-
Current Opinion in Microbiology Jun 2024Myxococcus relies on motility to efficiently invade and predate a prey colony. Upon contact with prey, Myxococcus temporarily halts its motility and initiates prey cell... (Review)
Review
Myxococcus relies on motility to efficiently invade and predate a prey colony. Upon contact with prey, Myxococcus temporarily halts its motility and initiates prey cell lysis, which involves two contact-dependent predatory machineries, the Kil system and the needleless T3SS*. Predatory cells grow as they invade and feed on prey cells. When dividing, Myxococcus cells systematically pause their movements before division. This highlights a high level of co-ordination between motility and contact-dependent killing but also with cell division. In this review, we give an overview of the different nanomachines used by Myxococcus to move on surfaces, kill by contact, and divide, and we discuss the potential regulatory mechanisms at play during these different processes.
PubMed: 38843560
DOI: 10.1016/j.mib.2024.102492 -
ACS Applied Bio Materials Jun 2024Protein compartments offer definitive structures with a large potential design space that are of particular interest for green chemistry and therapeutic applications....
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 reassembly studies, we first investigated the effectiveness of reassembly and cargo-loading of two size classes of encapsulins = 1 and = 3, using superfolder Green Fluorescent Protein. We show that the empty capsid reassembles with higher yield than the capsid and that loading promotes the formation of the = 3 capsid form over the = 1 form, while overloading with cargo results in malformed = 1 encapsulins. For the stability study, a Förster resonance energy transfer (FRET)-probed industrially relevant enzyme cargo, transketolase, was then loaded into the encapsulin. Our results show that site-specific orthogonal FRET labels can reveal changes in thermal unfolding of encapsulated cargo, suggesting that loading of transketolase into the = 1 encapsulin shell increases the thermal stability of the enzyme. This work supports the move toward fully harnessing structural, spatial, and functional control of assembled encapsulins with applications in cargo stabilization.
Topics: Transketolase; Enzyme Stability; Particle Size; Thermotoga maritima; Materials Testing; Biocompatible Materials
PubMed: 38835217
DOI: 10.1021/acsabm.3c01153 -
Experimental Biology and Medicine... 2024Currently, various functionalized nanocarrier systems are extensively studied for targeted delivery of drugs, peptides, and nucleic acids. Joining the approaches of...
Currently, various functionalized nanocarrier systems are extensively studied for targeted delivery of drugs, peptides, and nucleic acids. Joining the approaches of genetic and chemical engineering may produce novel carriers for precise targeting different cellular proteins, which is important for both therapy and diagnosis of various pathologies. Here we present the novel nanocontainers based on vectorized genetically encoded (Mx) encapsulin, confining a fluorescent photoactivatable mCherry (PAmCherry) protein. The shells of such encapsulins were modified using chemical conjugation of human transferrin (Tf) prelabeled with a fluorescein-6 (FAM) maleimide acting as a vector. We demonstrate that the vectorized encapsulin specifically binds to transferrin receptors (TfRs) on the membranes of mesenchymal stromal/stem cells (MSCs) followed by internalization into cells. Two spectrally separated fluorescent signals from Tf-FAM and PAmCherry are clearly distinguishable and co-localized. It is shown that Tf-tagged Mx encapsulins are internalized by MSCs much more efficiently than by fibroblasts. It has been also found that unlabeled Tf effectively competes with the conjugated Mx-Tf-FAM formulations. That indicates the conjugate internalization into cells by Tf-TfR endocytosis pathway. The developed nanoplatform can be used as an alternative to conventional nanocarriers for targeted delivery of, e.g., genetic material to MSCs.
Topics: Mesenchymal Stem Cells; Transferrin; Humans; Myxococcus xanthus; Endocytosis; Receptors, Transferrin; Luminescent Proteins
PubMed: 38774281
DOI: 10.3389/ebm.2024.10055 -
MBio Jun 2024Clonal reproduction of unicellular organisms ensures the stable inheritance of genetic information. However, this means of reproduction lacks an intrinsic basis for... (Review)
Review
Clonal reproduction of unicellular organisms ensures the stable inheritance of genetic information. However, this means of reproduction lacks an intrinsic basis for genetic variation, other than spontaneous mutation and horizontal gene transfer. To make up for this lack of genetic variation, many unicellular organisms undergo the process of cell differentiation to achieve phenotypic heterogeneity within isogenic populations. Cell differentiation is either an inducible or obligate program. Induced cell differentiation can occur as a response to a stimulus, such as starvation or host cell invasion, or it can be a stochastic process. In contrast, obligate cell differentiation is hardwired into the organism's life cycle. Whether induced or obligate, bacterial cell differentiation requires the activation of a signal transduction pathway that initiates a global change in gene expression and ultimately results in a morphological change. While cell differentiation is considered a hallmark in the development of multicellular organisms, many unicellular bacteria utilize this process to implement survival strategies. In this review, we describe well-characterized cell differentiation programs to highlight three main survival strategies used by bacteria capable of differentiation: (i) environmental adaptation, (ii) division of labor, and (iii) bet-hedging.
Topics: Bacteria; Bacterial Physiological Phenomena; Cell Differentiation; Adaptation, Physiological; Microbial Viability; Signal Transduction
PubMed: 38771034
DOI: 10.1128/mbio.00758-24 -
Proceedings of the National Academy of... May 2024Encapsulins are protein nanocompartments that regulate cellular metabolism in several bacteria and archaea. encapsulins protect the bacterial cells against oxidative...
Encapsulins are protein nanocompartments that regulate cellular metabolism in several bacteria and archaea. encapsulins protect the bacterial cells against oxidative stress by sequestering cytosolic iron. These encapsulins are formed by the shell protein EncA and three cargo proteins: EncB, EncC, and EncD. EncB and EncC form rotationally symmetric decamers with ferroxidase centers (FOCs) that oxidize Fe to Fe for iron storage in mineral form. However, the structure and function of the third cargo protein, EncD, have yet to be determined. Here, we report the x-ray crystal structure of EncD in complex with flavin mononucleotide. EncD forms an α-helical hairpin arranged as an antiparallel dimer, but unlike other flavin-binding proteins, it has no β-sheet, showing that EncD and its homologs represent a unique class of bacterial flavin-binding proteins. The cryo-EM structure of EncA-EncD encapsulins confirms that EncD binds to the interior of the EncA shell via its C-terminal targeting peptide. With only 100 amino acids, the EncD α-helical dimer forms the smallest flavin-binding domain observed to date. Unlike EncB and EncC, EncD lacks a FOC, and our biochemical results show that EncD instead is a NAD(P)H-dependent ferric reductase, indicating that the encapsulins act as an integrated system for iron homeostasis. Overall, this work contributes to our understanding of bacterial metabolism and could lead to the development of technologies for iron biomineralization and the production of iron-containing materials for the treatment of various diseases associated with oxidative stress.
Topics: Myxococcus xanthus; Bacterial Proteins; FMN Reductase; Crystallography, X-Ray; Flavin Mononucleotide; Iron; Models, Molecular; Cryoelectron Microscopy
PubMed: 38748579
DOI: 10.1073/pnas.2400426121 -
MSystems Jun 2024The clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) system widely occurs in prokaryotic organisms to recognize and...
UNLABELLED
The clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) system widely occurs in prokaryotic organisms to recognize and destruct genetic invaders. Systematic collation and characterization of endogenous CRISPR-Cas systems are conducive to our understanding and potential utilization of this natural genetic machinery. In this study, we screened 39 complete and 692 incomplete genomes of myxobacteria using a combined strategy to dispose of the abridged genome information and revealed at least 19 CRISPR-Cas subtypes, which were distributed with a taxonomic difference and often lost stochastically in intraspecies strains. The genes in each subtype were evolutionarily clustered but deeply separated, while most of the CRISPRs were divided into four types based on the motif characteristics of repeat sequences. The spacers recorded in myxobacterial CRISPRs were in high G+C content, matching lots of phages, tiny amounts of plasmids, and, surprisingly, massive organismic genomes. We experimentally demonstrated the immune and self-target immune activities of three endogenous systems in DK1622 against artificial genetic invaders and revealed the microhomology-mediated end-joining mechanism for the immunity-induced DNA repair but not homology-directed repair. The panoramic view and immune activities imply potential omnipotent immune functions and applications of the endogenous CRISPR-Cas machinery.
IMPORTANCE
Serving as an adaptive immune system, clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) empower prokaryotes to fend off the intrusion of external genetic materials. Myxobacteria are a collective of swarming Gram-stain-negative predatory bacteria distinguished by intricate multicellular social behavior. An in-depth analysis of their intrinsic CRISPR-Cas systems is beneficial for our understanding of the survival strategies employed by host cells within their environmental niches. Moreover, the experimental findings presented in this study not only suggest the robust immune functions of CRISPR-Cas in myxobacteria but also their potential applications.
Topics: CRISPR-Cas Systems; Genome, Bacterial; Myxococcales; Phylogeny; Clustered Regularly Interspaced Short Palindromic Repeats
PubMed: 38747603
DOI: 10.1128/msystems.01210-23 -
Journal of Mathematical Biology May 2024We study traveling wave solutions for a reaction-diffusion model, introduced in the article Calvez et al. (Regime switching on the propagation speed of travelling waves...
We study traveling wave solutions for a reaction-diffusion model, introduced in the article Calvez et al. (Regime switching on the propagation speed of travelling waves of some size-structured myxobacteriapopulation models, 2023), describing the spread of the social bacterium Myxococcus xanthus. This model describes the spatial dynamics of two different cluster sizes: isolated bacteria and paired bacteria. Two isolated bacteria can coagulate to form a cluster of two bacteria and conversely, a pair of bacteria can fragment into two isolated bacteria. Coagulation and fragmentation are assumed to occur at a certain rate denoted by k. In this article we study theoretically the limit of fast coagulation fragmentation corresponding mathematically to the limit when the value of the parameter k tends to . For this regime, we demonstrate the existence and uniqueness of a transition between pulled and pushed fronts for a certain critical ratio between the diffusion coefficient of isolated bacteria and the diffusion coefficient of paired bacteria. When the ratio is below , the critical front speed is constant and corresponds to the linear speed. Conversely, when the ratio is above the critical threshold, the critical spreading speed becomes strictly greater than the linear speed.
Topics: Models, Biological; Mathematical Concepts; Myxococcus xanthus; Computer Simulation; Diffusion
PubMed: 38739209
DOI: 10.1007/s00285-024-02099-4 -
Proceedings of the National Academy of... May 2024Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry...
Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from , a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.
Topics: Point Mutation; Capsid; Capsid Proteins; Cryoelectron Microscopy; Myxococcus xanthus; Models, Molecular
PubMed: 38722807
DOI: 10.1073/pnas.2321260121 -
Frontiers in Microbiology 2024This study aimed to study the characterization and the potential lipid-lowering effects of new isolated lactic acid bacteria from the feces of healthy adult cats.
INTRODUCTION
This study aimed to study the characterization and the potential lipid-lowering effects of new isolated lactic acid bacteria from the feces of healthy adult cats.
METHODS
We collected 85 cat fecal samples, isolated, screening lactic acid bacteria strains from samples, and investigated their and biological properties.
RESULTS
A total of 221 lactic acid bacteria strains were isolated from 85 cat fecal samples. Sixteen strains with calcium dissolution rings greater than 1 mm were identified and selected for further characterization. Three lactic acid bacteria strains, L-27-2, L-14-1, and , were identified as showing the most promising rates of cholesterol degradation (greater than 20%) and bacteriostatic radius (over 15 mm). These three strains exhibited robust growth and adherence to epithelial cells, along with adaptability to low pH (greater than 70%) and high bile salt conditions (greater than 60%), and remarkable cholesterol degradation and anti-pathogen activity. Sixteen mice were fed a high-fat diet (HFD) from 4 to 8 weeks of age, while a control group of the same size received a normal diet (ND). At 8 weeks of age, serum, feces and adipose tissue were collected. The results showed that, compared with mice fed an HFD diet alone, all mice fed an HFD diet plus lactic acid bacteria could decrease weight gain. < 0.05 and the pathological changes of adipose tissue were alleviated. In addition, mice fed L-14-1 and F203 showed abdominal fat accumulation decreased ( < 0.05). Mice fed L-27-2 showed serum and liver triglyceride (TG) decreased ( < 0.05) and mice fed F203 showed serum high density lipoprotein cholesterol (HDL-C) increased ( < 0.01). mice fed L-27-2 and L-14-1 showed inflammatory cytokines (IL-6) was decreased ( < 0.01) Analysis of the fecal microbiota of mice fed these three lactic acid bacteria strains revealed alterations in the gut microbial community. There were common changes in intestinal microbes in mice fed these three lactic acid bacteria: (1) decreased; (2) increased; (3) decreased. The microbes mentioned are all part of the core intestinal flora.
DISCUSSION
This study provided three potential lactic acid bacteria for alleviating animal obesity and inflammation.
PubMed: 38721604
DOI: 10.3389/fmicb.2024.1392864 -
The ISME Journal May 2024Bacterial predators are decisive organisms that shape microbial ecosystems. In this study, we investigated the role of iron and siderophores during the predatory...
Bacterial predators are decisive organisms that shape microbial ecosystems. In this study, we investigated the role of iron and siderophores during the predatory interaction between two rhizosphere bacteria: Myxococcus xanthus, an epibiotic predator, and Sinorhizobium meliloti, a bacterium that establishes nitrogen-fixing symbiosis with legumes. The results show that iron enhances the motility of the predator and facilitates its predatory capability, and that intoxication by iron is not used by the predator to prey, although oxidative stress increases in both bacteria during predation. However, competition for iron plays an important role in the outcome of predatory interactions. Using combinations of predator and prey mutants (non-producers and overproducers of siderophores), we have investigated the importance of competition for iron in predation. The results demonstrate that the competitor that, via the production of siderophores, obtains sufficient iron for growth and depletes metal availability for the opponent will prevail in the interaction. Consequently, iron fluctuations in soils may modify the composition of microbial communities by altering the activity of myxobacterial predators. In addition, siderophore overproduction during predation can alter soil properties, affecting the productivity and sustainability of agricultural operations.
PubMed: 38696719
DOI: 10.1093/ismejo/wrae077