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1
Vaccari, Liana, Mehdi Molaei, Robert L. Leheny, and Kathleen J. Stebe. "Cargo carrying bacteria at interfaces." Soft Matter 14, no. 27 (2018): 5643–53. http://dx.doi.org/10.1039/c8sm00481a.
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The displacements of ensembles of colloids at the interface between oil and suspensions of the bacterium Pseudomonas aeruginosa PA14ΔpelA indicate enhanced colloid mobilities and apparently diffusive motion driven by interactions with the bacteria.
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Shklarsh, Adi, Alin Finkelshtein, Gil Ariel, Oren Kalisman, Colin Ingham, and Eshel Ben-Jacob. "Collective navigation of cargo-carrying swarms." Interface Focus 2, no. 6 (August 29, 2012): 786–98. http://dx.doi.org/10.1098/rsfs.2012.0029.
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Much effort has been devoted to the study of swarming and collective navigation of micro-organisms, insects, fish, birds and other organisms, as well as multi-agent simulations and to the study of real robots. It is well known that insect swarms can carry cargo. The studies here are motivated by a less well-known phenomenon: cargo transport by bacteria swarms. We begin with a concise review of how bacteria swarms carry natural, micrometre-scale objects larger than the bacteria (e.g. fungal spores) as well as man-made beads and capsules (for drug delivery). A comparison of the trajectories of virtual beads in simulations (using different putative coupling between the virtual beads and the bacteria) with the observed trajectories of transported fungal spores implies the existence of adaptable coupling. Motivated by these observations, we devised new, multi-agent-based studies of cargo transport by agent swarms. As a first step, we extended previous modelling of collective navigation of simple bacteria-inspired agents in complex terrain, using three putative models of agent–cargo coupling. We found that cargo-carrying swarms can navigate efficiently in a complex landscape. We further investigated how the stability, elasticity and other features of agent–cargo bonds influence the collective motion and the transport of the cargo, and found sharp phase shifts and dual successful strategies for cargo delivery. Further understanding of such mechanisms may provide valuable clues to understand cargo-transport by smart swarms of other organisms as well as by man-made swarming robots.
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Fernandes, Rohan, Mary Zuniga, Fritz R. Sassine, Mert Karakoy, and David H. Gracias. "Enabling Cargo-Carrying Bacteria via Surface Attachment and Triggered Release." Small 7, no. 5 (February 2, 2011): 588–92. http://dx.doi.org/10.1002/smll.201002036.
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Trivedi, Rishi R., Rina Maeda, Nicholas L. Abbott, Saverio E. Spagnolie, and Douglas B. Weibel. "Bacterial transport of colloids in liquid crystalline environments." Soft Matter 11, no. 43 (2015): 8404–8. http://dx.doi.org/10.1039/c5sm02041g.
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Harrison, Ellie, Julie Truman, Rosanna Wright, Andrew J. Spiers, Steve Paterson, and Michael A. Brockhurst. "Plasmid carriage can limit bacteria–phage coevolution." Biology Letters 11, no. 8 (August 2015): 20150361. http://dx.doi.org/10.1098/rsbl.2015.0361.
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Coevolution with bacteriophages is a major selective force shaping bacterial populations and communities. A variety of both environmental and genetic factors has been shown to influence the mode and tempo of bacteria–phage coevolution. Here, we test the effects that carriage of a large conjugative plasmid, pQBR103, had on antagonistic coevolution between the bacterium Pseudomonas fluorescens and its phage, SBW25 ϕ 2. Plasmid carriage limited bacteria–phage coevolution; bacteria evolved lower phage-resistance and phages evolved lower infectivity in plasmid-carrying compared with plasmid-free populations. These differences were not explained by effects of plasmid carriage on the costs of phage resistance mutations. Surprisingly, in the presence of phages, plasmid carriage resulted in the evolution of high frequencies of mucoid bacterial colonies. Mucoidy can provide weak partial resistance against SBW25 ϕ 2, which may have limited selection for qualitative resistance mutations in our experiments. Taken together, our results suggest that plasmids can have evolutionary consequences for bacteria that go beyond the direct phenotypic effects of their accessory gene cargo.
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Macia, Laurence, Ralph Nanan, Elham Hosseini-Beheshti, and Georges E. Grau. "Host- and Microbiota-Derived Extracellular Vesicles, Immune Function, and Disease Development." International Journal of Molecular Sciences 21, no. 1 (December 22, 2019): 107. http://dx.doi.org/10.3390/ijms21010107.
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Extracellular vesicles (EVs) are blebs of either plasma membrane or intracellular membranes carrying a cargo of proteins, nucleic acids, and lipids. EVs are produced by eukaryotic cells both under physiological and pathological conditions. Genetic and environmental factors (diet, stress, etc.) affecting EV cargo, regulating EV release, and consequences on immunity will be covered. EVs are found in virtually all body fluids such as plasma, saliva, amniotic fluid, and breast milk, suggesting key roles in immune development and function at different life stages from in utero to aging. These will be reviewed here. Under pathological conditions, plasma EV levels are increased and exacerbate immune activation and inflammatory reaction. Sources of EV, cells targeted, and consequences on immune function and disease development will be discussed. Both pathogenic and commensal bacteria release EV, which are classified as outer membrane vesicles when released by Gram-negative bacteria or as membrane vesicles when released by Gram-positive bacteria. Bacteria derived EVs can affect host immunity with pathogenic bacteria derived EVs having pro-inflammatory effects of host immune cells while probiotic derived EVs mostly shape the immune response towards tolerance.
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Jiang, Min, Zhongxing Wang, Fufang Xia, Zhe Wen, Rui Chen, Dongyu Zhu, Min Wang, Xiangkai Zhuge, and Jianjun Dai. "Reductions in bacterial viability stimulate the production of Extra-intestinal Pathogenic Escherichia coli (ExPEC) cytoplasm-carrying Extracellular Vesicles (EVs)." PLOS Pathogens 18, no. 10 (October 19, 2022): e1010908. http://dx.doi.org/10.1371/journal.ppat.1010908.
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Extra-intestinal Pathogenic Escherichia coli (ExPEC) is defined as an extra-intestinal foodborne pathogen, and several dominant sequence types (STs) ExPEC isolates are highly virulent, with zoonotic potential. Bacteria extracellular vesicles (EVs) carry specific subsets of molecular cargo, which affect various biological processes in bacteria and host. The mechanisms of EVs formation in ExPEC remains to be elucidated. Here, the purified EVs of ExPEC strains of different STs were isolated with ultracentrifugation processes. A comparative analysis of the strain proteomes showed that cytoplasmic proteins accounted for a relatively high proportion of the proteins among ExPEC EVs. The proportion of cytoplasm-carrying vesicles in ExPEC EVs was calculated with a simple green fluorescent protein (GFP) expression method. The RecA/LexA-dependent SOS response is a critical mediator of generation of cytoplasm-carrying EVs. The SOS response activates the expression of prophage-associated endolysins, Epel1, Epel2.1, and Epel2.2, which triggered cell lysis, increasing the production of ExPEC cytoplasm-carrying EVs. The repressor LexA controlled directly the expression of these endolysins by binding to the SOS boxes in the endolysin promoter regions. Reducing bacterial viability stimulated the production of ExPEC EVs, especially cytoplasm-carrying EVs. The imbalance in cell division caused by exposure to H2O2, the deletion of ftsK genes, or t6A synthesis defects activated the RecA/LexA-dependent SOS response, inducing the expression of endolysins, and thus increasing the proportion of cytoplasm-carrying EVs in the total ExPEC EVs. Antibiotics, which decreased bacterial viability, also increase the production of ExPEC cytoplasm-carrying EVs through the SOS response. Changes in the proportion of cytoplasm-carrying EVs affected the total DNA content of ExPEC EVs. When macrophages are exposed to a higher proportion of cytoplasm-carrying vesicles, ExPEC EVs were more cytotoxic to macrophages, accompanied with more-severe mitochondrial disruption and a higher level of induced intrinsic apoptosis. In summary, we offered comprehensive insight into the proteome analysis of ExPEC EVs. This study demonstrated the novel formation mechanisms of E. coli cytoplasm-carrying EVs.
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Polikovsky, Mark, Eshel Ben-Jacob, and Alin Finkelshtein. "P. vortex-mediated strategies for polysaccharides decomposition." TECHNOLOGY 03, no. 02n03 (June 2015): 80–83. http://dx.doi.org/10.1142/s2339547815400087.
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Cellulose hydrolysis has many industrial applications such as biofuel production, food, paper and textile manufacture. Here, we present a novel approach to cellulose hydrolysis using a consortium of motile bacteria, Paenibacillus vortex, that can swarm on solid medium carrying a non-motile recombinant E. coli cargo strain expressing the β-glucosidase and cellulase genes that facilitate the hydrolysis of cellulose. These two species cooperate; the relationship is mutually beneficial: the E. coli is dispersed over long distances, while the P. vortex bacteria gain from the supply of cellulose degradation products. This enables the use of such consortia in this area of biotechnology.
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Ivanenko, N. "BIOFILM AND TUMOR: INTERPRETATION OF INTERACTION AND TREATMENT STRATEGIES. Review." Medical Science of Ukraine (MSU) 17, no. 1 (March 30, 2021): 104–20. http://dx.doi.org/10.32345/2664-4738.1.2021.13.
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Relevance. Treatment of solid tumors and biofilm-derived infections face a common problem: drugs often fail to reach and kill cancer cells and microbial pathogens because of local microenvironment heterogeneities. There are remarkable challenges for current and prospective anticancer and antibiofilm agents to target and maintain activity in the microenvironments where cancer cells and microbial pathogens survive and cause the onset of disease. Bacterial infections in cancer formation will increase in the coming years. Collection of approaches such as ROS modulation in cells, the tumor is promoted by microbe’s inflammation can be a strategy to target cancer and bacteria. Besides that, bacteria may take the advantage of oxygen tension and permissive carbon sources, therefore the tumor microenvironment (TM) becomes a potential refuge for bacteria. It is noteworthy that the relationship between cancer and bacteria is intertwined.
Objective: To analyze similarities between biofilm and tumor milieu that is produced against stress conditions and heterogeneous microenvironment for a combination of approaches the bacteriotherapy with chemotherapy which can help in defeating the tumor heterogeneity accompanied with malignancy, drug-resistance, and metastasis.
Method: An analytical review of the literature on keywords from the scientometric databases PubMed, Wiley.
Results: Bacteria evade antimicrobial treatment is mainly due to persistence that has become dormant during the stationary phase and tolerance. Drug-tolerant persisters and cellular dormancy are crucial in the development of cancer, especially in understanding the development of metastases as a late relapse. Biofilms are formed by groups of cells in different states, growing or non-growing and metabolically active or inactive in variable fractions, depending on maturity and on chemical gradients (O2 and nutrients) of the biofilms producing physiological heterogeneity. Heterogeneity in the microenvironment of cancer can be described as a non-cell autonomous driver of cancer cell diversity; in a highly diverse microenvironment, different cellular phenotypes may be selected for or against in different regions of the tumor. Hypoxia, oxidative stress, and inflammation have been identified as positive regulators of metastatic potential, drug resistance, and tumorigenic properties in cancer. It is proven that, Escherichia coli (E. coli) and life-threatening infectious pathogens such as Staphylococcus aureus (SA) and Mycobacterium tuberculosis (Mtb) are noticeably sensitive to alterations in the intracellular oxidative environment. An alternative emerging paradigm is that many cancers may be promoted by commensal microbiota, either by translocation and adherence of microbes to cancer cells or by the distant release of inflammation-activating microbial metabolites. Microbial factors such as F. nucleatum, B. fragilis, and Enterobacteriaceae members may contribute to disease onset in patients with a hereditary form of colorectal cancer (CRC); familial adenomatous polyposis (FAP). These findings are linked with the creation of new biomarkers and therapy for identifying and treating biofilm-associated cancers. Currently, about 20% of neoplasms globally can be caused by infections, with approximately 1.2 million cases annually. Several antineoplastic drugs that exhibited activity against S. mutans, including tamoxifen, doxorubicin, and ponatinib, also possessed activity against other Gram-positive bacteria. Drug repurposing, also known as repositioning, has gained momentum, mostly due to its advantages over de novo drug discovery, including reduced risk to patients due to previously documented clinical trials, lower drug development costs, and faster benchtop-to-clinic transition. Although many bacteria are carcinogens and tumor promoters, some have shown great potential towards cancer therapy. Several species of bacteria have shown an impressive power to penetrate and colonize solid tumors, which has mainly led to neoplasm slower growth and tumor clearance. Different strains of Clostridia, Lactococcus, Bifidobacteria, Shigella, Vibrio, Listeria, Escherichia, and Salmonella have been evaluated against cancer in animal models.
Conclusion. Cancer is a multifactorial disease and the use of bacteria for cancer therapy as an immunostimulatory agent or as a vector for carrying the therapeutic cargo is a promising treatment method. Therefore, the world has turned to an alternative solution, which is the use of genetically engineered microorganisms; thus, the use of living bacteria targeting cancerous cells is the unique option to overcome these challenges. Bacterial therapies, whether used alone or combination with chemotherapy, give a positive effect to treat multiple conditions of cancer.
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Worawittayatada, Jaruwan, Kitipong Angsujinda, Rapee Sinnuengnong, Pongsopee Attasart, Duncan R. Smith, and Wanchai Assavalapsakul. "Simultaneous Production of a Virus-Like Particle Linked to dsRNA to Enhance dsRNA Delivery for Yellow Head Virus Inhibition." Viruses 14, no. 12 (November 22, 2022): 2594. http://dx.doi.org/10.3390/v14122594.
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A co-expressed Penaeus stylirostris densovirus (PstDNV) capsid and dsRNA specific to the yellow head virus (YHV) protease (CoEx cpPstDNV/dspro) has been shown to suppress YHV replication in the Pacific white-legged shrimp (Litopenaeus vannamei). However, maintaining two plasmids in a single bacterial cell is not desirable; therefore, a single plasmid harboring both the PstDNV capsid and the dsRNA-YHV-pro gene was constructed under the regulation of a single T7 promoter, designated pET28a-Linked cpPstDNV-dspro. Following induction, this novel construct expressed an approximately 37-kDa recombinant protein associated with a roughly 400-bp dsRNA (Linked cpPstDNV-dspro). Under a transmission electron microscope, the virus-like particles (VLP; Linked PstDNV VLPs-dspro) obtained were seen to be monodispersed, similar to the native PstDNV virion. A nuclease digestion assay indicated dsRNA molecules were both encapsulated and present outside the Linked PstDNV VLPs-dspro. In addition, the amount of dsRNA produced from this strategy was higher than that obtained with a co-expression strategy. In a YHV infection challenge, the Linked PstDNV VLPs-dspro was more effective in delaying and reducing mortality than other constructs tested. Lastly, the linked construct provides protection for the dsRNA cargo from nucleolytic enzymes present in the shrimp hemolymph. This is the first report of a VLP carrying virus-inhibiting dsRNA that could be produced without disassembly and reassembly to control virus infection in shrimp.
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LeBlanc, Philippe M., Richard C. Hamelin, and Martin Filion. "Alteration of Soil Rhizosphere Communities following Genetic Transformation of White Spruce." Applied and Environmental Microbiology 73, no. 13 (April 27, 2007): 4128–34. http://dx.doi.org/10.1128/aem.02590-06.
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ABSTRACT The application of plant genetic manipulations to agriculture and forestry with the aim of alleviating insect damage through Bacillus thuringiensis transformation could lead to a significant reduction in the release of pesticides into the environment. However, many groups have come forward with very valid and important questions related to potentially adverse effects, and it is crucial to assess and better understand the impact that this technology might have on ecosystems. In this study, we analyzed rhizosphere soil samples collected from the first B. thuringiensis-transformed trees [with insertion of the CryIA(b) toxin-encoding gene] grown in Canada (Val-Cartier, QC, Canada) as part of an ecological impact assessment project. Using a robust amplified rRNA gene restriction analysis approach coupled with 16S rRNA gene sequencing, the rhizosphere-inhabiting microbial communities of white spruce (Picea glauca) genetically modified by biolistic insertion of the cryIA(b), uidA (beta-glucuronidase), and nptII genes were compared with the microbial communities associated with non-genetically modified counterparts and with trees in which only the genetic marker genes uidA and nptII have been inserted. Analysis of 1,728 rhizosphere bacterial clones (576 clones per treatment) using a Cramér-von Mises statistic analysis combined with a Monte Carlo comparison clearly indicated that there was a statistically significant difference (P < 0.05) between the microbial communities inhabiting the rhizospheres of trees carrying the cryIA(b), uidA, and nptII transgenes, trees carrying only the uidA and nptII transgenes, and control trees. Clear rhizosphere microbial community alterations due to B. thuringiensis tree genetic modification have to our knowledge never been described previously and open the door to interesting questions related to B. thuringiensis genetic transformation and also to the impact of commonly used uidA and nptII genetic marker genes.
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Finkelshtein, Alin, Dalit Roth, Eshel Ben Jacob, and Colin J. Ingham. "Bacterial Swarms Recruit Cargo Bacteria To Pave the Way in Toxic Environments." mBio 6, no. 3 (May 12, 2015). http://dx.doi.org/10.1128/mbio.00074-15.
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ABSTRACTSwarming bacteria are challenged by the need to invade hostile environments. Swarms of the flagellated bacteriumPaenibacillus vortexcan collectively transport other microorganisms. Here we show thatP. vortexcan invade toxic environments by carrying antibiotic-degrading bacteria; this transport is mediated by a specialized, phenotypic subpopulation utilizing a process not dependent on cargo motility. Swarms of beta-lactam antibiotic (BLA)-sensitiveP. vortexused beta-lactamase-producing, resistant, cargo bacteria to detoxify BLAs in their path. In the presence of BLAs, both transporter and cargo bacteria gained from this temporary cooperation; there was a positive correlation between BLA resistance and dispersal.P. vortextransported only the most beneficial antibiotic-resistant cargo (including environmental and clinical isolates) in a sustained way.P. vortexdisplayed a bet-hedging strategy that promoted the colonization of nontoxic niches byP. vortexalone; when detoxifying cargo bacteria were not needed, they were lost. This work has relevance for the dispersal of antibiotic-resistant microorganisms and for strategies for asymmetric cooperation with agricultural and medical implications.IMPORTANCEAntibiotic resistance is a major health threat. We show a novel mechanism for the local spread of antibiotic resistance. This involves interactions between different bacteria: one species provides an enzyme that detoxifies the antibiotic (a sessile cargo bacterium carrying a resistance gene), while the other (Paenibacillus vortex) moves itself and transports the cargo.P. vortexused a bet-hedging strategy, colonizing new environments alone when the cargo added no benefit, but cooperating when the cargo was needed. This work is of interest in an evolutionary context and sheds light on fundamental questions, such as how environmental antibiotic resistance may lead to clinical resistance and also microbial social organization, as well as the costs, benefits, and risks of dispersal in the environment.
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Muzzeddu, Pietro Luigi, Edgar Roldan, Andrea Gambassi, and Abhinav Sharma. "Taxis of cargo-carrying microswimmers in traveling activity waves." Europhysics Letters, May 25, 2023. http://dx.doi.org/10.1209/0295-5075/acd8e9.
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Abstract Many fascinating properties of biological active matter crucially depend on the capacity of constituting entities to perform directed motion, e.g., molecular motors transporting vesicles inside cells or bacteria searching for food. While much effort has been devoted to mimicking biological functions in synthetic systems, such as transporting a cargo to a targeted zone, theoretical studies have primarily focused on single active particles subject to various spatial and temporal stimuli. Here we study the behavior of a self-propelled particle carrying a passive cargo in a
travelling activity wave and show that this active-passive dimer displays a rich, emergent tactic behavior. 
For cargoes with low mobility, the dimer always drifts in the direction of the wave propagation. For highly-mobile cargoes, instead, the dimer can also drift against the traveling wave. The transition between these two tactic behaviors is controlled by the ratio between the frictions of the cargo and the microswimmer. In slow activity waves the dimer can perform an \emph{active surfing} of the wave maxima, with an average drift velocity equal to the wave speed. These analytical predictions, which we confirm by numerical simulations, might be useful for the future efficient design of bio-hybrid microswimmers.
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Akolpoglu, Mukrime Birgul, Yunus Alapan, Nihal Olcay Dogan, Saadet Fatma Baltaci, Oncay Yasa, Gulsen Aybar Tural, and Metin Sitti. "Magnetically steerable bacterial microrobots moving in 3D biological matrices for stimuli-responsive cargo delivery." Science Advances 8, no. 28 (July 15, 2022). http://dx.doi.org/10.1126/sciadv.abo6163.
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Bacterial biohybrids, composed of self-propelling bacteria carrying micro/nanoscale materials, can deliver their payload to specific regions under magnetic control, enabling additional frontiers in minimally invasive medicine. However, current bacterial biohybrid designs lack high-throughput and facile construction with favorable cargoes, thus underperforming in terms of propulsion, payload efficiency, tissue penetration, and spatiotemporal operation. Here, we report magnetically controlled bacterial biohybrids for targeted localization and multistimuli-responsive drug release in three-dimensional (3D) biological matrices. Magnetic nanoparticles and nanoliposomes loaded with photothermal agents and chemotherapeutic molecules were integrated onto Escherichia coli with ~90% efficiency. Bacterial biohybrids, outperforming previously reported E. coli –based microrobots, retained their original motility and were able to navigate through biological matrices and colonize tumor spheroids under magnetic fields for on-demand release of the drug molecules by near-infrared stimulus. Our work thus provides a multifunctional microrobotic platform for guided locomotion in 3D biological networks and stimuli-responsive delivery of therapeutics for diverse medical applications.
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Verster, Kirsten I., Gyöngyi Cinege, Zoltán Lipinszki, Lilla B. Magyar, Éva Kurucz, Rebecca L. Tarnopol, Edit Ábrahám, et al. "Evolution of insect innate immunity through domestication of bacterial toxins." Proceedings of the National Academy of Sciences 120, no. 16 (April 10, 2023). http://dx.doi.org/10.1073/pnas.2218334120.
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Toxin cargo genes are often horizontally transferred by phages between bacterial species and are known to play an important role in the evolution of bacterial pathogenesis. Here, we show how these same genes have been horizontally transferred from phage or bacteria to animals and have resulted in novel adaptations. We discovered that two widespread bacterial genes encoding toxins of animal cells, cytolethal distending toxin subunit B ( cdtB ) and apoptosis-inducing protein of 56 kDa ( aip56) , were captured by insect genomes through horizontal gene transfer from bacteria or phages. To study the function of these genes in insects, we focused on Drosophila ananassae as a model. In the D. ananassae subgroup species, cdtB and aip56 are present as singular ( cdtB ) or fused copies ( cdtB::aip56 ) on the second chromosome. We found that cdtB and aip56 genes and encoded proteins were expressed by immune cells, some proteins were localized to the wasp embryo’s serosa, and their expression increased following parasitoid wasp infection. Species of the ananassae subgroup are highly resistant to parasitoid wasps, and we observed that D. ananassae lines carrying null mutations in cdtB and aip56 toxin genes were more susceptible to parasitoids than the wild type. We conclude that toxin cargo genes were captured by these insects millions of years ago and integrated as novel modules into their innate immune system. These modules now represent components of a heretofore undescribed defense response and are important for resistance to parasitoid wasps. Phage or bacterially derived eukaryotic toxin genes serve as macromutations that can spur the instantaneous evolution of novelty in animals.
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de Assis, Jéssica Catarine Silva, Osiel Silva Gonçalves, Alexia Suellen Fernandes, Marisa Vieira de Queiroz, Denise Mara Soares Bazzolli, and Mateus Ferreira Santana. "Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria." Mobile DNA 13, no. 1 (August 12, 2022). http://dx.doi.org/10.1186/s13100-022-00275-1.
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Abstract Background ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact. Results Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants. Conclusions Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria.
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Gluck-Thaler, Emile, Timothy Ralston, Zachary Konkel, Cristhian Grabowski Ocampos, Veena Devi Ganeshan, Anne E. Dorrance, Terry L. Niblack, et al. "Giant Starship elements mobilize accessory genes in fungal genomes." Molecular Biology and Evolution, May 19, 2022. http://dx.doi.org/10.1093/molbev/msac109.
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Abstract Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a newly discovered group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27-393 kb and last shared a common ancestor ca. 400 mya. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize 4 additional Starships whose activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager’s activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first dedicated agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.
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Frei, Dominik Michael, Erlend Hodneland, Ivan Rios-Mondragon, Anne Burtey, Beate Neumann, Jutta Bulkescher, Julia Schölermann, Rainer Pepperkok, Hans-Hermann Gerdes, and Tanja Kögel. "Novel microscopy-based screening method reveals regulators of contact-dependent intercellular transfer." Scientific Reports 5, no. 1 (August 14, 2015). http://dx.doi.org/10.1038/srep12879.
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Abstract Contact-dependent intercellular transfer (codeIT) of cellular constituents can have functional consequences for recipient cells, such as enhanced survival and drug resistance. Pathogenic viruses, prions and bacteria can also utilize this mechanism to spread to adjacent cells and potentially evade immune detection. However, little is known about the molecular mechanism underlying this intercellular transfer process. Here, we present a novel microscopy-based screening method to identify regulators and cargo of codeIT. Single donor cells, carrying fluorescently labelled endocytic organelles or proteins, are co-cultured with excess acceptor cells. CodeIT is quantified by confocal microscopy and image analysis in 3D, preserving spatial information. An siRNA-based screening using this method revealed the involvement of several myosins and small GTPases as codeIT regulators. Our data indicates that cellular protrusions and tubular recycling endosomes are important for codeIT. We automated image acquisition and analysis to facilitate large-scale chemical and genetic screening efforts to identify key regulators of codeIT.
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Kaplan, Elise, Nicholas P. Greene, Abigail E. Jepson, and Vassilis Koronakis. "Structural basis of lipoprotein recognition by the bacterial Lol trafficking chaperone LolA." Proceedings of the National Academy of Sciences 119, no. 36 (August 29, 2022). http://dx.doi.org/10.1073/pnas.2208662119.
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In gram-negative bacteria, lipoproteins are vital structural components of the outer membrane (OM) and crucial elements of machineries central to the physiology of the cell envelope. A dedicated apparatus, the Lol system, is required for the correct localization of OM lipoproteins and is essential for viability. The periplasmic chaperone LolA is central to this trafficking pathway, accepting triacylated lipoproteins from the inner membrane transporter LolCDE, before carrying them across the periplasm to the OM receptor LolB. Here, we report a crystal structure of liganded LolA, generated in vivo, revealing the molecular details of lipoprotein association. The structure highlights how LolA, initially primed to receive lipoprotein by interaction with LolC, further opens to accommodate the three ligand acyl chains in a precise conformation within its cavity. LolA forms extensive interactions with the acyl chains but not with any residue of the cargo, explaining the chaperone’s ability to transport structurally diverse lipoproteins. Structural characterization of a ligandedLolA variant incapable of lipoprotein release reveals aberrant association, demonstrating the importance of the LolCDE-coordinated, sequential opening of LolA for inserting lipoprotein in a manner productive for subsequent trafficking. Comparison with existing structures of LolA in complex with LolC or LolCDE reveals substantial overlap of the lipoprotein and LolC binding sites within the LolA cavity, demonstrating that insertion of lipoprotein acyl chains physically disengages the chaperone protein from the transporter by perturbing interaction with LolC. Taken together, our data provide a key step toward a complete understanding of a fundamentally important trafficking pathway.
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Rivard, Nicolas, Rita R. Colwell, and Vincent Burrus. "Antibiotic Resistance in Vibrio cholerae: Mechanistic Insights from IncC Plasmid-Mediated Dissemination of a Novel Family of Genomic Islands Inserted at trmE." mSphere 5, no. 4 (August 26, 2020). http://dx.doi.org/10.1128/msphere.00748-20.
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ABSTRACT Cholera remains a formidable disease, and reports of multidrug-resistant strains of the causative agent Vibrio cholerae have become common during the last 3 decades. The pervasiveness of resistance determinants has largely been ascribed to mobile genetic elements, including SXT/R391 integrative conjugative elements, IncC plasmids, and genomic islands (GIs). Conjugative transfer of IncC plasmids is activated by the master activator AcaCD whose regulatory network extends to chromosomally integrated GIs. MGIVchHai6 is a multidrug resistance GI integrated at the 3′ end of trmE (mnmE or thdF) in chromosome 1 of non-O1/non-O139 V. cholerae clinical isolates from the 2010 Haitian cholera outbreak. In the presence of an IncC plasmid expressing AcaCD, MGIVchHai6 excises from the chromosome and transfers at high frequency. Herein, the mechanism of mobilization of MGIVchHai6 GIs by IncC plasmids was dissected. Our results show that AcaCD drives expression of GI-borne genes, including xis and mobIM, involved in excision and mobilization. A 49-bp fragment upstream of mobIM was found to serve as the minimal origin of transfer (oriT) of MGIVchHai6. The direction of transfer initiated at oriT was determined using IncC plasmid-driven mobilization of chromosomal markers via MGIVchHai6. In addition, IncC plasmid-encoded factors, including the relaxase TraI, were found to be required for GI transfer. Finally, in silico exploration of Gammaproteobacteria genomes identified 47 novel related and potentially AcaCD-responsive GIs in 13 different genera. Despite sharing conserved features, these GIs integrate at trmE, yicC, or dusA and carry a diverse cargo of genes involved in phage resistance. IMPORTANCE The increasing association of the etiological agent of cholera, Vibrio cholerae serogroup O1 and O139, with multiple antibiotic resistance threatens to deprive health practitioners of this effective tool. Drug resistance in cholera results mainly from acquisition of mobile genetic elements. Genomic islands conferring multidrug resistance and mobilizable by IncC conjugative plasmids were reported to circulate in non-O1/non-O139 V. cholerae clinical strains isolated from the 2010 Haitian cholera outbreak. As these genomic islands can be transmitted to pandemic V. cholerae serogroups, their mechanism of transmission needed to be investigated. Our research revealed plasmid- and genomic island-encoded factors required for the resistance island excision, mobilization, and integration, as well as regulation of these functions. The discovery of related genomic islands carrying diverse phage resistance genes but lacking antibiotic resistance-conferring genes in a wide range of marine dwelling bacteria suggests that these elements are ancient and recently acquired drug resistance genes.
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Yao, Xiaohui, Qiangqiang Song, Wei Zhu, Jianchao Wei, Donghua Shao, Ke Liu, Zongjie Li, et al. "Characterization of small plasmids carrying florfenicol resistance gene floR in Actinobacillus pleuropneumoniae and Pasteurella multocida isolates from swine in China." Frontiers in Veterinary Science 10 (January 30, 2023). http://dx.doi.org/10.3389/fvets.2023.1084491.
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Actinobacillus pleuropneumoniae and Pasteurella multocida are two important bacterial pathogens in swine industry. In the present study, resistance profiles of nine commonly used antibiotics of A. pleuropneumoniae and P. multocida isolates of swine origin from different regions of China were investigated by determination of minimum inhibitory concentrations (MICs). In addition, genetic relationship of the florfenicol-resistant A. pleuropneumoniae and P. multocida isolates was determined by pulsed-field gel electrophoresis (PFGE). The genetic basis of florfenicol resistance in these isolates were explored by floR detection and whole genome sequencing. High resistance rates (>25%) of florfenicol, tetracycline and trimethoprim- sulfamethoxazole were observed for both bacteria. No ceftiofur- and tiamulin- resistant isolates were detected. Furthermore, all the 17 florfenicol-resistant isolates (nine for A. pleuropneumoniae and eight for P. multocida) were positive for floR gene. The presence of similar PFGE types in these isolates suggested that clonal expansion of some floR-producing strains occurred in the pig farms from same regions. WGS and PCR screening showed that three plasmids, named pFA11, pMAF5, and pMAF6, were the cargos of the floR genes in the 17 isolates. Plasmid pFA11 exhibited novel structure and carried several resistance genes, including floR, sul2, aacC2d, strA, strB, and blaROB − 1. Plasmids pMAF5 and pMAF6 were presented in A. pleuropneumoniae and P. multocida isolates from different regions, suggesting horizontal transfer of the two plasmids are important for the floR dissemination in these Pasteurellaceae pathogens. Further studies of florfenicol resistance and its transfer vectors in Pasteurellaceae bacteria of veterinary origin are warranted.
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Long, Xiaochun, Mary A. Georger, Vivian Liu, and Joseph M. Miano. "Abstract 985: BAC Transgenic Analysis of the Smooth Muscle Calponin Gene." Circulation 116, suppl_16 (October 16, 2007). http://dx.doi.org/10.1161/circ.116.suppl_16.ii_195-c.
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Regulatory elements controlling gene expression are often found in separate, sometimes remote, regions around gene loci. Artificial chromosomes offer a means to capture all regulatory elements for study of gene regulation in a near-correct genomic context. The smooth muscle calponin gene (CNN1) encodes for a multifunctional protein involved in signaling, contractile force generation, and growth regulation. While CNN1’s physiology has been studied extensively, its transcriptional regulation has proven to be intractable to conventional in vivo assays. Four evolutionarily-conserved serum response factor (SRF) binding sites (called CArG boxes) are present in the first intron of CNN1 and appear to be required for full transcriptional competence of CNN1 in cultured smooth muscle cells (SMC). To assess the functionality of CNN1 CArG elements in vivo , we exploited a 103-kb bacterial artificial chromosome (BAC) containing the human CNN1 locus shown previously to completely recapitulate endogenous mouse CNN1 expression in vivo . We now show similar SMC-restricted expression of human CNN1 from only 38-kb of BAC sequence. BAC recombineering studies in which the first intron (containing four CArG elements) of CNN1 is replaced with a bacterial selection gene ( galK ) reveal complete loss of human CNN1 expression in vascular SMC, with residual expression in some visceral SMC-containing tissues such as bladder. Transgenic mice carrying the 38-kb BAC with point mutations in all four intronic CArG elements show similar findings suggesting that SRF directly mediates in vivo expression of CNN1 primarily through intronic CArG elements. Bioinformatic, luciferase, and ChIP assays reveal the presence of distal, conserved CArG elements, including a previously unrecognized one located more than 3-kb upstream of the CNN1 transcription start site. The latter CArG-like element is responsive to the SRF coactivator myocardin and is essential for full CNN1 promoter activity in vitro . Moreover, this distal CArG-like element is embedded in a cis regulatory module with conserved binding sites to other distinct transcription factors. We propose that full in vivo CNN1 gene expression requires multiple elements, including five CArG boxes, spread over 14-kb of genomic sequence.
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Ichikawa, Shunsuke, Satoru Ogawa, Ayami Nishida, Yuzuki Kobayashi, Toshihito Kurosawa, and Shuichi Karita. "Cellulosomes localise on the surface of membrane vesicles from the cellulolytic bacterium Clostridium thermocellum." FEMS Microbiology Letters 366, no. 12 (June 1, 2019). http://dx.doi.org/10.1093/femsle/fnz145.
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ABSTRACTMembrane vesicles released from bacteria contribute to cell–cell communication by carrying various cargos such as proteins, nucleic acids and signaling molecules. Cellulolytic bacteria have been isolated from many environments, yet the function of membrane vesicles for cellulolytic ability has been rarely described. Here, we show that a Gram-positive cellulolytic bacterium Clostridium thermocellum released membrane vesicles, each approximately 50–300 nm in diameter, into the broth. The observations with immunoelectron microscopy also revealed that cellulosomes, which are carbohydrate-active enzyme complexes that give C. thermocellum high cellulolytic activity, localized on the surface of the membrane vesicles. The membrane vesicles collected by ultracentrifugation maintained the cellulolytic activity. Supplementation with the biosurfactant surfactin or sonication treatment disrupted the membrane vesicles in the exoproteome of C. thermocellum and significantly decreased the degradation activity of the exoproteome for microcrystalline cellulose. However, these did not affect the degradation activity for soluble carboxymethyl cellulose. These results suggest a novel function of membrane vesicles: C. thermocellum releases cellulolytic enzymes on the surface of membrane vesicles to enhance the cellulolytic activity of C. thermocellum for crystalline cellulose.
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Chen, Chen, Jun Kawamoto, Soichiro Kawai, Akihiro Tame, Chiaki Kato, Tomoya Imai, and Tatsuo Kurihara. "Isolation of a Novel Bacterial Strain Capable of Producing Abundant Extracellular Membrane Vesicles Carrying a Single Major Cargo Protein and Analysis of Its Transport Mechanism." Frontiers in Microbiology 10 (January 14, 2020). http://dx.doi.org/10.3389/fmicb.2019.03001.
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Nichols, Wright W., Patricia A. Bradford, and Gregory G. Stone. "The primary pharmacology of ceftazidime/avibactam: in vivo translational biology and pharmacokinetics/pharmacodynamics (PK/PD)." Journal of Antimicrobial Chemotherapy, June 4, 2022. http://dx.doi.org/10.1093/jac/dkac172.
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Abstract This review describes the translational in vivo and non-clinical pharmacokinetics/pharmacodynamics (PK/PD) research that supported clinical trialling and subsequently licensing approval of ceftazidime/avibactam, a new β-lactam/β-lactamase inhibitor combination aimed at the treatment of infections by Enterobacterales and Pseudomonas aeruginosa. The review thematically follows on from the co-published article, Nichols et al. (J Antimicrob Chemother 2022; dkac171). Avibactam protected ceftazidime in animal models of infection with ceftazidime-resistant, β-lactamase-producing bacteria. For example, a single subcutaneous dose of ceftazidime at 1024 mg/kg yielded little effect on the growth of ceftazidime-resistant, blaKPC-2-carrying Klebsiella pneumoniae in the thighs of neutropenic mice (final counts of 4 × 108 to 8 × 108 cfu/thigh). In contrast, co-administration of avibactam in a 4:1 ratio (ceftazidime:avibactam) was bactericidal in the same model (final counts of 2 × 104 to 3 × 104 cfu/thigh). In a rat abdominal abscess model, therapy with ceftazidime or ceftazidime/avibactam (4:1 w/w) against blaKPC-2-positive K. pneumoniae resulted in 9.3 versus 3.3 log cfu/abscess, respectively, after 52 h. With respect to PK/PD, in Monte Carlo simulations, attainment of unbound drug exposure targets (ceftazidime fT>8 mg/L and avibactam fT>1 mg/L, each for 50% of the dosing interval) for the labelled dose of ceftazidime/avibactam (2 and 0.5 g, respectively, q8h by 2 h IV infusion), including dose adjustments for patients with impaired renal function, ranged between 94.8% and 99.6% of patients, depending on the infection modelled.