamily. This result is in agreement with the previously proposed hypothesis that the morphological features traditionally used to group Mytilisepta spp. and Septifer spp. within the same clade are inappropriate due to homoplasy.

Hierarchical Chitin Fibers with Aligned Nanofibrillar Architectures: A Nonwoven-Mat Separator for Lithium Metal Batteries

Here, we introduce regenerated fibers of chitin (Chiber), the second most abundant biopolymer after cellulose, and propose its utility as a nonwoven fiber separator for lithium metal batteries (LMBs) that exhibits an excellent electrolyte-uptaking capability and Li-dendrite-mitigating performance. Chiber is produced by a centrifugal jet-spinning technique, which allows a simple and fast production of Chibers consisting of hierarchically aligned self-assembled chitin nanofibers. Following the scrutinization on the Chiber-Li-ion interaction via computational methods, we demonstrate the potential of Chiber as a nonwoven mat-type separator by monitoring it in Li-O₂ and Na-O₂ cells.

Supramolecular β-Sheets Stabilized Protein Nanocarriers for Drug Delivery and Gene Transfection

Suckerin proteins, recently discovered in the sucker ring teeth of squids, represent a family of promising structural biomacromolecules that can form supramolecular networks stabilized by nanoconfined β-sheets. Exploiting this feature as well as their specific amino acid composition, we demonstrate that artificial suckerin-19 (S-19) can be engineered into nanocarriers for efficient drug delivery and gene transfection in vitro and in vivo. First, we demonstrate that S-19 self-assembles into β-sheet stabilized nanoparticles with controlled particle sizes of 100-200 nm that are able to encapsulate hydrophobic drugs for pH-dependent release in vitro, and that can effectively inhibit tumor growth in vivo. We also show that S-19 can complex and stabilize plasmid DNA, with the complexes stabilized by hydrophobic interactions of the β-sheet domains as opposed to electrostatic interactions commonly achieved with cationic polymers, thus lowering cytotoxicity. The elevated Histidine content of S-19 appears critical to trigger endosomal escape by the proton sponge effect, thereby ensuring efficient gene transfection both in vitro and in vivo. Our study demonstrates that S-19 represents a promising functional protein nanocarrier that could be used for various drug and gene delivery applications.

De novo assembly and comparative transcriptome analysis of the foot from Chinese green mussel (Perna viridis) in response to cadmium stimulation

The Chinese green mussel, Perna viridis, is a marine bivalve with important economic values as well as biomonitoring roles for aquatic pollution. Byssus, secreted by the foot gland, has been proved to bind heavy metals effectively. In this study, using the RNA sequencing technology, we performed comparative transcriptomic analysis on the mussel feet with or without inducing by cadmium (Cd). Our current work is aiming at providing insights into the molecular mechanisms of byssus binding to heavy metal ions. The transcriptome sequencing generated a total of 26.13-Gb raw data. After a careful assembly of clean data, we obtained a primary set of 105,127 unigenes, in which 32,268 unigenes were annotated. Based on the expression profiles, we identified 9,048 differentially expressed genes (DEGs) between Cd treatment (50 or 100 μg/L) at 48 h and the control, suggesting an extensive transcriptome response of the mussels during the Cd stimulation. Moreover, we observed that the expression levels of 54 byssus protein coding genes increased significantly after the 48-h Cd stimulation. In addition, 16 critical byssus protein coding genes were picked for profiling by quantitative real-time PCR (qRT-PCR). Finally, we reached a primary conclusion that high content of tyrosine (Tyr), cysteine (Cys), histidine (His) residues or the special motif plays an important role in the accumulation of heavy metals in byssus. We also proposed an interesting model for the confirmed byssal Cd accumulation, in which biosynthesis of byssus proteins may play simultaneously critical roles since their transcription levels were significantly elevated.

Hierarchical Assembly of Tough Bioelastomeric Egg Capsules is Mediated by a Bundling Protein

Marine snail egg capsules are shock-absorbing bioelastomers made from precursor "egg case proteins" (ECPs) that initially lack long-range order. During capsule formation, these proteins self-assemble into coiled-coil filaments that subsequently align into microscopic layers, a multiscale process which is crucial to the capsules' shock-absorbing properties. In this study, we show that the self-assembly of ECPs into their functional capsule material is mediated by a bundling protein that facilitates the aggregation of coiled-coil building blocks and their gelation into a prefinal capsule prior to final stabilization. This low molecular weight bundling protein, termed Pugilina cochlidium Bundling Protein (PcBP), led to gelation of native extracts from gravid snails, whereas crude extracts lacking PcBP did not gelate and remained as a protein solution. Refolding and reconcentration of recombinant PcBP induced bundling and aggregation of ECPs, as evidenced by ECPs oligomerization. We propose that the secretion of PcBP in vivo is a time-specific event during the embryo encapsulation process prior to cross-linking in the ventral pedal gland (VPG). Using molecular dynamics (MD) simulations, we further propose plausible disulfide binding sites stabilizing two PcBP monomers, as well as a polarized surface charge distribution, which we suggest plays an important role in the bundling mechanism. Overall, this study shows that controlled bundling is a key step during the extra-cellular self-assembly of egg capsules, which has previously been overlooked.

Mussel adhesion - essential footwork

Robust adhesion to wet, salt-encrusted, corroded and slimy surfaces has been an essential adaptation in the life histories of sessile marine organisms for hundreds of millions of years, but it remains a major impasse for technology. Mussel adhesion has served as one of many model systems providing a fundamental understanding of what is required for attachment to wet surfaces. Most polymer engineers have focused on the use of 3,4-dihydroxyphenyl-l-alanine (Dopa), a peculiar but abundant catecholic amino acid in mussel adhesive proteins. The premise of this Review is that although Dopa does have the potential for diverse cohesive and adhesive interactions, these will be difficult to achieve in synthetic homologs without a deeper knowledge of mussel biology; that is, how, at different length and time scales, mussels regulate the reactivity of their adhesive proteins. To deposit adhesive proteins onto target surfaces, the mussel foot creates an insulated reaction chamber with extreme reaction conditions such as low pH, low ionic strength and high reducing poise. These conditions enable adhesive proteins to undergo controlled fluid-fluid phase separation, surface adsorption and spreading, microstructure formation and, finally, solidification.

Modular peptides from the thermoplastic squid sucker ring teeth form amyloid-like cross-β supramolecular networks

The hard sucker ring teeth (SRT) from decapodiforme cephalopods, which are located inside the sucker cups lining the arms and tentacles of these species, have recently emerged as a unique model structure for biomimetic structural biopolymers. SRT are entirely composed of modular, block co-polymer-like proteins that self-assemble into a large supramolecular network. In order to unveil the molecular principles behind SRT's self-assembly and robustness, we describe a combinatorial screening assay that maps the molecular-scale interactions between the most abundant modular peptide blocks of suckerin proteins. By selecting prominent interaction hotspots from this assay, we identified four peptides that exhibited the strongest homo-peptidic interactions, and conducted further in-depth biophysical characterizations complemented by molecular dynamic (MD) simulations to investigate the nature of these interactions. Circular Dichroism (CD) revealed conformations that transitioned from semi-extended poly-proline II (PII) towards β-sheet structure. The peptides spontaneously self-assembled into microfibers enriched with cross β-structures, as evidenced by Fourier-Transform Infrared Spectroscopy (FTIR) and Congo red staining. Nuclear Magnetic Resonance (NMR) experiments identified the residues involved in the hydrogen-bonded network and demonstrated that these self-assembled β-sheet-based fibers exhibit high protection factors that bear resemblance to amyloids. The high stability of the β-sheet network and an amyloid-like model of fibril assembly were supported by MD simulations. The work sheds light on how Nature has evolved modular sequence design for the self-assembly of mechanically robust functional materials, and expands our biomolecular toolkit to prepare load-bearing biomaterials from protein-based block co-polymers and self-assembled peptides.

STATEMENT OF SIGNIFICANCE

The sucker ring teeth (SRT) located on the arms and tentacles of cephalopods represent as a very promising protein-based biopolymer with the potential to rival silk in biomedical and engineering applications. SRT are made of modular, block co-polymer like proteins (suckerins), which assemble into a semicrystalline polymer reinforced by nano-confined β-sheets, resulting in a supramolecular network with mechanical properties that match those of the strongest engineering polymers. In this study, we aimed to understand the molecular mechanisms behind SRT's self-assembly and robustness. The most abundant modular peptidic blocks of suckerin proteins were studied by various spectroscopic methods, which demonstrate that SRT peptides form amyloid-like cross-β structures.

Sequence basis of Barnacle Cement Nanostructure is Defined by Proteins with Silk Homology

Barnacles adhere by producing a mixture of cement proteins (CPs) that organize into a permanently bonded layer displayed as nanoscale fibers. These cement proteins share no homology with any other marine adhesives, and a common sequence-basis that defines how nanostructures function as adhesives remains undiscovered. Here we demonstrate that a significant unidentified portion of acorn barnacle cement is comprised of low complexity proteins; they are organized into repetitive sequence blocks and found to maintain homology to silk motifs. Proteomic analysis of aggregate bands from PAGE gels reveal an abundance of Gly/Ala/Ser/Thr repeats exemplified by a prominent, previously unidentified, 43 kDa protein in the solubilized adhesive. Low complexity regions found throughout the cement proteome, as well as multiple lysyl oxidases and peroxidases, establish homology with silk-associated materials such as fibroin, silk gum sericin, and pyriform spidroins from spider silk. Distinct primary structures defined by homologous domains shed light on how barnacles use low complexity in nanofibers to enable adhesion, and serves as a starting point for unraveling the molecular architecture of a robust and unique class of adhesive nanostructures.

Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics

The differentiated ectodermal basal disc cells of the freshwater cnidarian Hydra secrete proteinaceous glue to temporarily attach themselves to underwater surfaces. Using transcriptome sequencing and a basal disc-specific RNA-seq combined with in situ hybridisation a highly specific set of candidate adhesive genes was identified. A de novo transcriptome assembly of 55,849 transcripts (>200 bp) was generated using paired-end and single reads from Illumina libraries constructed from different polyp conditions. Differential transcriptomics and spatial gene expression analysis by in situ hybridisation allowed the identification of 40 transcripts exclusively expressed in the ectodermal basal disc cells. Comparisons after mass spectrometry analysis of the adhesive secretion showed a total of 21 transcripts to be basal disc specific and eventually secreted through basal disc cells. This is the first study to survey adhesion-related genes in Hydra. The candidate list presented in this study provides a platform for unravelling the molecular mechanism of underwater adhesion of Hydra.

The role of water on the structure and mechanical properties of a thermoplastic natural block co-polymer from squid sucker ring teeth

Hard biological polymers exhibiting a truly thermoplastic behavior that can maintain their structural properties after processing are extremely rare and highly desirable for use in advanced technological applications such as 3D-printing, biodegradable plastics and robust composites. One exception are the thermoplastic proteins that comprise the sucker ring teeth (SRT) of the Humboldt jumbo squid (Dosidicus gigas). In this work, we explore the mechanical properties of reconstituted SRT proteins and demonstrate that the material can be re-shaped by simple processing in water and at relatively low temperature (below 100 °C). The post-processed material maintains a high modulus in the GPa range, both in the dry and the wet states. When transitioning from low to high humidity, the material properties change from brittle to ductile with an increase in plastic deformation, where water acts as a plasticizer. Using synchrotron x-ray scattering tools, we found that water mostly influences nano scale structure, whereas at the molecular level, the protein structure remains largely unaffected. Furthermore, through simultaneous in situ x-ray scattering and mechanical tests, we show that the supramolecular network of the reconstituted SRT material exhibits a progressive alignment along the strain direction, which is attributed to chain alignment of the amorphous domains of SRT proteins. The high modulus in both dry and wet states, combined with their efficient thermal processing characteristics, make the SRT proteins promising substitutes for applications traditionally reserved for petroleum-based thermoplastics.

Squid Sucker Ring Teeth: Multiscale Structure-Property Relationships, Sequencing, and Protein Engineering of a Thermoplastic Biopolymer

The arms and tentacles of Decapodiform cephalopods (squids and cuttlefish) are lined with suckers, each of which contains embedded sucker ring teeth (SRT), which are used by the animal for prey capture and handling. SRT exhibit intriguing physicochemical and thermomechanical characteristics that have so far not been observed in other protein-based biomaterials. Notably, despite their comparatively high mechanical properties, SRT are almost fully soluble in chaotropic solvents and can be readily reconstituted after solvent evaporation into three-dimensional structures. SRT also exhibit thermoplastic characteristics: they can be melted and reshaped multiple times with no-or only minimal-loss of mechanical performance postprocessing. Intrigued by these unusual material characteristics, in recent years, we have conducted in-depth fundamental studies to unveil structure/property relationships of SRT from the molecular (genetic) level to the macroscopic scale. These investigations have demonstrated that SRT are entirely assembled from a protein family called "suckerins" that self-assemble into semicrystalline polymer infinite networks. Suckerins are block copolymers at the molecular level, whose closest analogy appears to be silk fibroins, although significant differences exist between these two protein families. Parallel to these studies, there have been efforts to mimic and engineer suckerins by protein engineering and to demonstrate potential applications through proof-of-concept studies, with a focus on the biomedical field. Both fundamental aspects and emerging applications are presented in this short review. Given the rather unusual source of this model structure, we start by a brief historical account of SRT and suckerin discovery.

Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins

Many globular and structural proteins have repetitions in their sequences or structures. However, a clear relationship between these repeats and their contribution to the mechanical properties remains elusive. We propose a new approach for the design and production of synthetic polypeptides that comprise one or more tandem copies of a single unit with distinct amorphous and ordered regions. Our designed sequences are based on a structural protein produced in squid suction cups that has a segmented copolymer structure with amorphous and crystalline domains. We produced segmented polypeptides with varying repeat number, while keeping the lengths and compositions of the amorphous and crystalline regions fixed. We showed that mechanical properties of these synthetic proteins could be tuned by modulating their molecular weights. Specifically, the toughness and extensibility of synthetic polypeptides increase as a function of the number of tandem repeats. This result suggests that the repetitions in native squid proteins could have a genetic advantage for increased toughness and flexibility.