Bacterial collagen-like proteins that form triple-helical structures

Self-Assembling Triple-Helix Recombinant Collagen Hydrogel Enriched with Tyrosine

The self-assembly of collagen within the human body creates a complex 3D fibrous network, providing structural integrity and mechanical strength to connective tissues. Recombinant collagen plays a pivotal role in the realm of biomimetic natural collagen. However, almost all of the reported recombinant collagens lack the capability of self-assembly, severely hindering their application in tissue engineering and regenerative medicine. Herein, we have for the first time constructed a series of self-assembling tyrosine-rich triple helix recombinant collagens, mimicking the structure and functionality of natural collagen. The recombinant collagen consists of a central triple-helical domain characterized by the (Gly-Xaa-Yaa)n sequence, along with N-terminal and C-terminal domains featuring the GYY sequence. The introduction of GYY has a negligible impact on the stability of the triple-helical structure of recombinant collagen while simultaneously promoting its self-assembly into fibers. In the presence of [Ru(bpy)3]Cl2 and APS as catalysts, tyrosine residues in the recombinant collagen undergo covalent cross-linking, resulting in a hydrogel with exceptional mechanical properties. The recombinant collagen hydrogel exhibits outstanding biocompatibility and bioactivity, significantly enhancing the proliferation, adhesion, migration, and differentiation of HFF-1 cells. This innovative self-assembled triple-helix recombinant collagen demonstrates significant potential in the fields of tissue engineering and medical materials.

A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments

Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.

Designing collagens to shed light on the multi-scale structure-function mapping of matrix disorders

Collagens are the most abundant structural proteins in the extracellular matrix of animals and play crucial roles in maintaining the structural integrity and mechanical properties of tissues and organs while mediating important biological processes. Fibrillar collagens have a unique triple helix structure with a characteristic repeating sequence of (Gly-X-Y)n. Variations within the repetitive sequence can cause misfolding of the triple helix, resulting in heritable connective tissue disorders. The most common variations are single-point missense mutations that lead to the substitution of a glycine residue with a bulkier amino acid (Gly → X). In this review, we will first discuss the importance of collagen's triple helix structure and how single Gly substitutions can impact its folding, structure, secretion, assembly into higher-order structures, and biological functions. We will review the role of "designer collagens," i.e., synthetic collagen-mimetic peptides and recombinant bacterial collagen as model systems to include Gly → X substitutions observed in collagen disorders and investigate their impact on structure and function utilizing in vitro studies. Lastly, we will explore how computational modeling of collagen peptides, especially molecular and steered molecular dynamics, has been instrumental in probing the effects of Gly substitutions on structure, receptor binding, and mechanical stability across multiple length scales.

The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans

Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans (GAGs) on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual dynamic trimer arrangement with a positively charged external surface and a negatively charged solvent exposed internal cavity. Through Molecular Dynamics (MD) simulations, we show how the GAG chondroitin-4-sulphate associates with the Lcl-CTD surface via unique binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate binding mechanism.

Construction of a Collagen-like Protein Based on Elastin-like Polypeptide Fusion and Evaluation of Its Performance in Promoting Wound Healing

In the healing of wounds, human-like collagen (hCol) is essential. However, collagen-based composite dressings have poor stability in vivo, which severely limits their current therapeutic potential. Based on the above, we have developed a recombinant fusion protein named hCol-ELP, which consists of hCol and an elastin-like peptide (ELP). Then, we examined the physicochemical and biological properties of hCol-ELP. The results indicated that the stability of the hCol-ELP fusion protein exhibited a more compact and homogeneous lamellar microstructure along with collagen properties, it was found to be significantly superior to the stability of free hCol. The compound hCol-ELP demonstrated a remarkable capacity to induce the proliferation and migration of mouse embryo fibroblast cells (NIH/3T3), as well as enhance collagen synthesis in human skin fibroblasts (HSF) when tested in vitro. In vivo, hCol-ELP demonstrated significant enhancements in healing rate and a reduction in the time required for scab removal, thereby exhibiting a scar-free healing effect. The findings provide a crucial theoretical foundation for the implementation of an hCol-ELP protein dressing in fields associated with the healing of traumatic injuries.

In-Silico Analysis Highlights the Existence in Members of Burkholderia cepacia Complex of a New Class of Adhesins Possessing Collagen-like Domains

Burkholderia cenocepacia is a multi-drug-resistant lung pathogen. This species synthesizes various virulence factors, among which cell-surface components (adhesins) are critical for establishing the contact with host cells. This work in the first part focuses on the current knowledge about the adhesion molecules described in this species. In the second part, through in silico approaches, we perform a comprehensive analysis of a group of unique bacterial proteins possessing collagen-like domains (CLDs) that are strikingly overrepresented in the Burkholderia species, representing a new putative class of adhesins. We identified 75 CLD-containing proteins in Burkholderia cepacia complex (Bcc) members (Bcc-CLPs). The phylogenetic analysis of Bcc-CLPs revealed the evolution of the core domain denominated "Bacterial collagen-like, middle region". Our analysis remarkably shows that these proteins are formed by extensive sets of compositionally biased residues located within intrinsically disordered regions (IDR). Here, we discuss how IDR functions may increase their efficiency as adhesion factors. Finally, we provided an analysis of a set of five homologs identified in B. cenocepacia J2315. Thus, we propose the existence in Bcc of a new type of adhesion factors distinct from the described collagen-like proteins (CLPs) found in Gram-positive bacteria.

Comparative Genomic and Metagenomic Investigations of the Corynebacterium tuberculostearicum Species Complex Reveals Potential Mechanisms Underlying Associations To Skin Health and Disease

Corynebacterium are a diverse genus and dominant member of the human skin microbiome. Recently, we reported that the most prevalent Corynebacterium species found on skin, including Corynebacterium tuberculostearicum and Corynebacterium kefirresidentii, comprise a narrow species complex despite the diversity of the genus. Here, we apply high-resolution phylogenomics and comparative genomics to describe the structure of the C. tuberculostearicum species complex and highlight genetic traits which are enriched or depleted in it relative to other Corynebacterium. Through metagenomic investigations, we also find that individual species within the complex can associate with specific body sites. Finally, we discover that one species from the complex, C. kefirresidentii, increases in relative abundance during atopic dermatitis flares, and show that most genomes of this species encode a colocalized set of putative virulence genes. IMPORTANCE Corynebacterium are commonly found bacteria on the human skin. In this study, we perform comparative genomics to gain insight into genetic traits which differentiate a phylogenetically related group of Corynebacterium, the Corynebacterium tuberculostearicum species complex, that includes the most prevalent species from the genus in skin microbiomes. After resolving the presence of distinct species within the complex, we applied metagenomic analysis to uncover biogeographic associations of individual species within the complex with specific body sites and discovered that one species, commonly found in the nares of individuals, increases in abundance across multiple body sites during atopic dermatitis flares.

Regulation of Collagen I and Collagen III in Tissue Injury and Regeneration

The structure of connective tissues including cartilage, tendons, and ligaments as well as many organs, like the skin, heart, liver, kidney, lungs, blood vessels, and bones, depend on collagen. The bulk of the network of structural proteins that make up the extracellular matrix of the heart is composed of collagen type I and type III, which provide structural support for the muscle cells and are crucial for cardiac function. The prognosis and progression of a disease or diseased state may be significantly impacted by the upregulation or downregulation of the collagen types, particularly Col I and Col III. For example, increasing Col I protein levels may impose increasing myocardial stiffness, impairing the diastolic and systolic function of the myocardium. Collagen I is a stiff fibrillar protein that gives tensile strength, whereas Col III produces an elastic network that stores kinetic energy as an elastic rebound. These two collagen proteins have distinct physical properties in nature. Therefore, the control of Col I and Col III as well as the potential relevance of the Col I/Col III ratio in many biological processes serve as the foundation for this comprehensive review article.

Purification of recombinant bacterial collagens containing structural perturbations

Streptococcus pyogenes-derived recombinant bacterial collagen-like proteins (CLPs) are emerging as a potential biomaterial for biomedical research and applications. Bacterial CLPs form stable triple helices and lack specific interactions with human cell surface receptors, thus enabling the design of novel biomaterials with specific functional attributes. Bacterial collagens have been instrumental in understanding collagen structure and function in normal and pathological conditions. These proteins can be readily produced in E. coli, purified using affinity chromatography, and subsequently isolated after cleavage of the affinity tag. Trypsin is a widely used protease during this purification step since the triple helix structure is resistant to trypsin digestion. However, the introduction of Gly→X mutations or natural interruptions within CLPs can perturb the triple helix structure, making them susceptible to trypsin digestion. Consequently, removing the affinity tag and isolating collagen-like (CL) domains containing mutations is impossible without degradation of the product. We present an alternative method to isolate CL domains containing Gly→X mutations utilizing a TEV protease cleavage site. Protein expression and purification conditions were optimized for designed protein constructs to achieve high yield and purity. Enzymatic digestion assays demonstrated that CL domains from wild-type CLPs could be isolated by digestion with either trypsin or TEV protease. In contrast, CLPs containing Gly→Arg mutations are readily digested by trypsin while digestion with TEV protease cleaved the His6-tag, enabling the isolation of mutant CL domains. The developed method can be adapted to CLPs containing various new biological sequences to develop multifunctional biomaterials for tissue engineering applications.

Hydrated Collagen: Where Physical Chemistry, Medical Imaging, and Bioengineering Meet

It is well-known that collagen is the most abundant protein in the human body; however, what is not often appreciated is its fascinating physical chemistry and molecular physics. In this Perspective, we aim to expose some of the physicochemical phenomena associated with the hydration of collagen and to examine the role collagen's hydration water plays in determining its biological function as well as applications ranging from radiology to bioengineering. The main focus is on the Magic-Angle Effect, a phenomenon observed in Nuclear Magnetic Resonance (NMR) spectroscopy and Magnetic Resonance Imaging (MRI) of anisotropic collagenous tissues such as articular cartilage and tendon. While the effect has been known in NMR and MRI for decades, its exact molecular mechanism remains a topic of debate and continuing research in scientific literature. We survey some of the latest research aiming to develop a comprehensive molecular-level model of the Magic-Angle Effect. We also touch on other fields where understanding of collagen hydration is important, particularly nanomechanics and mechanobiology, biomaterials, and piezoelectric sensors.

Characterization of recombinant humanized collagen type III and its influence on cell behavior and phenotype

Collagen made a tremendous impact in the field of regenerative medicine as a bioactive material. For decades, collagen has been used not only as a scaffolding material but also as an active component in regulating cells' biological behavior and phenotype. However, animal-derived collagen as a major source suffered from problems of immunogenicity, risk of viral infection, and the unclear relationship between bioactive sequence and function. Recombinant humanized collagen (rhCol) provided alternatives for regenerative medicine with more controllable risks. However, the characterization of rhCol and the interaction between rhCol and cells still need further investigation, including cell behavior and phenotype. The current study preliminarily demonstrated that recombinant humanized collagen type III (rhCol III) conformed to the theoretical amino acid sequence and had an advanced structure resembling bovine collagen. Furthermore, rhCol III could facilitate basal biological behaviors of human skin fibroblasts, such as adhesion, proliferation and migration. rhCol III was beneficial for some extracellular matrix-expressing cell phenotypes. The study would shed light on the mechanism research of rhCol and cell interactions and further understanding of effectiveness in tissue regeneration.

Graphical abstract

Recombinant protein polymer-antibody conjugates for applications in nanotechnology and biomedicine

Currently, there are over 100 antibody-based therapeutics on the market for the treatment of various diseases. The increasing importance of antibody treatment is further highlighted by the recent FDA emergency use authorization of certain antibody therapies for COVID-19 treatment. Protein-based materials have gained momentum for antibody delivery due to their biocompatibility, tunable chemistry, monodispersity, and straightforward synthesis and purification. In this review, we discuss progress in engineering the molecular features of protein-based biomaterials, in particular recombinant protein polymers, for introducing novel functionalities and enhancing the delivery properties of antibodies and related binding protein domains.

Design of synthetic collagens that assemble into supramolecular banded fibers as a functional biomaterial testbed

Collagens are the most abundant proteins of the extracellular matrix, and the hierarchical folding and supramolecular assembly of collagens into banded fibers is essential for mediating cell-matrix interactions and tissue mechanics. Collagen extracted from animal tissues is a valuable commodity, but suffers from safety and purity issues, limiting its biomaterials applications. Synthetic collagen biomaterials could address these issues, but their construction requires molecular-level control of folding and supramolecular assembly into ordered banded fibers, comparable to those of natural collagens. Here, we show an innovative class of banded fiber-forming synthetic collagens that recapitulate the morphology and some biological properties of natural collagens. The synthetic collagens comprise a functional-driver module that is flanked by adhesive modules that effectively promote their supramolecular assembly. Multiscale simulations support a plausible molecular-level mechanism of supramolecular assembly, allowing precise design of banded fiber morphology. We also experimentally demonstrate that synthetic fibers stimulate osteoblast differentiation at levels comparable to natural collagen. This work thus deepens understanding of collagen biology and disease by providing a ready source of safe, functional biomaterials that bridge the current gap between the simplicity of peptide biophysical models and the complexity of in vivo animal systems.

Bacterial collagen-templated synthesis and assembly of inorganic particles

Collagen has been used as a common template for mineralization and assembly of inorganic particles, because of the special arrangement of its fibrils and the presence of charged residues. Streptococcal bacterial collagen, which is inherently secreted on the surface ofStreptococcus pyogenes, has been progressively used as an alternative for type I animal collagen. Bacterial collagen is rich in charged amino acids, which can act as a substrate for the nucleation and growth of inorganic particles. Here, we show that bacterial collagen can be used to nucleate three different inorganic materials: hydroxyapatite crystals, silver nanoparticles, and silica nanoparticles. Collagen/mineral composites show an even distribution of inorganic particles along the collagen fibers, and the particles have a more homogenous size compared with minerals that are formed in the absence of the collagen scaffold. Furthermore, the gelation of silica occurring during mineralization represents a means to produce processable self-standing collagen composites, which is challenging to achieve with bacterial collagen alone. Overall, we highlight the advantage of simply combining bacterial collagen with minerals to expand their applications in the fields of biomaterials and tissue engineering, especially for bone regenerative scaffolds.

Recombinant and genetic code expanded collagen-like protein as a tailorable biomaterial

Collagen occurs in nature with a dedicated triple helix structure and is the most preferred biomaterial in commercialized medical products. However, concerns on purity, disease transmission, and the reproducibility of animal derived collagen restrict its applications and warrants alternate recombinant sources. The expression of recombinant collagen in different prokaryotic and eukaryotic hosts has been reported with varying degrees of success, however, it is vital to elucidate the structural and biological characteristics of natural collagen. The recombinant production of biologically functional collagen is restricted by its high molecular weight and post-translational modification (PTM), especially the hydroxylation of proline to hydroxyproline. Hydroxyproline plays a key role in the structural stability and higher order self-assembly to form fibrillar matrices. Advancements in synthetic biology and recombinant technology are being explored for improving the yield and biomimicry of recombinant collagen. It emerges as reliable, sustainable source of collagen, promises tailorable properties and thereby custom-made protein biomaterials. Remarkably, the evolutionary existence of collagen-like proteins (CLPs) has been identified in single-cell organisms. Interestingly, CLPs exhibit remarkable ability to form stable triple helical structures similar to animal collagen and have gained increasing attention. Strategies to expand the genetic code of CLPs through the incorporation of unnatural amino acids promise the synthesis of highly tunable next-generation triple helical proteins required for the fabrication of smart biomaterials. The review outlines the importance of collagen, sources and diversification, and animal and recombinant collagen-based biomaterials and highlights the limitations of the existing collagen sources. The emphasis on genetic code expanded tailorable CLPs as the most sought alternate for the production of functional collagen and its advantages as translatable biomaterials has been highlighted.

Discovering design principles of collagen molecular stability using a genetic algorithm, deep learning, and experimental validation

Collagen is the most abundant structural protein in humans, providing crucial mechanical properties, including high strength and toughness, in tissues. Collagen-based biomaterials are, therefore, used for tissue repair and regeneration. Utilizing collagen effectively during materials processing ex vivo and subsequent function in vivo requires stability over wide temperature ranges to avoid denaturation and loss of structure, measured as melting temperature (T_m). Although significant research has been conducted on understanding how collagen primary amino acid sequences correspond to T_m values, a robust framework to facilitate the design of collagen sequences with specific T_m remains a challenge. Here, we develop a general model using a genetic algorithm within a deep learning framework to design collagen sequences with specific T_m values. We report 1,000 de novo collagen sequences, and we show that we can efficiently use this model to generate collagen sequences and verify their T_m values using both experimental and computational methods. We find that the model accurately predicts T_m values within a few degrees centigrade. Further, using this model, we conduct a high-throughput study to identify the most frequently occurring collagen triplets that can be directly incorporated into collagen. We further discovered that the number of hydrogen bonds within collagen calculated with molecular dynamics (MD) is directly correlated to the experimental measurement of triple-helical quality. Ultimately, we see this work as a critical step to helping researchers develop collagen sequences with specific T_m values for intended materials manufacturing methods and biomedical applications, realizing a mechanistic materials by design paradigm.

The application of collagen in the repair of peripheral nerve defect

Collagen is a natural polymer expressed in the extracellular matrix of the peripheral nervous system. It has become increasingly crucial in peripheral nerve reconstruction as it was involved in regulating Schwann cell behaviors, maintaining peripheral nerve functions during peripheral nerve development, and being strongly upregulated after nerve injury to promote peripheral nerve regeneration. Moreover, its biological properties, such as low immunogenicity, excellent biocompatibility, and biodegradability make it a suitable biomaterial for peripheral nerve repair. Collagen provides a suitable microenvironment to support Schwann cells’ growth, proliferation, and migration, thereby improving the regeneration and functional recovery of peripheral nerves. This review aims to summarize the characteristics of collagen as a biomaterial, analyze its role in peripheral nerve regeneration, and provide a detailed overview of the recent advances concerning the optimization of collagen nerve conduits in terms of physical properties and structure, as well as the application of the combination with the bioactive component in peripheral nerve regeneration.

Recombinant collagen hydrogels induced by disulfide bonds

With the characteristics of low toxicity and biodegradability, recombinant collagen‐like proteins have been chemically and genetically engineered as a scaffold for cell adhesion and proliferation. However, most of the existing hydrogels crosslinked with peptides or polymers are not pure collagen, limiting their utility as biomaterials. A major roadblock in the development of biomaterials is the need for high purity collagen that can self‐assemble into hydrogels under mild conditions. In this work, we designed a recombinant protein, S‐VCL‐S, by introducing cysteine residues into the Streptococcus pyogenes collagen‐like protein at both the N‐and C‐termini of the collagen with a trimerization domain (V) and a collagen domain (CL). The S‐VCL‐S protein was properly folded in complete triple helices and formed self‐supporting hydrogels without polymer modifications. In addition, the introduction of cysteines was found to play a key role in the properties of the hydrogels, including their microstructure, pore size, mechanical properties, and drug release capability. Moreover, two/three‐dimensional cell‐culture assays showed that the hydrogels are noncytotoxic and can promote long‐term cell viability. This study explored a crosslinking collagen hydrogel based on disulfide bonds and provides a design strategy for collagen‐based biomaterials.

N'-terminal- and Ca2+-induced stabilization of high-order oligomers of full-length Danio rerio and Homo sapiens otolin-1

Otolin-1 is a C1q family member and a major component of the organic matrix of fish otoliths and human otoconia. To date, the protein molecular properties have not been characterized. In this work, we describe biochemical characterization and comparative studies on saccular-specific otolin-1 derived from Danio rerio and Homo sapiens. Due to the low abundance of proteins in the otoconial matrix, we developed a production and purification method for both recombinant homologues of otolin-1. Danio rerio and Homo sapiens otolin-1 forms higher-order oligomers that can be partially disrupted under reducing conditions. The presence of Ca²⁺ stabilizes the oligomers and significantly increases the thermal stability of the proteins. Despite the high sequence coverage, the oligomerization of Danio rerio otolin-1 is more affected by the reducing conditions and presence of Ca²⁺ than the human homologue. The results show differences in molecular behaviour, which may be reflected in Danio rerio and Homo sapiens otolin-1 role in otolith and otoconia formation.

Prokaryotic Collagen-Like Proteins as Novel Biomaterials

Collagens are the major structural component in animal extracellular matrices and are critical signaling molecules in various cell-matrix interactions. Its unique triple helical structure is enabled by tripeptide Gly-X-Y repeats. Understanding of sequence requirements for animal-derived collagen led to the discovery of prokaryotic collagen-like protein in the early 2000s. These prokaryotic collagen-like proteins are structurally similar to mammalian collagens in many ways. However, unlike the challenges associated with recombinant expression of mammalian collagens, these prokaryotic collagen-like proteins can be readily expressed in E. coli and are amenable to genetic modification. In this review article, we will first discuss the properties of mammalian collagen and provide a comparative analysis of mammalian collagen and prokaryotic collagen-like proteins. We will then review the use of prokaryotic collagen-like proteins to both study the biology of conventional collagen and develop a new biomaterial platform. Finally, we will describe the application of Scl2 protein, a streptococcal collagen-like protein, in thromboresistant coating for cardiovascular devices, scaffolds for bone regeneration, chronic wound dressing and matrices for cartilage regeneration.

Recent Advances in Collagen Mimetic Peptide Structure and Design

Collagen mimetic peptides (CMPs) fold into a polyproline type II triple helix, allowing the study of the structure and function (or misfunction) of the collagen family of proteins. This Perspective will focus on recent developments in the use of CMPs toward understanding the structure and controlling the stability of the triple helix. Triple helix assembly is influenced by various factors, including the single amino acid propensity for the triple helix fold, pairwise interactions between these amino acids, and long-range effects observed across the helix, such as bend, twist, and fraying. Important progress in creating a comprehensive and predictive understanding of these factors for peptides with exclusively natural amino acids has been made. In contrast, several groups have successfully developed unnatural amino acids that are engineered to stabilize the triple helical structure. A third approach to controlling the triple helical structure includes covalent cross-linking of the triple helix to stabilize the assembly, which eliminates the problematic equilibrium of unfolding into monomers and enforces compositional control. Advances in all these areas have resulted in significant improvements to our understanding and control of this important class of protein, allowing for the design and application of more chemically complex and well-controlled collagen mimetic biomaterials.

ColGen: An end-to-end deep learning model to predict thermal stability of de novo collagen sequences

Collagen is the most abundant structural protein in humans, with dozens of sequence variants accounting for over 30% of the protein in an animal body. The fibrillar and hierarchical arrangements of collagen are critical in providing mechanical properties with high strength and toughness. Due to this ubiquitous role in human tissues, collagen-based biomaterials are commonly used for tissue repairs and regeneration, requiring chemical and thermal stability over a range of temperatures during materials preparation ex vivo and subsequent utility in vivo. Collagen unfolds from a triple helix to a random coil structure during a temperature interval in which the midpoint or T_m is used as a measure to evaluate the thermal stability of the molecules. However, finding a robust framework to facilitate the design of a specific collagen sequence to yield a specific T_m remains a challenge, including using conventional molecular dynamics modeling. Here we propose a de novo framework to provide a model that outputs the T_m values of input collagen sequences by incorporating deep learning trained on a large data set of collagen sequences and corresponding T_m values. By using this framework, we are able to quickly evaluate how mutations and order in the primary sequence affect the stability of collagen triple helices. Specifically, we confirm that mutations to glycines, mutations in the middle of a sequence, and short sequence lengths cause the greatest drop in T_m values.

VNTR Typing of the Bacterial Rice Pathogen Burkholderia glumae Reveals the Coexistence of Several Diverging Lineages in a Single Field in Colombia

Burkholderia glumae is responsible for the panicle blight disease of rice. This disease is present worldwide and can result in significant drop in yields. To estimate the genetic diversity of the bacterial strains present in a rice paddy field in Colombia, we sampled 109 strains from infected panicles. To detect fine genetic relationships among related haplotypes, and to overcome a very low nucleotide diversity detected in previous studies, we designed primers to amplify and sequence several highly variable minisatellite loci, or variable number tandem repeats (VNTRs), as well as part of the Toxoflavin toxA gene in all strains. Results show that the toxA nucleotide diversity defined four lineages and was similar to that detected in several fields in Japan; data suggest that B. glumae has spread from Asia to America without major loss of genetic diversity, and that five VNTR loci discriminated the strains within the field revealing single and multi-infections of the rice panicles with a wide distribution of the haplotypes among the different plots. Even though disease levels vary considerably from year to year, the bacterial genetic diversity is maintained within a field. We do not detect any geographical structuring within the field, nor any effect of the rice cultivar on the observed diversity. The consequences on the origin and evolution of the bacteria are discussed.

An artificial virus-like triblock protein shows low in vivo humoral immune response and high stability

The use of viral vectors for in vivo gene therapy can be severely limited by their immunogenicity. Non-viral vectors may represent an alternative, however, reports analyzing their immunogenicity are still lacking. Here, we studied the humoral immune response in a murine model triggered by artificial virus-like particles (AVLPs) carrying plasmid or antisense DNA. The AVLPs were assembled using a family of modular proteins based on bioinspired collagen-like and silk-like sequences that produce virus-like particles. We compared our AVLPs against an Adeno Associated Virus 1 (AAV), a widely used viral vector for in vivo gene delivery that has been approved by the FDA and EMA for gene therapy. We found that a 1000-fold higher mass of AVLPs than AAV are necessary to obtain similar specific antibody titters. Furthermore, we studied the stability of AVLPs against relevant biological reagents such as heparin and fetal bovine serum to ensure nucleic acid protection in biological media. Our study demonstrates that the AVLPs are stable in physiological conditions and can overcome safety limitations such as immunogenicity. The scarce humoral immunogenicity and high stability found with AVLPs suggest that they have potential to be used as stealth non-viral gene delivery systems for in vivo studies or gene therapy.

"Here we go again": the inspection of collagen extraction protocols for 14C dating and palaeodietary analysis

Archaeological bone collagen is highly useful for radiocarbon (¹⁴C) dating and palaeodietary reconstruction. However, collagen preservation and carbon contamination are essential considerations when extracting collagen, becoming especially crucial close to the limit of the method (50,000 years before present = BP). Strong progress has been achieved in the past two decades by ¹⁴C and stable isotopic laboratories in removing contamination from archaeological bones, but different pretreatment protocols have been proven to produce varying results. Here we compare three collagen extraction protocols used for palaeodietary studies and ¹⁴C dating, considering collagen yield, elemental and stable isotopic data, FTIR analysis, and ¹⁴C dates. We focus on the impact of ultrafiltration on the yield and quality of the extracted material. The results again underline the importance of rigorous decontamination methods to gain accurate ¹⁴C dates and demonstrate that different protocols have significant effects on the quality and yield of extracted collagen.

A Significantly High Abundance of "Candidatus Liberibacter asiaticus" in Citrus Fruit Pith: in planta Transcriptome and Anatomical Analyses

Huanglongbing, a highly destructive disease of citrus, is associated with the non-culturable phloem-limited α-proteobacterium "Candidatus Liberibacter asiaticus" (CLas). The distribution patterns of CLas in infected plant are variable and not consistent, which make the CLas detection and characterization more challenging. Here, we performed a systemic analysis of CLas distribution in citrus branches and fruits of 14 cultivars. A significantly high concentration of CLas was detected in fruit pith (dorsal vascular bundle) of 14 citrus cultivars collected at fruit maturity season. A 2-year monitoring assay of CLas population in citrus branches of "Shatangju" mandarin (Citrus reticulata Blanco "Shatangju") revealed that CLas population already exhibited a high level even before the appearance of visual symptoms in the fruit rind. Quantitative analyses of CLas in serial 1.5-cm segments of fruit piths showed the CLas was unevenly distributed within fruit pith and tended to colonize in the middle or distal (stylar end) regions of pith. The use of CLas-abundant fruit pith for dual RNA-seq generated higher-resolution CLas transcriptome data compared with the leaf samples. CLas genes involved in transport system, flagellar assembly, lipopolysaccharide biosynthesis, virulence, stress response, and cell surface structure, as well as host genes involved in biosynthesis of antimicrobial-associated secondary metabolites, was up-regulated in leaf midribs compared with fruit pith. In addition, CLas infection caused the severe collapse in phloem and callose deposition in the plasmodesmata of fruit pith. The ability of fruit pith to support multiplication of CLas to high levels makes it an ideal host tissue for morphological studies and in planta transcriptome analyses of CLas-host interactions.

Applications of bacteria and their derived biomaterials for repair and tissue regeneration

Microorganisms such as bacteria and their derived biopolymers can be used in biomaterials and tissue regeneration. Various methods have been applied to regenerate damaged tissues, but using probiotics and biomaterials derived from bacteria with improved economic-production efficiency and highly applicable properties can be a new solution in tissue regeneration. Bacteria can synthesize numerous types of biopolymers. These biopolymers possess many desirable properties such as biocompatibility and biodegradability, making them good candidates for tissue regeneration. Here, we reviewed different types of bacterial-derived biopolymers and highlight their applications for tissue regeneration.

Toward Activatable Collagen Mimics: Combining DEPSI "Switch" Defects and Template-Guided Self-Organization to Control Collagen Mimetic Peptides

Collagen mimetic peptides (CMPs), which imitate various structural or functional features of natural collagen, constitute advanced models illuminating the folding aspects of the collagen triple helix (CTH) motif. In this study, the CMPs of repeating Gly-Pro-Pro (GPP) triplets are tethered to an organic scaffold based on a tris(2-aminoethyl) amine (TREN) derivative (TREN(sucOH)₃ ). These three templated peptide strands are further expanded via native chemical ligation to increase the number of GPP triplets and lead to a TREN(sucGPPGPPG(Ψ)SPGPPCPP[GPP]₄ )₃ construct. The incorporation of an ester switch segment, G(Ψ)S, as a positional O-acyl isopeptide (DEPSI) defect into the peptide strands allows the pH-controlled acceleration of CTH formation. The strand assembly process is monitored by circular dichroism (CD) spectroscopy. The results of pH jump experiments and thermal denaturation studies provide new insights into the contributions of structural DEPSI defects to the template-guided self-assembly of the CTH motif. While the organic scaffold drives the CTH formation, the switch defects act as temporary opponents and slow down the folding. CD spectroscopy data confirm that the switch defects contribute to the formation of a more stable CTH motif by enhancing the structural dynamics at the early stage of the folding process.

Genome-Wide Association Analysis Identifies a Genetic Basis of Infectivity in a Model Bacterial Pathogen

Knowledge of the genetic architecture of pathogen infectivity and host resistance is essential for a mechanistic understanding of coevolutionary processes, yet the genetic basis of these interacting traits remains unknown for most host-pathogen systems. We used a comparative genomic approach to explore the genetic basis of infectivity in Pasteuria ramosa, a Gram-positive bacterial pathogen of planktonic crustaceans that has been established as a model for studies of Red Queen host-pathogen coevolution. We sequenced the genomes of a geographically, phenotypically, and genetically diverse collection of P. ramosa strains and performed a genome-wide association study to identify genetic correlates of infection phenotype. We found multiple polymorphisms within a single gene, Pcl7, that correlate perfectly with one common and widespread infection phenotype. We then confirmed this perfect association via Sanger sequencing in a large and diverse sample set of P. ramosa clones. Pcl7 codes for a collagen-like protein, a class of adhesion proteins known or suspected to be involved in the infection mechanisms of a number of important bacterial pathogens. Consistent with expectations under Red Queen coevolution, sequence variation of Pcl7 shows evidence of balancing selection, including extraordinarily high diversity and absence of geographic structure. Based on structural homology with a collagen-like protein of Bacillus anthracis, we propose a hypothesis for the structure of Pcl7 and the physical location of the phenotype-associated polymorphisms. Our results offer strong evidence for a gene governing infectivity and provide a molecular basis for further study of Red Queen dynamics in this model host-pathogen system.

Current Insights on the Diverse Structures and Functions in Bacterial Collagen-like Proteins

The dearth of knowledge on the diverse structures and functions in bacterial collagen-like proteins is in stark contrast to the deep grasp of structures and functions in mammalian collagen, the ubiquitous triple-helical scleroprotein that plays a central role in tissue architecture, extracellular matrix organization, and signal transduction. To fill and highlight existing gaps due to the general paucity of data on bacterial CLPs, we comprehensively reviewed the latest insight into their functional and structural diversity from multiple perspectives of biology, computational simulations, and materials engineering. The origins and discovery of bacterial CLPs were explored. Their genetic distribution and molecular architecture were analyzed, and their structural and functional diversity in various bacterial genera was examined. The principal roles of computational techniques in understanding bacterial CLPs' structural stability, mechanical properties, and biological functions were also considered. This review serves to drive further interest and development of bacterial CLPs, not only for addressing fundamental biological problems in collagen but also for engineering novel biomaterials. Hence, both biology and materials communities will greatly benefit from intensified research into the diverse structures and functions in bacterial collagen-like proteins.

Enhanced Collagen-like Protein for Facile Biomaterial Fabrication

We present a collagen-mimetic protein of bacterial origin based upon a modified subdomain of the collagen-like Sc12 protein from Streptococcus pyogenes, as an alternative collagen-like biomaterial platform that is highly soluble, forms stable, homogeneous, fluid-like solutions at elevated concentrations, and that can be efficiently fabricated into hydrogel materials over a broad range of pH conditions. This extended bacterial collagen-like (eBCL) protein is expressed in a bacterial host and purified as a trimeric assembly exhibiting a triple helical secondary structure in its collagen-like subdomain that is stable near physiological solution conditions (neutral pH and 37 °C), as well as over a broad range of pH conditions. We also show how this sequence can be modified to include biofunctional attributes, in particular, the Arg-Gly-Asp (RGD) sequence to elicit integrin-specific cell binding, without loss of structural function. Furthermore, through the use of EDC-NHS chemistry, we demonstrate that members of this eBCL protein system can be covalently cross-linked to fabricate transparent hydrogels with high protein concentrations (at least to 20% w/w). These hydrogels are shown to possess material properties and resistance to enzymatic degradation that are comparable or superior to a type I collagen control. Moreover, such hydrogels containing the constructs with the RGD integrin-binding sequence are shown to promote the adhesion, spreading, and proliferation of C2C12 and 3T3 cells in vitro. Due to its enhanced solubility, structural stability, fluidity at elevated concentrations, ease of modification, and facility of cross-linking, this eBCL collagen-mimetic system has potential for numerous biomedical material applications, where the ease of processing and fabrication and the facility to tailor the sequence for specific biological functionality are desired.

Synthesis and Application of Collagens for Assembling a Corneal Implant

Recombinant or artificial designer collagens have developed to a point where they are viable candidates for replacing extracted animal collagens in regenerative medicine applications. Biomimetic corneas made have shown promise as replacements for human donor corneas, and have previously been fabricated from several different collagens or collagen-like peptides (CLPs). Prokaryotic expression systems allow for cheap, rapid, gram scale production of collagens/CLPs. Here, we describe a procedure for production of collagen-like peptides for the manufacture of a biomimetic cornea.

Biopolymer-based Scaffolds for Tissue Engineering Applications

Tissue engineering is governed by the use of cells and polymers. The cells may be accounted for the type of tissue to be targeted, while polymers may vary from natural to synthetic. The natural polymers have advantages such as non-immunogenic and complex structures that help in the formation of bonds in comparison to the synthetic ones. Various targeted drug delivery systems have been prepared using polymers and cells, such as nanoparticles, hydrogels, nanofibers, and microspheres. The design of scaffolds depends on the negative impact of material used on the human body and they have been prepared using surface modification technique or neo material synthesis. The dermal substitutes are a distinctive array that aims at the replacement of skin parts either through grafting or some other means. This review focuses on biomaterials for their use in tissue engineering. This article shall provide the bird's eye view of the scaffolds and dermal substitutes, which are naturally derived.

Collagen Binding Proteins of Gram-Positive Pathogens

Collagens are the primary structural components of mammalian extracellular matrices. In addition, collagens regulate tissue development, regeneration and host defense through interaction with specific cellular receptors. Their unique triple helix structure, which requires a glycine residue every third amino acid, is the defining structural feature of collagens. There are 28 genetically distinct collagens in humans. In addition, several other unrelated human proteins contain a collagen domain. Gram-positive bacteria of the genera Staphylococcus, Streptococcus, Enterococcus, and Bacillus express cell surface proteins that bind to collagen. These proteins of Gram-positive pathogens are modular proteins that can be classified into different structural families. This review will focus on the different structural families of collagen binding proteins of Gram-positive pathogen. We will describe how these proteins interact with the triple helix in collagens and other host proteins containing a collagenous domain and discuss how these interactions can contribute to the pathogenic processes.

Collagen Mimetic Peptides

Since their first synthesis in the late 1960s, collagen mimetic peptides (CMPs) have been used as a molecular tool to study collagen, and as an approach to develop novel collagen mimetic biomaterials. Collagen, a major extracellular matrix (ECM) protein, plays vital roles in many physiological and pathogenic processes. Applications of CMPs have advanced our understanding of the structure and molecular properties of a collagen triple helix-the building block of collagen-and the interactions of collagen with important molecular ligands. The accumulating knowledge is also paving the way for developing novel CMPs for biomedical applications. Indeed, for the past 50 years, CMP research has been a fast-growing, far-reaching interdisciplinary field. The major development and achievement of CMPs were documented in a few detailed reviews around 2010. Here, we provided a brief overview of what we have learned about CMPs-their potential and their limitations. We focused on more recent developments in producing heterotrimeric CMPs, and CMPs that can form collagen-like higher order molecular assemblies. We also expanded the traditional view of CMPs to include larger designed peptides produced using recombinant systems. Studies using recombinant peptides have provided new insights on collagens and promoted progress in the development of collagen mimetic fibrillar self-assemblies.

Dynamic Evolution of the Cthrc1 Genes, a Newly Defined Collagen-Like Family

Collagen triple helix repeat containing protein 1 (Cthrc1) is a secreted glycoprotein reported to regulate collagen deposition and to be linked to the Transforming growth factor β/Bone morphogenetic protein and the Wnt/planar cell polarity pathways. It was first identified as being induced upon injury to rat arteries and was found to be highly expressed in multiple human cancer types. Here, we explore the phylogenetic and evolutionary trends of this metazoan gene family, previously studied only in vertebrates. We identify Cthrc1 orthologs in two distant cnidarian species, the sea anemone Nematostella vectensis and the hydrozoan Clytia hemisphaerica, both of which harbor multiple copies of this gene. We find that Cthrc1 clade-specific diversification occurred multiple times in cnidarians as well as in most metazoan clades where we detected this gene. Many other groups, such as arthropods and nematodes, have entirely lost this gene family. Most vertebrates display a single highly conserved gene, and we show that the sequence evolutionary rate of Cthrc1 drastically decreased within the gnathostome lineage. Interestingly, this reduction coincided with the origin of its conserved upstream neighboring gene, Frizzled 6 (FZD6), which in mice has been shown to functionally interact with Cthrc1. Structural modeling methods further reveal that the yet uncharacterized C-terminal domain of Cthrc1 is similar in structure to the globular C1q superfamily domain, also found in the C-termini of collagens VIII and X. Thus, our studies show that the Cthrc1 genes are a collagen-like family with a variable short collagen triple helix domain and a highly conserved C-terminal domain structure resembling the C1q family.

Growth factor-mimicking 3,4-dihydroxyphenylalanine-encoded bioartificial extracellular matrix like protein promotes wound closure and angiogenesis

The present work reports a new route to prepare a "smart biomaterial" by mimicking long-acting cellular growth factor showing enhanced cell-material interactions by promoting cell proliferation and angiogenesis. For that, reactive non-proteogenic amino acid 3,4-dihydroxyphenylalanine (DOPA) was genetically introduced into an intrinsic triple-helical hierarchical structure forming protein to initiate hierarchical self-assembly to form a macromolecular structure. The self-assembled scaffold displayed vascular endothelial growth factor mimicking the pro-angiogenic reactive group for repairing and remodeling of damaged tissue cells. We customized the recombinant collagen-like protein (CLP) with DOPA to promote rapid wound healing and cell migrations. Selective incorporation of catechol in variable and C-terminal region of CLP enhanced interaction between inter- and intra-triple-helical collagen molecules that resulted in a structure resembling higher-order native collagen fibril. Turbidity analysis indicated that the triple-helical CLP self-assembled at neutral pH via a catechol intra-crosslinking mechanism. After self-assembly, only DOPA-encoded CLP formed branched filamentous structures suggesting that catechol mediated network coordination. The catechol-encoded CLP also acted as a "smart material" by mimicking long-acting cellular growth factor showing enhanced cell-material interactions by promoting cell proliferation and angiogenesis. It eliminates release rate, stability, and shelf-life of hybrid growth factor conjugated biomaterials. The newly synthesized CLP has the potential to promote accelerated cell migration, pro-angiogenesis, and biocompatibility and could be used in the field of implantable medical devices and tissue engineering.

Three Decades of Research on Recombinant Collagens: Reinventing the Wheel or Developing New Biomedical Products?

Collagens provide the building blocks for diverse tissues and organs. Furthermore, these proteins act as signaling molecules that control cell behavior during organ development, growth, and repair. Their long half-life, mechanical strength, ability to assemble into fibrils and networks, biocompatibility, and abundance from readily available discarded animal tissues make collagens an attractive material in biomedicine, drug and food industries, and cosmetic products. About three decades ago, pioneering experiments led to recombinant human collagens' expression, thereby initiating studies on the potential use of these proteins as substitutes for the animal-derived collagens. Since then, scientists have utilized various systems to produce native-like recombinant collagens and their fragments. They also tested these collagens as materials to repair tissues, deliver drugs, and serve as therapeutics. Although many tests demonstrated that recombinant collagens perform as well as their native counterparts, the recombinant collagen technology has not yet been adopted by the biomedical, pharmaceutical, or food industry. This paper highlights recent technologies to produce and utilize recombinant collagens, and it contemplates their prospects and limitations.

Interaction Patterns for Staggered Assembly of Fibrils from Semiflexible Chains

The design of colloidal interactions to achieve target self-assembled structures has especially been done for compact objects such as spheres with isotropic interaction potentials, patchy spheres and other compact objects with patchy interactions. Inspired by the self-assembly of collagen-I fibrils and intermediate filaments, we here consider the design of interaction patterns on semiflexible chains that could drive their staggered assembly into regular (para)crystalline fibrils. We consider semiflexible chains composed of a finite number of types of interaction beads (uncharged hydrophilic, hydrophobic, positively charged and negatively charged) and optimize the sequence of these interaction beads with respect to the interaction energy of the semiflexible chains in a number of target-staggered crystalline packings. We find that structures with the lowest interaction energies, that form simple lattices, also have low values of L/D (where L is chain length and D is stagger). In the low interaction energy sequences, similar types of interaction beads cluster together to form stretches. Langevin Dynamics simulations confirm that semiflexible chains with optimal sequences self-assemble into the designed staggered (para)crystalline fibrils. We conclude that very simple interaction patterns should suffice to drive the assembly of long semiflexible chains into staggered (para)crystalline fibrils.

Sea Cucumber Derived Type I Collagen: A Comprehensive Review

Collagen is the major fibrillar protein in most living organisms. Among the different types of collagen, type I collagen is the most abundant one in tissues of marine invertebrates. Due to the health-related risk factors and religious constraints, use of mammalian derived collagen has been limited. This triggers the search for alternative sources of collagen for both food and non-food applications. In this regard, numerous studies have been conducted on maximizing the utilization of seafood processing by-products and address the need for collagen. However, less attention has been given to marine invertebrates and their by-products. The present review has focused on identifying sea cucumber as a potential source of collagen and discusses the general scope of collagen extraction, isolation, characterization, and physicochemical properties along with opportunities and challenges for utilizing marine-derived collagen.

Role for Cell-Surface Collagen of Streptococcus pyogenes in Infections

Group A Streptococcus (GAS) displays cell-surface proteins that resemble human collagen. We find that a fluorophore-labeled collagen mimetic peptide (CMP) labels GAS cells but not Escherichia coli or Bacillus subtilis cells, which lack such proteins. The CMP likely engages in a heterotrimeric helix with endogenous collagen, as the nonnatural d enantiomer of the CMP does not label GAS cells. To identify a molecular target, we used reverse genetics to "knock-in" the GAS genes that encode two proteins with collagen-like domains, Scl1 and Scl2, into B. subtilis. The fluorescent CMP labels the cells of these B. subtilis strains. Moreover, these strains bind tightly to a surface of mammalian collagen. These data are consistent with streptococcal collagen forming triple helices with damaged collagen in a wound bed and thus have implications for microbial virulence.

The predominant roles of the sequence periodicity in the self-assembly of collagen-mimetic mini-fibrils

Collagen fibrils represent a unique case of protein folding and self‐association. We have recently successfully developed triple‐helical peptides that can further self‐assemble into collagen‐mimetic mini‐fibrils. The 35 nm axially repeating structure of the mini‐fibrils, which is designated the d‐period, is highly reminiscent of the well‐known 67 nm D‐period of native collagens when examined using TEM and atomic force spectroscopy. We postulate that it is the pseudo‐identical repeating sequence units in the primary structure of the designed peptides that give rise to the d‐period of the quaternary structure of the mini‐fibrils. In this work, we characterize the self‐assembly of two additional designed peptides: peptide Col877 and peptide Col108rr. The triple‐helix domain of Col877 consists of three pseudo‐identical amino acid sequence units arranged in tandem, whereas that of Col108rr consists of three sequence units identical in amino acid composition but different in sequence. Both peptides form stable collagen triple helices, but only triple helices Col877 self‐associate laterally under fibril forming conditions to form mini‐fibrils having the predicted d‐period. The Co108rr triple helices, however, only form nonspecific aggregates having no identifiable structural features. These results further accentuate the critical involvement of the repeating sequence units in the self‐assembly of collagen mini‐fibrils; the actual amino acid sequence of each unit has only secondary effects. Collagen is essential for tissue development and function. This novel approach to creating collagen‐mimetic fibrils can potentially impact fundamental research and have a wide range of biomedical and industrial applications.

Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.

The SAR11 clade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of myophages that putatively infect the SAR11 clade. They have been retrieved by mining ca. 45 Gbp aquatic assembled cellular metagenomes and viromes. Most of the myophages were obtained from the cellular fraction (0.2 μm), indicating a bias against this type of virus in viromes. We have found the first myophages that putatively infect Candidatus Fonsibacter (freshwater SAR11) and another group putatively infecting bathypelagic SAR11 phylogroup Ic. The genomes have similar sizes and maintain overall synteny in spite of low average nucleotide identity values, revealing high similarity to marine cyanomyophages. Pelagimyophages recruited metagenomic reads widely from several locations but always much more from cellular metagenomes than from viromes, opposite to what happens with pelagipodophages. Comparing the genomes resulted in the identification of a hypervariable island that is related to host recognition. Interestingly, some genes in these islands could be related to host cell wall synthesis and coinfection avoidance. A cluster of curli-related proteins was widespread among the genomes, although its function is unclear.

IMPORTANCE SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.

Expression and Purification of Collagen-Like Proteins of Group A Streptococcus

Prokaryotic proteins with extended collagen domain are found in many bacterial species that are pathogenic to humans and animals. The collagen domain is often fused to additional ligand-binding domains and plays both structural and functional roles in modular "bacterial collagens." Here, we describe the step-by-step expression and purification of the recombinant streptococcal collagen-like proteins, rScl, using the Strep-tag II system. The integrity and structural characterization of recombinant collagen-like proteins is very important for defining their function.

Collagen-like sequences encoded by extremophilic and extremotolerant bacteria

Collagens and collagen-like proteins are found in a wide range of organisms. The common feature of these proteins is a triple helix fold, requiring a characteristic pattern of amino acid sequences, composed of Gly-X-Y tripeptide repeats. Collagen-like proteins from bacteria are heterogeneous in terms of length and amino acid composition of their collagenous sequences. However, different bacteria live in different environments, some at extreme temperatures and conditions. This study explores the occurrence of collagen-like sequences in the genomes of different extreme condition-adapted bacteria, and investigates features that could be linked to conditions where they thrive. Our results show that proteins containing collagen-like sequences are encoded by genomes of various extremophiles. Some of these proteins contain conservative domains, characteristic of cell or endospore surface proteins, while most other proteins are unknown. The characteristics of collagenous sequences may depend on both, the phylogenetic relationship and the living conditions of the bacteria.

Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum

Bifidobacterium longum colonizes mammalian gastrointestinal tracts where it could metabolize host-indigestible oligosaccharides. Although B. longum strains are currently segregated into three subspecies that reflect common metabolic capacities and genetic similarity, heterogeneity within subspecies suggests that these taxonomic boundaries may not be completely resolved. To address this, the B. longum pangenome was analyzed from representative strains isolated from a diverse set of sources. As a result, the B. longum pangenome is open and contains almost 17,000 genes, with over 85% of genes found in ≤28 of 191 strains. B. longum genomes share a small core gene set of only ~500 genes, or ~3% of the total pangenome. Although the individual B. longum subspecies pangenomes share similar relative abundances of clusters of orthologous groups, strains show inter- and intrasubspecies differences with respect to carbohydrate utilization gene content and growth phenotypes.

Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex

The idea that original soft tissue structures and the native structural proteins comprising them can persist across geological time is controversial, in part because rigorous and testable mechanisms that can occur under natural conditions, resulting in such preservation, have not been well defined. Here, we evaluate two non-enzymatic structural protein crosslinking mechanisms, Fenton chemistry and glycation, for their possible contribution to the preservation of blood vessel structures recovered from the cortical bone of a Tyrannosaurus rex (USNM 555000 [formerly, MOR 555]). We demonstrate the endogeneity of the fossil vessel tissues, as well as the presence of type I collagen in the outermost vessel layers, using imaging, diffraction, spectroscopy, and immunohistochemistry. Then, we use data derived from synchrotron FTIR studies of the T. rex vessels to analyse their crosslink character, with comparison against two non-enzymatic Fenton chemistry- and glycation-treated extant chicken samples. We also provide supporting X-ray microprobe analyses of the chemical state of these fossil tissues to support our conclusion that non-enzymatic crosslinking pathways likely contributed to stabilizing, and thus preserving, these T. rex vessels. Finally, we propose that these stabilizing crosslinks could play a crucial role in the preservation of other microvascular tissues in skeletal elements from the Mesozoic.