Encapsulin carrier proteins for enhanced expression of antimicrobial peptides

Antimicrobial Peptides and Their Mimetics: Promising Candidates of Next-Generation Therapeutic Agents Combating Multidrug-Resistant Bacteria

The increasing morbidity and mortality caused by multidrug-resistant bacteria alerts human beings to the fact that conventional antibiotics are no longer reliable and effective alternatives are imperatively needed. Owing to wide range of sources, diverse structures, and unique mode of action, antimicrobial peptides have been highly anticipated and extensively studied in recent years. Besides, the integration of artificial intelligence helps researchers gain access to the vast unexplored chemical space, which opens more opportunities for the optimization and design of novel structures. Moreover, Due to advances in chemistry and synthetic biology, researchers have also begun to focus on the potential of chemical mimetics of antimicrobial peptides. In this review, a comprehensive discussion about natural and synthesized antimicrobial peptides as well as their chemical mimetics is made, so as to provide a comprehensive summary of this field and inspire follow-up research.

Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing

Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments that self-assemble into icosahedral structures with external diameters ranging from 24 to 42 nm. Encapsulins from Myxococcus xanthus were designed to package bacterial RNA when produced in E. coli and were shown to have immunogenic and self-adjuvanting properties enhanced by this RNA. We genetically incorporated a 20-mer peptide derived from a mutant strain of the SARS-CoV-2 receptor binding domain (RBD) into the encapsulin protomeric coat protein for presentation on the exterior surface of the particle, inducing the formation of several nonicosahedral structures that were characterized by cryogenic electron microscopy. This immunogen elicited conformationally relevant humoral responses to the SARS-CoV-2 RBD. Immunological recognition was enhanced when the same peptide was presented in a heterologous prime/boost vaccination strategy using the engineered encapsulin and a previously reported variant of the PP7 virus-like particle, leading to the development of a selective antibody response against a SARS-CoV-2 RBD point mutant. While generating epitope-focused antibody responses is an interplay between inherent vaccine properties and B/T cells, here we demonstrate the use of orthogonal nanoparticles to fine-tune the control of epitope focusing.

Prokaryotic Expression and Functional Verification of Antimicrobial Peptide LRGG

The antimicrobial peptide LRGG (LLRLLRRGGRRLLRLL-NH2) was designed and chemically synthesized in a study conducted by Jia et al. Gram-negative bacteria were found to be sensitive to LRGG and exhibited a high therapeutic index. Genetic engineering methods were used to create the prokaryotic fusion expression vector pQE-GFP-LRGG, and the resulting corresponding fusion protein GFP-LRGG was subsequently expressed and purified. The precursor GFP was then removed by TEV proteolysis, and pure LRGG was obtained after another round of purification and endotoxin removal. The prokaryotic-expressed antimicrobial peptide LRGG displays a broad-spectrum antibacterial effect on Gram-negative bacteria, and its minimum inhibitory activity (MIC) against Escherichia coli can reach 2 μg/mL. Compared to the chemically synthesized LRGG, the prokaryotic-expressed LRGG exhibits similar temperature, pH, salt ion, serum stability, and cell selectivity. Furthermore, prokaryotic-expressed LRGG showed excellent therapeutic effects in both the infection model of cell selectivity and no embryotoxicity in a Galleria mellonella infection model. The mechanism by which LRGG causes bacterial death was found to be the disruption of the Gram-negative cell membrane.

Encapsulation of Transketolase into In Vitro-Assembled Protein Nanocompartments Improves Thermal Stability

Protein compartments offer definitive structures with a large potential design space that are of particular interest for green chemistry and therapeutic applications. One family of protein compartments, encapsulins, are simple prokaryotic nanocompartments that self-assemble from a single monomer into selectively permeable cages of between 18 and 42 nm. Over the past decade, encapsulins have been developed for a diverse application portfolio utilizing their defined cargo loading mechanisms and repetitive surface display. Although it has been demonstrated that encapsulation of non-native cargo proteins provides protection from protease activity, the thermal effects arising from enclosing cargo within encapsulins remain poorly understood. This study aimed to establish a methodology for loading a reporter protein into thermostable encapsulins to determine the resulting stability change of the cargo. Building on previous in vitro reassembly studies, we first investigated the effectiveness of in vitro reassembly and cargo-loading of two size classes of encapsulins Thermotoga maritima T = 1 and Myxococcus xanthus T = 3, using superfolder Green Fluorescent Protein. We show that the empty T. maritima capsid reassembles with higher yield than the M. xanthus capsid and that in vitro loading promotes the formation of the M. xanthus T = 3 capsid form over the T = 1 form, while overloading with cargo results in malformed T. maritima T = 1 encapsulins. For the stability study, a Förster resonance energy transfer (FRET)-probed industrially relevant enzyme cargo, transketolase, was then loaded into the T. maritima encapsulin. Our results show that site-specific orthogonal FRET labels can reveal changes in thermal unfolding of encapsulated cargo, suggesting that in vitro loading of transketolase into the T. maritima T = 1 encapsulin shell increases the thermal stability of the enzyme. This work supports the move toward fully harnessing structural, spatial, and functional control of in vitro assembled encapsulins with applications in cargo stabilization.

Heterologous Prime-Boost with Immunologically Orthogonal Protein Nanoparticles for Peptide Immunofocusing

Protein nanoparticles are effective platforms for antigen presentation and targeting effector immune cells in vaccine development. Encapsulins are a class of protein-based microbial nanocompartments that self-assemble into icosahedral structures with external diameters ranging from 24 to 42 nm. Encapsulins from Mxyococcus xanthus were designed to package bacterial RNA when produced in E. coli and were shown to have immunogenic and self-adjuvanting properties enhanced by this RNA. We genetically incorporated a 20-mer peptide derived from a mutant strain of the SARS-CoV-2 receptor binding domain (RBD) into the encapsulin protomeric coat protein for presentation on the exterior surface of the particle. This immunogen elicited conformationally-relevant humoral responses to the SARS-CoV-2 RBD. Immunological recognition was enhanced when the same peptide was presented in a heterologous prime/boost vaccination strategy using the engineered encapsulin and a previously reported variant of the PP7 virus-like particle, leading to the development of a selective antibody response against a SARS-CoV-2 RBD point mutant. While generating epitope-focused antibody responses is an interplay between inherent vaccine properties and B/T cells, here we demonstrate the use of orthogonal nanoparticles to fine-tune the control of epitope focusing.

Encapsulins: Nanotechnology's future in a shell

Encapsulins, virus capsid-like bacterial nanocompartments have emerged as promising tools in medicine, imaging, and material sciences. Recent work has shown that these protein-bound icosahedral 'organelles' possess distinct properties that make them exceptionally usable for nanotechnology applications. A key factor contributing to their appeal is their ability to self-assemble, coupled with their capacity to encapsulate a wide range of cargos. Their genetic manipulability, stability, biocompatibility, and nano-size further enhance their utility, offering outstanding possibilities for practical biotechnology applications. In particular, their amenability to engineering has led to their extensive modification, including the packaging of non-native cargos and the utilization of the shell surface for displaying immunogenic or targeting proteins and peptides. This inherent versatility, combined with the ease of expressing encapsulins in heterologous hosts, promises to provide broad usability. Although mostly not yet commercialized, encapsulins have started to demonstrate their vast potential for biotechnology, from drug delivery to biofuel production and the synthesis of valuable inorganic materials. In this review, we will initially discuss the structure, function and diversity of encapsulins, which form the basis for these emerging applications, before reviewing ongoing practical uses and highlighting promising applications in medicine, engineering and environmental sciences.

Encapsulin cargo loading: progress and potential

Encapsulins are a recently discovered class of prokaryotic self-assembling icosahedral protein nanocompartments measuring between 24 and 42 nm in diameter, capable of selectively encapsulating dedicated cargo proteins in vivo. They have been classified into four families based on sequence identity and operon structure, and thousands of encapsulin systems have recently been computationally identified across a wide range of bacterial and archaeal phyla. Cargo encapsulation is mediated by the presence of specific targeting motifs found in all native cargo proteins that interact with the interior surface of the encapsulin shell during self-assembly. Short C-terminal targeting peptides (TPs) are well documented in Family 1 encapsulins, while more recently, larger N-terminal targeting domains (TDs) have been discovered in Family 2. The modular nature of TPs and their facile genetic fusion to non-native cargo proteins of interest has made cargo encapsulation, both in vivo and in vitro, readily exploitable and has therefore resulted in a range of rationally engineered nano-compartmentalization systems. This review summarizes current knowledge on cargo protein encapsulation within encapsulins and highlights select studies that utilize TP fusions to non-native cargo in creative and useful ways.

Modification and Production of Encapsulin

Encapsulins are a class of protein nanocages that are found in bacteria, which are easy to produce and engineer in E. coli expression systems. The encapsulin from Thermotoga maritima (Tm) is well studied, its structure is available, and without modification it is barely taken up by cells, making it promising candidates for targeted drug delivery. In recent years, encapsulins are engineered and studied for potential use as drug delivery carriers, imaging agents, and as nanoreactors. Consequently, it is important to be able to modify the surface of these encapsulins, for example, by inserting a peptide sequence for targeting or other functions. Ideally, this is combined with high production yields and straightforward purification methods. In this chapter, we describe a method to genetically modify the surface of Tm and Brevibacterium linens (Bl) encapsulins, as model systems, to purify them and characterize the obtain nanocages.

Engineered Protein Nanocages for Concurrent RNA and Protein Packaging In Vivo

Protein nanocages have emerged as an important engineering platform for biotechnological and biomedical applications. Among naturally occurring protein cages, encapsulin nanocompartments have recently gained prominence due to their favorable physico-chemical properties, ease of shell modification, and highly efficient and selective intrinsic protein packaging capabilities. Here, we expand encapsulin function by designing and characterizing encapsulins for concurrent RNA and protein encapsulation in vivo. Our strategy is based on modifying encapsulin shells with nucleic acid-binding peptides without disrupting the native protein packaging mechanism. We show that our engineered encapsulins reliably self-assemble in vivo, are capable of efficient size-selective in vivo RNA packaging, can simultaneously load multiple functional RNAs, and can be used for concurrent in vivo packaging of RNA and protein. Our engineered encapsulation platform has potential for codelivery of therapeutic RNAs and proteins to elicit synergistic effects and as a modular tool for other biotechnological applications.

Strategies for improving antimicrobial peptide production

Antimicrobial peptides (AMPs) found in a wide range of animal, insect, and plant species are host defense peptides forming an integral part of their innate immunity. Although the exact mode of action of some AMPs is yet to be deciphered, many exhibit membrane lytic activity or interact with intracellular targets. The ever-growing threat of antibiotic resistance has brought attention to research on AMPs to enhance their clinical use as a therapeutic alternative. AMPs have several advantages over antibiotics such as broad range of antimicrobial activities including anti-fungal, anti-viral and anti-bacterial, and have not reported to contribute to resistance development. Despite the numerous studies to develop efficient production methods for AMPs, limitations including low yield, degradation, and loss of activity persists in many recombinant approaches. In this review, we outline available approaches for AMP production and various expression systems used to achieve higher yield and quality. In addition, recent advances in recombinant strategies, suitable fusion protein partners, and other molecular engineering strategies for improved AMP production are surveyed.

Protein Cages: From Fundamentals to Advanced Applications

Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.

Introduction of Surface Loops as a Tool for Encapsulin Functionalization

Encapsulin-based protein cages are nanoparticles with potential biomedical applications, such as targeted drug delivery or imaging. These particles are biocompatible and can be produced in bacteria, allowing large-scale production and protein engineering. In order to use these bacterial nanocages in different applications, it is important to further explore their surface modification and optimize their production. In this study, we design and show new surface modifications of Thermotoga maritima (Tm) and Brevibacterium linens (Bl) encapsulins. Two new loops on the Tm encapsulin with a His-tag insertion after residue 64 and residue 127 and the modification of the C-terminus on the Bl encapsulin are reported. The multimodification of the Tm encapsulin enables up to 240 functionalities on the cage surface, resulting from four potential modifications per protein subunit. We further report an improved production protocol giving a better stability and good production yield of the cages. Finally, we tested the stability of different encapsulin variants over a year, and the results show a difference in stability arising from the tag insertion position. These first insights in the structure–property relationship of encapsulins, with respect to the position of a functional loop, allow for further study of the use of these protein nanocages in biomedical applications.

Bacterial Nanocompartments: Structures, Functions and Applications

Increasing efficiency is an important driving force behind cellular organization and often achieved through compartmentalization. Long recognized as a core principle of eukaryotic cell organization, its widespread occurrence in prokaryotes has only recently come to light. Despite the early discovery of a few microcompartments such as gas vesicles and carboxysomes, the vast majority of these structures in prokaryotes are less than 100 nm in diameter - too small for conventional light microscopy and electron microscopic thin sectioning. Consequently, these smaller-sized nanocompartments have therefore been discovered serendipitously and then through bioinformatics shown to be broadly distributed. Their small uniform size, robust self-assembly, high stability, excellent biocompatibility, and large cargo capacity make them excellent candidates for biotechnology applications. This review will highlight our current knowledge of nanocompartments, the prospects for applications as well as open question and challenges that need to be addressed to fully understand these important structures.

Artificial Organelles: Towards Adding or Restoring Intracellular Activity

Compartmentalization is one of the main characteristics that define living systems. Creating a physically separated microenvironment allows nature a better control over biological processes, as is clearly specified by the role of organelles in living cells. Inspired by this phenomenon, researchers have developed a range of different approaches to create artificial organelles: compartments with catalytic activity that add new function to living cells. In this review we will discuss three complementary lines of investigation. First, orthogonal chemistry approaches are discussed, which are based on the incorporation of catalytically active transition metal-containing nanoparticles in living cells. The second approach involves the use of premade hybrid nanoreactors, which show transient function when taken up by living cells. The third approach utilizes mostly genetic engineering methods to create bio-based structures that can be ultimately integrated with the cell's genome to make them constitutively active. The current state of the art and the scope and limitations of the field will be highlighted with selected examples from the three approaches.

Nanotechnological Applications Based on Bacterial Encapsulins

Encapsulins are proteinaceous nanocontainers, constructed by a single species of shell protein that self-assemble into 20-40 nm icosahedral particles. Encapsulins are structurally similar to the capsids of viruses of the HK97-like lineage, to which they are evolutionarily related. Nearly all these nanocontainers encase a single oligomeric protein that defines the physiological role of the complex, although a few encapsulate several activities within a single particle. Encapsulins are abundant in bacteria and archaea, in which they participate in regulation of oxidative stress, detoxification, and homeostasis of key chemical elements. These nanocontainers are physically robust, contain numerous pores that permit metabolite flux through the shell, and are very tolerant of genetic manipulation. There are natural mechanisms for efficient functionalization of the outer and inner shell surfaces, and for the in vivo and in vitro internalization of heterologous proteins. These characteristics render encapsulin an excellent platform for the development of biotechnological applications. Here we provide an overview of current knowledge of encapsulin systems, summarize the remarkable toolbox developed by researchers in this field, and discuss recent advances in the biomedical and bioengineering applications of encapsulins.

Engineering spatiotemporal organization and dynamics in synthetic cells

Constructing synthetic cells has recently become an appealing area of research. Decades of research in biochemistry and cell biology have amassed detailed part lists of components involved in various cellular processes. Nevertheless, recreating any cellular process in vitro in cell-sized compartments remains ambitious and challenging. Two broad features or principles are key to the development of synthetic cells-compartmentalization and self-organization/spatiotemporal dynamics. In this review article, we discuss the current state of the art and research trends in the engineering of synthetic cell membranes, development of internal compartmentalization, reconstitution of self-organizing dynamics, and integration of activities across scales of space and time. We also identify some research areas that could play a major role in advancing the impact and utility of engineered synthetic cells. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.

Advances in encapsulin nanocompartment biology and engineering

Compartmentalization is an essential feature of all cells. It allows cells to segregate and coordinate physiological functions in a controlled and ordered manner. Different mechanisms of compartmentalization exist, with the most relevant to prokaryotes being encapsulation via self-assembling protein-based compartments. One widespread example of such is that of encapsulins-cage-like protein nanocompartments able to compartmentalize specific reactions, pathways, and processes in bacteria and archaea. While still relatively nascent bioengineering tools, encapsulins exhibit many promising characteristics, including a number of defined compartment sizes ranging from 24 to 42 nm, straightforward expression, the ability to self-assemble via the Hong Kong 97-like fold, marked physical robustness, and internal and external handles primed for rational genetic and molecular manipulation. Moreover, encapsulins allow for facile and specific encapsulation of native or heterologous cargo proteins via naturally or rationally fused targeting peptide sequences. Taken together, the attributes of encapsulins promise substantial customizability and broad usability. This review discusses recent advances in employing engineered encapsulins across various fields, from their use as bionanoreactors to targeted delivery systems and beyond. A special focus will be provided on the rational engineering of encapsulin systems and their potential promise as biomolecular research tools.