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Chan WJ, Li H. Recent advances in nano/micro systems for improved circulation stability, enhanced tumor targeting, penetration, and intracellular drug delivery: a review. Biomed Phys Eng Express 2024; 10:022001. [PMID: 38086099 DOI: 10.1088/2057-1976/ad14f0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024]
Abstract
In recent years, nanoparticles (NPs) have been extensively developed as drug carriers to overcome the limitations of cancer therapeutics. However, there are several biological barriers to nanomedicines, which include the lack of stability in circulation, limited target specificity, low penetration into tumors and insufficient cellular uptake, restricting the active targeting toward tumors of nanomedicines. To address these challenges, a variety of promising strategies were developed recently, as they can be designed to improve NP accumulation and penetration in tumor tissues, circulation stability, tumor targeting, and intracellular uptake. In this Review, we summarized nanomaterials developed in recent three years that could be utilized to improve drug delivery for cancer treatments.
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Affiliation(s)
- Wei-Jen Chan
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, United States of America
| | - Huatian Li
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, United States of America
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Villa-Torrealba A, Navia S, Soto R. Kinetic modeling of the chemotactic process in run-and-tumble bacteria. Phys Rev E 2023; 107:034605. [PMID: 37072994 DOI: 10.1103/physreve.107.034605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 03/14/2023] [Indexed: 04/20/2023]
Abstract
The chemotactic process of run-and-tumble bacteria results from modulating the tumbling rate in response to changes in chemoattractant gradients felt by the bacteria. The response has a characteristic memory time and is subject to important fluctuations. These ingredients are considered in a kinetic description of chemotaxis, allowing the computation of the stationary mobility and the relaxation times needed to reach the steady state. For large memory times, these relaxation times become large, implying that finite-time measurements give rise to nonmonotonic currents as a function of the imposed chemoattractant gradient, contrary to the stationary regime where the response is monotonic. The case of an inhomogeneous signal is analyzed. Contrary to the usual Keller-Segel model, the response is nonlocal, and the bacterial profile is smoothed with a characteristic length that grows with the memory time. Finally, the case of traveling signals is considered, where appreciable differences appear compared to memoryless chemotactic descriptions.
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Affiliation(s)
- Andrea Villa-Torrealba
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Avenida Blanco Encalada 2008, Santiago, Chile
| | - Simón Navia
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Avenida Blanco Encalada 2008, Santiago, Chile
| | - Rodrigo Soto
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Avenida Blanco Encalada 2008, Santiago, Chile
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Kavela S, Vyas P, CP J, Kushwaha SK, Majumdar SS, Faisal SM. Use of an Integrated Multi-Omics Approach To Identify Molecular Mechanisms and Critical Factors Involved in the Pathogenesis of Leptospira. Microbiol Spectr 2023; 11:e0313522. [PMID: 36853003 PMCID: PMC10100824 DOI: 10.1128/spectrum.03135-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023] Open
Abstract
Leptospirosis, a bacterial zoonosis caused by pathogenic Leptospira spp., is prevalent worldwide and has become a serious threat in recent years. Limited understanding of Leptospira pathogenesis and host response has hampered the development of effective vaccine and diagnostics. Although Leptospira is phagocytosed by innate immune cells, it resists its destruction, and the evading mechanism involved is unclear. In the present study, we used an integrative multi-omics approach to identify the critical molecular factors of Leptospira involved in pathogenesis during interaction with human macrophages. Transcriptomic and proteomic analyses were performed at 24 h postinfection of human macrophages (phorbol-12-myristate-13-acetate differentiated THP-1 cells) with the pathogenic Leptospira interrogans serovar Icterohaemorrhagiae strain RGA (LEPIRGA). Our results identified a total of 1,528 transcripts and 871 proteins that were significantly expressed with an adjusted P value of <0.05. The correlations between the transcriptomic and proteomic data were above average (r = 0.844), suggesting the role of the posttranscriptional processes during host interaction. The conjoint analysis revealed the expression of several virulence-associated proteins such as adhesins, invasins, and secretory and chemotaxis proteins that might be involved in various processes of attachment and invasion and as effectors during pathogenesis in the host. Further, the interaction of bacteria with the host cell (macrophages) was a major factor in the differential expression of these proteins. Finally, eight common differentially expressed RNA-protein pairs, predicted as virulent, outer membrane/extracellular proteins were validated by quantitative PCR. This is the first report using integrated multi-omics approach to identify critical factors involved in Leptospira pathogenesis. Validation of these critical factors may lead to the identification of target antigens for the development of improved diagnostics and vaccines against leptospirosis. IMPORTANCE Leptospirosis is a zoonotic disease of global importance. It is caused by a Gram-negative bacterial spirochete of the genus Leptospira. The current challenge is to detect the infection at early stage for treatment or to develop potent vaccines that can induce cross-protection against various pathogenic serovars. Understanding host-pathogen interactions is important to identify the critical factors involved in pathogenesis and host defense for developing improved vaccines and diagnostics. Utilizing an integrated multi-omics approach, our study provides important insight into the interaction of Leptospira with human macrophages and identifies a few critical factors (such as virulence-associated proteins) involved in pathogenesis. These factors can be exploited for the development of novel tools for the detection, treatment, or prevention of leptospirosis.
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Affiliation(s)
- Sridhar Kavela
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
| | - Pallavi Vyas
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Jusail CP
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Sandeep K. Kushwaha
- Bioinformatics Lab, National Institute of Animal Biotechnology, Hyderabad, India
| | - Subeer S. Majumdar
- Gene and Protein Engineering Lab, National Institute of Animal Biotechnology, Hyderabad, India
| | - Syed M. Faisal
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
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Singh AK, Awasthi R, Malviya R. Bioinspired microrobots: Opportunities and challenges in targeted cancer therapy. J Control Release 2023; 354:439-452. [PMID: 36669531 DOI: 10.1016/j.jconrel.2023.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 01/21/2023]
Abstract
Chemotherapy is still the most effective technique to treat many forms of cancer. However, it also carries a high risk of side effects. Numerous nanomedicines have been developed to avoid unintended consequences and significant negative effects of conventional therapies. Achieving targeted drug delivery also has several challenges. In this context, the development of microrobots is receiving considerable attention of formulation scientists and clinicians to overcome such challenges. Due to their mobility, microrobots can infiltrate tissues and reach tumor sites more quickly. Different types of microrobots, like custom-made moving bacteria, microengines powered by small bubbles, and hybrid spermbots, can be designed with complex features that are best for precise targeting of a wide range of cancers. In this review, we mainly focus on the idea of how microrobots can quickly target cancer cells and discuss specific advantages of microrobots. A brief summary of the microrobots' drug loading and release behavior is provided in this manuscript. This manuscript will assist clinicians and other medical professionals in diagnosing and treating cancer without surgery.
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Affiliation(s)
- Arun Kumar Singh
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India
| | - Rajendra Awasthi
- Department of Pharmaceutical Sciences, School of Health Sciences & Technology, University of Petroleum and Energy Studies (UPES), Energy Acres, P.O. Bidholi, Via-Prem Nagar, Dehradun 248 007, Uttarakhand, India
| | - Rishabha Malviya
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India.
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Taha, Elgamoudi BA, Andrianova EP, Haselhorst T, Day CJ, Hartley-Tassell LE, King RM, Najnin T, Zhulin IB, Korolik V. Diverse Sensory Repertoire of Paralogous Chemoreceptors Tlp2, Tlp3, and Tlp4 in Campylobacter jejuni. Microbiol Spectr 2022; 10:e0364622. [PMID: 36374080 PMCID: PMC9769880 DOI: 10.1128/spectrum.03646-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Campylobacter jejuni responds to extracellular stimuli via transducer-like chemoreceptors (Tlps). Here, we describe receptor-ligand interactions of a unique paralogue family of dCache_1 (double Calcium channels and chemotaxis) chemoreceptors: Tlp2, Tlp3, and Tlp4. Phylogenetic analysis revealed that Tlp2, Tlp3, and Tlp4 receptors may have arisen through domain duplications, followed by a divergent evolutionary drift, with Tlp3 emerging more recently, and unexpectedly, responded to glycans, as well as multiple organic and amino acids with overlapping specificities. All three Tlps interacted with five monosaccharides and complex glycans, including Lewis's antigens, P antigens, and fucosyl GM1 ganglioside, indicating a potential role in host-pathogen interactions. Analysis of chemotactic motility of single, double, and triple mutants indicated that these chemoreceptors are likely to work together to balance responses to attractants and repellents to modulate chemotaxis in C. jejuni. Molecular docking experiments, in combination with saturation transfer difference nuclear magnetic resonance spectroscopy and competition surface plasmon resonance analysis, illustrated that the ligand-binding domain of Tlp3 possess one major binding pocket with two overlapping, but distinct binding sites able to interact with multiple ligands. A diverse sensory repertoire could provide C. jejuni with the ability to modulate responses to attractant and repellent signals and allow for adaptation in host-pathogen interactions. IMPORTANCE Campylobacter jejuni responds to extracellular stimuli via transducer-like chemoreceptors (Tlps). This remarkable sensory perception mechanism allows bacteria to sense environmental changes and avoid unfavorable conditions or to maneuver toward nutrient sources and host cells. Here, we describe receptor-ligand interactions of a unique paralogue family of chemoreceptors, Tlp2, Tlp3, and Tlp4, that may have arisen through domain duplications, followed by a divergent evolutionary drift, with Tlp3 emerging more recently. Unlike previous reports of ligands interacting with sensory proteins, Tlp2, Tlp3, and Tlp4 responded to many types of chemical compounds, including simple and complex sugars such as those present on human blood group antigens and gangliosides, indicating a potential role in host-pathogen interactions. Diverse sensory repertoire could provide C. jejuni with the ability to modulate responses to attractant and repellent signals and allow for adaptation in host-pathogen interactions.
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Affiliation(s)
- Taha
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Bassam A. Elgamoudi
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Ekaterina P. Andrianova
- Department of Microbiology and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Christopher J. Day
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | | | - Rebecca M. King
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Tahria Najnin
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Igor B. Zhulin
- Department of Microbiology and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Victoria Korolik
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
- School of Pharmacy and Medical Science, Griffith University, Gold Coast, Queensland, Australia
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Progress of engineered bacteria for tumor therapy. Adv Drug Deliv Rev 2022; 185:114296. [PMID: 35439571 DOI: 10.1016/j.addr.2022.114296] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/25/2022] [Accepted: 04/10/2022] [Indexed: 02/08/2023]
Abstract
Recently, with the rapid development of bioengineering technology and nanotechnology, natural bacteria were modified to change their physiological activities and therapeutic functions for improved therapeutic efficiency of diseases. These engineered bacteria were equipped to achieve directed genetic reprogramming, selective functional reorganization and precise spatio-temporal control. In this review, research progress in the basic modification methodologies of engineered bacteria were summarized, and representative researches about their therapeutic performances for tumor treatment were illustrated. Moreover, the strategies for the construction of engineered colonies based on engineering of individual bacteria were summarized, providing innovative ideas for complex functions and efficient anti-tumor treatment. Finally, current limitation and challenges of tumor therapy utilizing engineered bacteria were discussed.
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Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. mSystems 2022; 7:e0151821. [PMID: 35311563 PMCID: PMC9040814 DOI: 10.1128/msystems.01518-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Shewanella spp. play important ecological and biogeochemical roles, due in part to their versatile metabolism and swift integration of stimuli. While Shewanella spp. are primarily considered environmental microbes, Shewanella algae is increasingly recognized as an occasional human pathogen. S. algae shares the broad metabolic and respiratory repertoire of Shewanella spp. and thrives in similar ecological niches. In S. algae, nitrate and dimethyl sulfoxide (DMSO) respiration promote biofilm formation strain specifically, with potential implication of taxis and cyclic diguanosine monophosphate (c-di-GMP) signaling. Signal transduction systems in S. algae have not been investigated. To fill these knowledge gaps, we provide here an inventory of the c-di-GMP turnover proteome and chemosensory networks of the type strain S. algae CECT 5071 and compare them with those of 41 whole-genome-sequenced clinical and environmental S. algae isolates. Besides comparative analysis of genetic content and identification of laterally transferred genes, the occurrence and topology of c-di-GMP turnover proteins and chemoreceptors were analyzed. We found S. algae strains to encode 61 to 67 c-di-GMP turnover proteins and 28 to 31 chemoreceptors, placing S. algae near the top in terms of these signaling capacities per Mbp of genome. Most c-di-GMP turnover proteins were predicted to be catalytically active; we describe in them six novel N-terminal sensory domains that appear to control their catalytic activity. Overall, our work defines the c-di-GMP and chemosensory signal transduction pathways in S. algae, contributing to a better understanding of its ecophysiology and establishing S. algae as an auspicious model for the analysis of metabolic and signaling pathways within the genus Shewanella. IMPORTANCEShewanella spp. are widespread aquatic bacteria that include the well-studied freshwater model strain Shewanella oneidensis MR-1. In contrast, the physiology of the marine and occasionally pathogenic species Shewanella algae is poorly understood. Chemosensory and c-di-GMP signal transduction systems integrate environmental stimuli to modulate gene expression, including the switch from a planktonic to sessile lifestyle and pathogenicity. Here, we systematically dissect the c-di-GMP proteome and chemosensory pathways of the type strain S. algae CECT 5071 and 41 additional S. algae isolates. We provide insights into the activity and function of these proteins, including a description of six novel sensory domains. Our work will enable future analyses of the complex, intertwined c-di-GMP metabolism and chemotaxis networks of S. algae and their ecophysiological role.
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Pérez‐Rodríguez S, García‐Aznar JM, Gonzalo‐Asensio J. Microfluidic devices for studying bacterial taxis, drug testing and biofilm formation. Microb Biotechnol 2022; 15:395-414. [PMID: 33645897 PMCID: PMC8867988 DOI: 10.1111/1751-7915.13775] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
Some bacteria have coevolved to establish symbiotic or pathogenic relationships with plants, animals or humans. With human association, the bacteria can cause a variety of diseases. Thus, understanding bacterial phenotypes at the single-cell level is essential to develop beneficial applications. Traditional microbiological techniques have provided great knowledge about these organisms; however, they have also shown limitations, such as difficulties in culturing some bacteria, the heterogeneity of bacterial populations or difficulties in recreating some physical or biological conditions. Microfluidics is an emerging technique that complements current biological assays. Since microfluidics works with micrometric volumes, it allows fine-tuning control of the test conditions. Moreover, it allows the recruitment of three-dimensional (3D) conditions, in which several processes can be integrated and gradients can be generated, thus imitating physiological 3D environments. Here, we review some key microfluidic-based studies describing the effects of different microenvironmental conditions on bacterial response, biofilm formation and antimicrobial resistance. For this aim, we present different studies classified into six groups according to the design of the microfluidic device: (i) linear channels, (ii) mixing channels, (iii) multiple floors, (iv) porous devices, (v) topographic devices and (vi) droplet microfluidics. Hence, we highlight the potential and possibilities of using microfluidic-based technology to study bacterial phenotypes in comparison with traditional methodologies.
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Affiliation(s)
- Sandra Pérez‐Rodríguez
- Aragón Institute of Engineering Research (I3A)Department of Mechanical EngineeringUniversity of ZaragozaZaragoza50018Spain
- Multiscale in Mechanical and Biological Engineering (M2BE)IIS‐AragónZaragozaSpain
- Grupo de Genética de MicobacteriasDepartment of Microbiology, Faculty of MedicineUniversity of ZaragozaIIS AragónZaragoza50009Spain
| | - José Manuel García‐Aznar
- Aragón Institute of Engineering Research (I3A)Department of Mechanical EngineeringUniversity of ZaragozaZaragoza50018Spain
- Multiscale in Mechanical and Biological Engineering (M2BE)IIS‐AragónZaragozaSpain
| | - Jesús Gonzalo‐Asensio
- Grupo de Genética de MicobacteriasDepartment of Microbiology, Faculty of MedicineUniversity of ZaragozaIIS AragónZaragoza50009Spain
- CIBER Enfermedades RespiratoriasInstituto de Salud Carlos IIIMadrid28029Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI)Zaragoza50018Spain
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García-Álvarez R, Vallet-Regí M. Bacteria and cells as alternative nano-carriers for biomedical applications. Expert Opin Drug Deliv 2022; 19:103-118. [PMID: 35076351 PMCID: PMC8802895 DOI: 10.1080/17425247.2022.2029844] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/12/2022] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Nano-based systems have received a lot of attention owing to their particular properties and, hence, have been proposed for a wide variety of biomedical applications. These nanosystems could be potentially employed for diagnosis and therapy of different medical issues. Although these nanomaterials are designed for specific tasks, interactions, and transformations when administered to the human body affect their performance and behavior. In this regard, bacteria and other cells have been presented as alternative nanocarriers. These microorganisms can be genetically modified and customized for a more specific therapeutic action and, in combination with nanomaterials, can lead to bio-hybrids with a unique potential for biomedical purposes. AREAS COVERED Literature regarding bacteria and cells employed in combination with nanomaterials for biomedical applications is revised and discussed in this review. The potential as well as the limitations of these novel bio-hybrid systems are evaluated. Several examples are presented to show the performance of these alternative nanocarriers. EXPERT OPINION Bio-hybrid systems have shown their potential as alternative nanocarriers as they contribute to better performance than traditional nano-based systems. Nevertheless, their limitations must be studied, and advantages and drawbacks assessed before their application to medicine.
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Affiliation(s)
- Rafaela García-Álvarez
- Departamento de Química En Ciencias Farmacéuticas, Unidad de Química Inorgánica Y Bioinorgánica, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre I+12, Madrid, Spain
- Ciber de Bioingeniería, Biomateriales Y Nanomedicina, Madrid, Spain
| | - María Vallet-Regí
- Departamento de Química En Ciencias Farmacéuticas, Unidad de Química Inorgánica Y Bioinorgánica, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre I+12, Madrid, Spain
- Ciber de Bioingeniería, Biomateriales Y Nanomedicina, Madrid, Spain
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Wang H, Zhang M, Xu Y, Zong R, Xu N, Guo M. Agrobacterium fabrum atu0526-Encoding Protein Is the Only Chemoreceptor That Regulates Chemoattraction toward the Broad Antibacterial Agent Formic Acid. BIOLOGY 2021; 10:biology10121345. [PMID: 34943260 PMCID: PMC8698456 DOI: 10.3390/biology10121345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 12/25/2022]
Abstract
Soil-born plant pathogens, especially Agrobacterium, generally navigate their way to hosts through recognition of the root exudates by chemoreceptors. However, there is still a lack of appropriate identification of chemoreceptors and their ligands in Agrobacterium. Here, Atu0526, a sCache-type chemoreceptor from Agrobacterium fabrum C58, was confirmed as the receptor of a broad antibacterial agent, formic acid. The binding of formic acid to Atu0526 was screened using a thermo shift assay and verified using isothermal titration calorimetry. Inconsistent with the previously reported antimicrobial properties, formic acid was confirmed to be a chemoattractant to A. fabrum and could promote its growth. The chemotaxis of A. fabrum C58 toward formic acid was completely lost with the knock-out of atu0526, and regained with the complementation of the gene, indicating that Atu0526 is the only chemoreceptor for formic acid in A. fabrum C58. The affinity of formic acid to Atu0526LBD significantly increased after the arginine at position 115 was replaced by alanine. However, in vivo experiments showed that the R115A mutation fully abolished the chemotaxis of A. fabrum toward formic acid. Molecular docking based on a predicted 3D structure of Atu0526 suggested that the arginine may provide "an anchorage" for formic acid to pull the minor loop, thereby forming a conformational change that generates the ligand-binding signal. Collectively, our findings will promote an understanding of sCache-type chemoreceptors and their signal transduction mechanism.
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Feng H, Fu R, Hou X, Lv Y, Zhang N, Liu Y, Xu Z, Miao Y, Krell T, Shen Q, Zhang R. Chemotaxis of Beneficial Rhizobacteria to Root Exudates: The First Step towards Root-Microbe Rhizosphere Interactions. Int J Mol Sci 2021; 22:ijms22136655. [PMID: 34206311 PMCID: PMC8269324 DOI: 10.3390/ijms22136655] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/28/2022] Open
Abstract
Chemotaxis, the ability of motile bacteria to direct their movement in gradients of attractants and repellents, plays an important role during the rhizosphere colonization by rhizobacteria. The rhizosphere is a unique niche for plant-microbe interactions. Root exudates are highly complex mixtures of chemoeffectors composed of hundreds of different compounds. Chemotaxis towards root exudates initiates rhizobacteria recruitment and the establishment of bacteria-root interactions. Over the last years, important progress has been made in the identification of root exudate components that play key roles in the colonization process, as well as in the identification of the cognate chemoreceptors. In the first part of this review, we summarized the roles of representative chemoeffectors that induce chemotaxis in typical rhizobacteria and discussed the structure and function of rhizobacterial chemoreceptors. In the second part we reviewed findings on how rhizobacterial chemotaxis and other root-microbe interactions promote the establishment of beneficial rhizobacteria-plant interactions leading to plant growth promotion and protection of plant health. In the last part we identified the existing gaps in the knowledge and discussed future research efforts that are necessary to close them.
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Affiliation(s)
- Haichao Feng
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Ruixin Fu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Xueqin Hou
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Yu Lv
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Correspondence: ; Tel.: +86-025-84396477
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Abstract
The natural world has provided a host of materials and inspiration for the field of nanomedicine. By taking design cues from naturally occurring systems, the nanoengineering of advanced biomimetic platforms has significantly accelerated over the past decade. In particular, the biomimicry of bacteria, with their motility, taxis, immunomodulation, and overall dynamic host interactions, has elicited substantial interest and opened up exciting avenues of research. More recently, advancements in genetic engineering have given way to more complex and elegant systems with tunable control characteristics. Furthermore, bacterial derivatives such as membrane ghosts, extracellular vesicles, spores, and toxins have proven advantageous for use in nanotherapeutic applications, as they preserve many of the features from the original bacteria while also offering distinct advantages. Overall, bacteria-inspired nanomedicines can be employed in a range of therapeutic settings, from payload delivery to immunotherapy, and have proven successful in combatting both cancer and infectious disease.
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Affiliation(s)
- Maya Holay
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhongyuan Guo
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Jessica Pihl
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Jiyoung Heo
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Joon Ho Park
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Ronnie H. Fang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Liangfang Zhang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
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Zheng P, Fan M, Liu H, Zhang Y, Dai X, Li H, Zhou X, Hu S, Yang X, Jin Y, Yu N, Guo S, Zhang J, Liang XJ, Cheng K, Li Z. Self-Propelled and Near-Infrared-Phototaxic Photosynthetic Bacteria as Photothermal Agents for Hypoxia-Targeted Cancer Therapy. ACS NANO 2021; 15:1100-1110. [PMID: 33236885 DOI: 10.1021/acsnano.0c08068] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hypoxia can increase the resistance of tumor cells to radiotherapy and chemotherapy. However, the dense extracellular matrix, high interstitial fluid pressure, and irregular blood supply often serve as physical barriers to inhibit penetration of drugs or nanodrugs across tumor blood microvessels into hypoxic regions. Therefore, it is of great significance and highly desirable to improve the efficiency of hypoxia-targeted therapy. In this work, living photosynthetic bacteria (PSB) are utilized as hypoxia-targeted carriers for hypoxic tumor therapy due to their near-infrared (NIR) chemotaxis and their physiological characteristics as facultative aerobes. More interestingly, we discovered that PSB can serve as a kind of photothermal agent to generate heat through nonradiative relaxation pathways due to their strong photoabsorption in the NIR region. Therefore, PSB integrate the properties of hypoxia targeting and photothermal therapeutic agents in an "all-in-one" manner, and no postmodification is needed to achieve hypoxia-targeted cancer therapy. Moreover, as natural bacteria, noncytotoxic PSB were found to enhance immune response that induced the infiltration of cytotoxicity T lymphocyte. Our results indicate PSB specifically accumulate in hypoxic tumor regions, and they show a high efficiency in the elimination of cancer cells. This proof of concept may provide a smart therapeutic system in the field of hypoxia-targeted photothermal therapeutic platforms.
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Affiliation(s)
- Pengli Zheng
- College of Chemistry & Environmental Science, Analytical Chemistry Key Laboratory of Hebei Province, Hebei University, Baoding 071002, P.R. China
| | - Miao Fan
- College of Chemistry & Environmental Science, Analytical Chemistry Key Laboratory of Hebei Province, Hebei University, Baoding 071002, P.R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding 071002, P.R. China
| | - Huifang Liu
- College of Pharmaceutical Science, Hebei University, Baoding 071002, P.R. China
| | - Yinghua Zhang
- College of Chemistry & Environmental Science, Analytical Chemistry Key Laboratory of Hebei Province, Hebei University, Baoding 071002, P.R. China
| | - Xinyue Dai
- College of Chemistry & Environmental Science, Analytical Chemistry Key Laboratory of Hebei Province, Hebei University, Baoding 071002, P.R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding 071002, P.R. China
| | - Hang Li
- College of Chemistry & Environmental Science, Analytical Chemistry Key Laboratory of Hebei Province, Hebei University, Baoding 071002, P.R. China
| | - Xiaohan Zhou
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding 071002, P.R. China
| | - Shiqi Hu
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27607, United States
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Xinjian Yang
- College of Chemistry & Environmental Science, Analytical Chemistry Key Laboratory of Hebei Province, Hebei University, Baoding 071002, P.R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding 071002, P.R. China
| | - Yi Jin
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding 071002, P.R. China
| | - Na Yu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, P.R. China
| | - Shutao Guo
- Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, P.R. China
| | - Jinchao Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding 071002, P.R. China
| | - Xing-Jie Liang
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, P.R. China
| | - Ke Cheng
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27607, United States
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Zhenhua Li
- College of Chemistry & Environmental Science, Analytical Chemistry Key Laboratory of Hebei Province, Hebei University, Baoding 071002, P.R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Institute of Life Science and Green Development, Hebei University, Baoding 071002, P.R. China
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27607, United States
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, North Carolina 27695, United States
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14
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Luo GF, Chen WH, Zeng X, Zhang XZ. Cell primitive-based biomimetic functional materials for enhanced cancer therapy. Chem Soc Rev 2021; 50:945-985. [PMID: 33226037 DOI: 10.1039/d0cs00152j] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cell primitive-based functional materials that combine the advantages of natural substances and nanotechnology have emerged as attractive therapeutic agents for cancer therapy. Cell primitives are characterized by distinctive biological functions, such as long-term circulation, tumor specific targeting, immune modulation etc. Moreover, synthetic nanomaterials featuring unique physical/chemical properties have been widely used as effective drug delivery vehicles or anticancer agents to treat cancer. The combination of these two kinds of materials will catalyze the generation of innovative biomaterials with multiple functions, high biocompatibility and negligible immunogenicity for precise cancer therapy. In this review, we summarize the most recent advances in the development of cell primitive-based functional materials for cancer therapy. Different cell primitives, including bacteria, phages, cells, cell membranes, and other bioactive substances are introduced with their unique bioactive functions, and strategies in combining with synthetic materials, especially nanoparticulate systems, for the construction of function-enhanced biomaterials are also summarized. Furthermore, foreseeable challenges and future perspectives are also included for the future research direction in this field.
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Affiliation(s)
- Guo-Feng Luo
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, P. R. China.
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15
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The phosphorylated regulator of chemotaxis is crucial throughout biofilm biogenesis in Shewanella oneidensis. NPJ Biofilms Microbiomes 2020; 6:54. [PMID: 33188190 PMCID: PMC7666153 DOI: 10.1038/s41522-020-00165-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/13/2020] [Indexed: 02/04/2023] Open
Abstract
The core of the chemotaxis system of Shewanella oneidensis is made of the CheA3 kinase and the CheY3 regulator. When appropriated, CheA3 phosphorylates CheY3, which, in turn, binds to the rotor of the flagellum to modify the swimming direction. In this study, we showed that phosphorylated CheY3 (CheY3-P) also plays an essential role during biogenesis of the solid-surface-associated biofilm (SSA-biofilm). Indeed, in a ΔcheY3 strain, the formation of this biofilm is abolished. Using the phospho-mimetic CheY3D56E mutant, we showed that CheY-P is required throughout the biogenesis of the biofilm but CheY3 phosphorylation is independent of CheA3 during this process. We have recently found that CheY3 interacts with two diguanylate cyclases (DGCs) and with MxdA, the c-di-GMP effector, probably triggering exopolysaccharide synthesis by the Mxd machinery. Here, we discovered two additional DGCs involved in SSA-biofilm development and showed that one of them interacts with CheY3. We therefore propose that CheY3-P acts together with DGCs to control SSA-biofilm formation. Interestingly, two orthologous CheY regulators complement the biofilm defect of a ΔcheY3 strain, supporting the idea that biofilm formation could involve CheY regulators in other bacteria.
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16
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Schmidt CK, Medina-Sánchez M, Edmondson RJ, Schmidt OG. Engineering microrobots for targeted cancer therapies from a medical perspective. Nat Commun 2020; 11:5618. [PMID: 33154372 PMCID: PMC7645678 DOI: 10.1038/s41467-020-19322-7] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Systemic chemotherapy remains the backbone of many cancer treatments. Due to its untargeted nature and the severe side effects it can cause, numerous nanomedicine approaches have been developed to overcome these issues. However, targeted delivery of therapeutics remains challenging. Engineering microrobots is increasingly receiving attention in this regard. Their functionalities, particularly their motility, allow microrobots to penetrate tissues and reach cancers more efficiently. Here, we highlight how different microrobots, ranging from tailor-made motile bacteria and tiny bubble-propelled microengines to hybrid spermbots, can be engineered to integrate sophisticated features optimised for precision-targeting of a wide range of cancers. Towards this, we highlight the importance of integrating clinicians, the public and cancer patients early on in the development of these novel technologies.
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Affiliation(s)
- Christine K Schmidt
- Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester, M20 4GJ, UK.
| | - Mariana Medina-Sánchez
- Institute for Integrative Nanosciences, Leibniz IFW Dresden, Helmholtzstraße 20, 01069, Dresden, Germany.
| | - Richard J Edmondson
- Gynaecological Oncology, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- St. Mary's Hospital, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Level 5, Research Floor, Oxford Road, Manchester, M13 9WL, UK
| | - Oliver G Schmidt
- Institute for Integrative Nanosciences, Leibniz IFW Dresden, Helmholtzstraße 20, 01069, Dresden, Germany.
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17
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Duca DR, Glick BR. Indole-3-acetic acid biosynthesis and its regulation in plant-associated bacteria. Appl Microbiol Biotechnol 2020; 104:8607-8619. [PMID: 32875364 DOI: 10.1007/s00253-020-10869-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 11/28/2022]
Abstract
Numerous studies have reported the stimulation of plant growth following inoculation with an IAA-producing PGPB. However, the specific mode of IAA production by the PGPB is rarely elucidated. In part, this is due to the overwhelming complexity of IAA biosynthesis and regulation. The promiscuity of the enzymes implicated in IAA biosynthesis adds another element of complexity when attempting to decipher their role in IAA biosynthesis. To date, the majority of research on IAA biosynthesis describes three separate pathways classified in terms of their intermediates-indole acetonitrile (IAN), indole acetamide (IAM), and indole pyruvic acid (IPA). Each of these pathways is mediated by a set of enzymes, many of which are traditionally assumed to exist for that specific catalytic role. This lends the possibility of missing other, novel, enzymes that may also incidentally serve that function. Some of these pathways are constitutively expressed, while others are inducible. Some enzymes involved in IAA biosynthesis are known to be regulated by IAA or by IAA precursors, as well as by a multitude of environmental cues. This review aims to provide an update to our current understanding of the biosynthesis and regulation of IAA in bacteria. KEY POINTS: • IAA produced by PGPB improves bacterial stress tolerance and promotes plant growth. • Bacterial IAA biosynthesis is convoluted; multiple interdependent pathways. • Biosynthesis of IAA is regulated by IAA, IAA-precursors, and environmental factors.
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Affiliation(s)
- Daiana R Duca
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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18
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Wu Z, He R, Zhang R, Yuan J. Swarming Motility Without Flagellar Motor Switching by Reversal of Swimming Direction in E. coli. Front Microbiol 2020; 11:1042. [PMID: 32670212 PMCID: PMC7326100 DOI: 10.3389/fmicb.2020.01042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/27/2020] [Indexed: 01/08/2023] Open
Abstract
In a crowded environment such as a bacterial swarm, cells frequently got jammed and came to a stop, but were able to escape the traps by backing up in their moving course with a head-to-tail change (a reversal). Reversals are essential for the expansion of a bacterial swarm. Reversal for a wildtype cell usually involved polymorphic transformation of the flagellar filaments induced by directional switching of the flagellar motors. Here we discovered a new way of reversal in cells without motor switching and characterized its mechanisms. We further found that this type of reversal was not limited to swarmer cells, but also occurred for cells grown in a bulk solution. Therefore, reversal was a general way of escaping when cells got jammed in their natural complex habitats. The new way of reversal we discovered here offered a general strategy for cells to escape traps and explore their environment.
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Affiliation(s)
- Zhengyu Wu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, China
| | - Rui He
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, China
| | - Rongjing Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, China
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, China
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19
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Menon SN, Varuni P, Menon GI. Information integration and collective motility in phototactic cyanobacteria. PLoS Comput Biol 2020; 16:e1007807. [PMID: 32352961 PMCID: PMC7237038 DOI: 10.1371/journal.pcbi.1007807] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 05/19/2020] [Accepted: 03/20/2020] [Indexed: 11/19/2022] Open
Abstract
Cells in microbial colonies integrate information across multiple spatial and temporal scales while sensing environmental cues. A number of photosynthetic cyanobacteria respond in a directional manner to incident light, resulting in the phototaxis of individual cells. Colonies of such bacteria exhibit large-scale changes in morphology, arising from cell-cell interactions, during phototaxis. These interactions occur through type IV pili-mediated physical contacts between cells, as well as through the secretion of complex polysaccharides (‘slime’) that facilitates cell motion. Here, we describe a computational model for such collective behaviour in colonies of the cyanobacterium Synechocystis. The model is designed to replicate observations from recent experiments on the emergent response of the colonies to varied light regimes. It predicts the complex colony morphologies that arise as a result. We ask if changes in colony morphology during phototaxis can be used to infer if cells integrate information from multiple light sources simultaneously, or respond to these light sources separately at each instant of time. We find that these two scenarios cannot be distinguished from the shapes of colonies alone. However, we show that tracking the trajectories of individual cyanobacteria provides a way of determining their mode of response. Our model allows us to address the emergent nature of this class of collective bacterial motion, linking individual cell response to the dynamics of colony shape. Microbial colonies in the wild often consist of large groups of heterogeneous cells that coordinate and integrate information across multiple spatio-temporal scales. We describe a computational model for one such collective behaviour, phototaxis, in colonies of the cyanobacterium Synechocystis that move in response to light. The model replicates experimental observations of the response of cyanobacterial colonies to varied light regimes, and predicts the complex colony morphologies that arise as a result. The results suggest that tracking the trajectories of individual cyanobacteria may provide a way of determining their mode of information integration. Our model allows us to address the emergent nature of this class of collective bacterial motion, linking individual cell response to the large scale dynamics of the colony.
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Affiliation(s)
- Shakti N. Menon
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, Tamil Nadu, India
| | - P. Varuni
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, Tamil Nadu, India
| | - Gautam I. Menon
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai, Tamil Nadu, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India
- Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
- * E-mail:
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20
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Bioinspired reorientation strategies for application in micro/nanorobotic control. JOURNAL OF MICRO-BIO ROBOTICS 2020. [DOI: 10.1007/s12213-020-00130-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractEngineers have recently been inspired by swimming methodologies of microorganisms in creating micro-/nanorobots for biomedical applications. Future medicine may be revolutionized by the application of these small machines in diagnosing, monitoring, and treating diseases. Studies over the past decade have often concentrated on propulsion generation. However, there are many other challenges to address before the practical use of robots at the micro-/nanoscale. The control and reorientation ability of such robots remain as some of these challenges. This paper reviews the strategies of swimming microorganisms for reorientation, including tumbling, reverse and flick, direction control of helical-path swimmers, by speed modulation, using complex flagella, and the help of mastigonemes. Then, inspired by direction change in microorganisms, methods for orientation control for microrobots and possible directions for future studies are discussed. Further, the effects of solid boundaries on the swimming trajectories of microorganisms and microrobots are examined. In addition to propulsion systems for artificial microswimmers, swimming microorganisms are promising sources of control methodologies at the micro-/nanoscale.
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21
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Ud-Din AIMS, Khan MF, Roujeinikova A. Broad Specificity of Amino Acid Chemoreceptor CtaA of Pseudomonas fluorescens Is Afforded by Plasticity of Its Amphipathic Ligand-Binding Pocket. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:612-623. [PMID: 31909676 DOI: 10.1094/mpmi-10-19-0277-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Motile bacteria follow gradients of nutrients or other environmental cues. Many bacterial chemoreceptors that sense exogenous amino acids contain a double Cache (dCache; calcium channels and chemotaxis receptors) ligand-binding domain (LBD). A growing number of studies suggest that broad-specificity dCache-type receptors that sense more than one amino acid are common. Here, we present an investigation into the mechanism by which the dCache LBD of the chemoreceptor CtaA from a plant growth-promoting rhizobacterium, Pseudomonas fluorescens, recognizes several chemically distinct amino acids. We established that amino acids that signal by directly binding to the CtaA LBD include ones with aliphatic (l-alanine, l-proline, l-leucine, l-isoleucine, l-valine), small polar (l-serine), and large charged (l-arginine) side chains. We determined the structure of CtaA LBD in complex with different amino acids, revealing that its ability to recognize a range of structurally and chemically distinct amino acids is afforded by its easily accessible plastic pocket, which can expand or contract according to the size of the ligand side chain. The amphipathic character of the pocket enables promiscuous interactions with both polar and nonpolar amino acids. The results not only clarify the means by which various amino acids are recognized by CtaA but also reveal that a conserved mobile lid over the ligand-binding pocket adopts the same conformation in all complexes, consistent with this being an important and invariant part of the signaling mechanism.
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Affiliation(s)
- Abu I M S Ud-Din
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Australia, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Mohammad F Khan
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Australia, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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22
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Mannan T, Rafique MW, Bhatti MH, Matin A, Ahmad I. Type 1 Fimbriae and Motility Play a Pivotal Role During Interactions of Salmonella typhimurium with Acanthamoeba castellanii (T4 Genotype). Curr Microbiol 2020; 77:836-845. [PMID: 31932998 DOI: 10.1007/s00284-019-01868-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
Amoebic bacterial interactions are the most ancient form of host pathogen interactions. Here, we investigate the fate of Salmonella typhimurium and Acanthamoeba castellanii T4 genotype upon mutual interactions in a nutrition free environment. The role of type 1 fimbriae and motility of S. typhimurium during interactions with A. castellanii has also been investigated. Deletion of genes encoding the type 1 fimbriae subunit FimA, type 1 fimbriae tip protein FimH, chemotaxis regulatory proteins CheA and CheY and major flagella subunits FliC and FljB was performed through homologous recombination. In vitro association, invasion and survival assays of S. typhimurium wild-type and mutant strains were performed upon co-incubation of bacteria with A. castellanii trophozoites in a nutrition free environment. The deletion gene encoding type 1 fimbriae subunit FimA reduced, whereas the deletion of genes encoding flagella subunits FliC and FljB of flagella enhanced the association capability of S. typhimurium with A. castellanii. Invasion of A. castellanii by Salmonella was significantly reduced upon the loss of type 1 fimbriae subunit FimA and type 1 fimbriae tip protein FimH. Co-incubation of S. typhimurium with A. castellanii in phosphate buffered saline medium stimulated the growth of S. typhimurium wild-type and mutant strains. Viable A. castellanii trophozoites count became significantly reduced upon co-incubation with S. typhimurium within 48 h. Type 1 fimbriae play a pivotal role in the adherence of S. typhimurium to the A. castellanii cell surface. Subsequently, this interaction provides S. typhimurium an advantage in growth.
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Affiliation(s)
- Talha Mannan
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences Lahore, Lahore, 54600, Pakistan
| | - Muhammad Wasim Rafique
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences Lahore, Lahore, 54600, Pakistan
| | - Muhammad Haroon Bhatti
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences Lahore, Lahore, 54600, Pakistan
| | - Abdul Matin
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, 11952, Saudi Arabia.,Department of Medical Laboratory Technology, University of Haripur, Hattar Road, Haripur, Khyber Pakhtunkhwa, 22620, Pakistan
| | - Irfan Ahmad
- Institute of Biomedical and Allied Health Sciences, University of Health Sciences Lahore, Lahore, 54600, Pakistan.
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23
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Aschtgen MS, Brennan CA, Nikolakakis K, Cohen S, McFall-Ngai M, Ruby EG. Insights into flagellar function and mechanism from the squid-vibrio symbiosis. NPJ Biofilms Microbiomes 2019; 5:32. [PMID: 31666982 PMCID: PMC6814793 DOI: 10.1038/s41522-019-0106-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023] Open
Abstract
Flagella are essential and multifunctional nanomachines that not only move symbionts towards their tissue colonization site, but also play multiple roles in communicating with the host. Thus, untangling the activities of flagella in reaching, interacting, and signaling the host, as well as in biofilm formation and the establishment of a persistent colonization, is a complex problem. The squid-vibrio system offers a unique model to study the many ways that bacterial flagella can influence a beneficial association and, generally, other bacteria-host interactions. Vibrio fischeri is a bioluminescent bacterium that colonizes the Hawaiian bobtail squid, Euprymna scolopes. Over the last 15 years, the structure, assembly, and functions of V. fischeri flagella, including not only motility and chemotaxis, but also biofilm formation and symbiotic signaling, have been revealed. Here we discuss these discoveries in the perspective of other host-bacteria interactions.
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Affiliation(s)
- Marie-Stephanie Aschtgen
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, 171 76 Sweden
| | - Caitlin A. Brennan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Kiel Nikolakakis
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: Department of Natural and Applied Sciences, University of Wisconsin – Green Bay, Green Bay, WI 54311 USA
| | - Stephanie Cohen
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, and Center for Advanced Surface Analysis, Institute of Earth Sciences, Université de Lausanne, CH-1015 Lausanne, Switzerland
- Kewalo Marine Laboratory, University of Hawaii-Manoa, Honolulu, HI 96813 USA
| | | | - Edward G. Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa, Honolulu, HI 96813 USA
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Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni. Int J Mol Sci 2019; 20:ijms20112701. [PMID: 31159416 PMCID: PMC6600141 DOI: 10.3390/ijms20112701] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 02/07/2023] Open
Abstract
Chemotaxis is an important physiological adaptation that allows many motile bacteria to orientate themselves for better niche adaptation. Chemotaxis is best understood in Escherichia coli. Other representative bacteria, such as Rhodobacter sphaeroides, Pseudomonas species, Helicobacter pylori, and Bacillus subtilis, also have been deeply studied and systemically summarized. These bacteria belong to α-, γ-, ε-Proteobacteria, or Firmicutes. However, β-Proteobacteria, of which many members have been identified as holding chemotactic pathways, lack a summary of chemotaxis. Comamonas testosteroni, belonging to β-Proteobacteria, grows with and chemotactically responds to a range of aromatic compounds. This paper summarizes the latest research on chemotaxis towards aromatic compounds, mainly from investigations of C. testosteroni and other Comamonas species.
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Hashem A, Tabassum B, Fathi Abd Allah E. Bacillus subtilis: A plant-growth promoting rhizobacterium that also impacts biotic stress. Saudi J Biol Sci 2019; 26:1291-1297. [PMID: 31516360 PMCID: PMC6734152 DOI: 10.1016/j.sjbs.2019.05.004] [Citation(s) in RCA: 247] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/18/2019] [Accepted: 05/19/2019] [Indexed: 12/04/2022] Open
Abstract
Plants encounter many biotic agents, such as viruses, bacteria, nematodes, weeds, and arachnids. These entities induce biotic stress in their hosts by disrupting normal metabolism, and as a result, limit plant growth and/or are the cause of plant mortality. Some biotic agents, however, interact symbiotically or synergistically with their host plants. Some microbes can be beneficial to plants and perform the same role as chemical fertilizers and pesticides, acting as a biofertilizer and/or biopesticide. Plant growth promoting rhizobacteria (PGPR) can significantly enhance plant growth and represent a mutually helpful plant-microbe interaction. Bacillus species are a major type of rhizobacteria that can form spores that can survive in the soil for long period of time under harsh environmental conditions. Plant growth is enhanced by PGPR through the induction of systemic resistance, antibiosis, and competitive omission. Thus, the application of microbes can be used to induce systemic resistance in plants against biotic agents and enhance environmental stress tolerance. Bacillus subtilis exhibits both a direct and indirect biocontrol mechanism to suppress disease caused by pathogens. The direct mechanism includes the synthesis of many secondary metabolites, hormones, cell-wall-degrading enzymes, and antioxidants that assist the plant in its defense against pathogen attack. The indirect mechanism includes the stimulation of plant growth and the induction of acquired systemic resistance. Bacillus subtilis can also solubilize soil P, enhance nitrogen fixation, and produce siderophores that promote its growth and suppresses the growth of pathogens. Bacillus subtilis enhances stress tolerance in their plant hosts by inducing the expression of stress-response genes, phytohormones, and stress-related metabolites. The present review discusses the activity of B. subtilis in the rhizosphere, its role as a root colonizer, its biocontrol potential, the associated mechanisms of biocontrol and the ability of B. subtilis to increase crop productivity under conditions of biotic and abiotic stress.
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Key Words
- ABA, abscisic acid
- ACC, 1-aminocyclopropane-1-carboxylate deaminase
- Abiotic stress
- Bacillus subtilis
- Biocontrol mechanism
- Biocontrol potential
- Biotic stress
- GA3, gibberellic acid
- IAA, indole acetic acid
- ISR, induced systemic resistance
- JA, jasmonic acid
- LPs, lipopeptides
- PAL, phenylalanine ammonialyase
- PGP, plant growth promotion
- PGPR, plant growth promoting rhizobacteria
- POD, peroxidase
- PPO, polyphenol oxidase
- Rhizobacteria
- SOD, superoxide dismutase
- VOCs, volatile organic compounds
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Affiliation(s)
- Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia.,Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, Egypt
| | - Baby Tabassum
- Toxicology Laboratory, Department of Zoology, Government Raza PG College, Rampur, UP, India
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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Ramakrishnan B, Venkateswarlu K, Sethunathan N, Megharaj M. Local applications but global implications: Can pesticides drive microorganisms to develop antimicrobial resistance? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:177-189. [PMID: 30445319 DOI: 10.1016/j.scitotenv.2018.11.041] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 05/07/2023]
Abstract
Pesticides are an important agricultural input, and the introduction of new active ingredients with increased efficiencies drives their higher production and consumption worldwide. Inappropriate application and storage of these chemicals often contaminate plant tissues, air, water, or soil environments. The presence of pesticides can lead to developing tolerance, resistance or persistence and even the capabilities to degrade them by the microbiomes of theses environments. The pesticide-degrading microorganisms gain and employ several mechanisms for attraction (chemotaxis), membrane transport systems, efflux pumps, enzymes and genetical make-up with plasmid and chromosome encoded catabolic genes for degradation. Even the evolution and the mechanisms of inheritance for pesticide-degradation as a functional trait in several microorganisms are beginning to be understood. Because of the commonalities in the microbial responses of sensing and uptake, and adaptation due to the selection pressures of pesticides and antimicrobial substances including antibiotics, the pesticide-degraders have higher chances of possessing antimicrobial resistance as a surplus functional trait. This review critically examines the probabilities of pesticide contamination of soil and foliage, the knowledge gaps in the regulation and storage of pesticide chemicals, and the human implications of pesticide-degrading microorganisms with antimicrobial resistance in the global strategy of 'One Health'.
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Affiliation(s)
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapur 515055, India
| | - Nambrattil Sethunathan
- Flat No. 103, Ushodaya Apartments, Sri Venkateswara Officers Colony, Ramakrishnapuram, Secunderabad 500056, India
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER) and Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), University of Newcastle, ATC Building, Callaghan, NSW 2308, Australia.
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Sinorhizobium meliloti Chemoreceptor McpV Senses Short-Chain Carboxylates via Direct Binding. J Bacteriol 2018; 200:JB.00519-18. [PMID: 30201781 DOI: 10.1128/jb.00519-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium meliloti is a soil-dwelling endosymbiont of alfalfa that has eight chemoreceptors to sense environmental stimuli during its free-living state. The functions of two receptors have been characterized, with McpU and McpX serving as general amino acid and quaternary ammonium compound sensors, respectively. Both receptors use a dual Cache (calcium channels and chemotaxis receptors) domain for ligand binding. We identified that the ligand-binding periplasmic region (PR) of McpV contains a single Cache domain. Homology modeling revealed that McpVPR is structurally similar to a sensor domain of a chemoreceptor with unknown function from Anaeromyxobacter dehalogenans, which crystallized with acetate in its binding pocket. We therefore assayed McpV for carboxylate binding and S. meliloti for carboxylate sensing. Differential scanning fluorimetry identified 10 potential ligands for McpVPR Nine of these are monocarboxylates with chain lengths between two and four carbons. We selected seven compounds for capillary assay analysis, which established positive chemotaxis of the S. meliloti wild type, with concentrations of peak attraction at 1 mM for acetate, propionate, pyruvate, and glycolate, and at 100 mM for formate and acetoacetate. Deletion of mcpV or mutation of residues essential for ligand coordination abolished positive chemotaxis to carboxylates. Using microcalorimetry, we determined that dissociation constants of the seven ligands with McpVPR were in the micromolar range. An McpVPR variant with a mutation in the ligand coordination site displayed no binding to isobutyrate or propionate. Of all the carboxylates tested as attractants, only glycolate was detected in alfalfa seed exudates. This work examines the relevance of carboxylates and their sensor to the rhizobium-legume interaction.IMPORTANCE Legumes share a unique association with certain soil-dwelling bacteria known broadly as rhizobia. Through concerted interorganismal communication, a legume allows intracellular infection by its cognate rhizobial species. The plant then forms an organ, the root nodule, dedicated to housing and supplying fixed carbon and nutrients to the bacteria. In return, the engulfed rhizobia, differentiated into bacteroids, fix atmospheric N2 into ammonium for the plant host. This interplay is of great benefit to the cultivation of legumes, such as alfalfa and soybeans, and is initiated by chemotaxis to the host plant. This study on carboxylate chemotaxis contributes to the understanding of rhizobial survival and competition in the rhizosphere and aids the development of commercial inoculants.
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In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides. BMC Genomics 2018; 19:757. [PMID: 30340510 PMCID: PMC6194562 DOI: 10.1186/s12864-018-5151-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/08/2018] [Indexed: 11/23/2022] Open
Abstract
Background An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to external cues, the internal metabolic state of any bacterium plays a major role in determining its ability to reside and thrive in its current environment. Similar to external signaling molecules, cytoplasmic signals are also sensed by methyl-accepting chemotaxis proteins (MCPs) via diverse ligand binding domains. Myxobacteria are complex soil-dwelling social microbes that can perform a variety of physiologic and metabolic activities ranging from gliding motility, sporulation, biofilm formation, carotenoid and secondary metabolite biosynthesis, predation, and slime secretion. To live such complex lifestyles, they have evolved efficient signal transduction systems with numerous one- and two-component regulatory system along with a large array of chemosensory systems to perceive and integrate both external and internal cues. Results Here we report the in silico characterization of a putative energy taxis cluster, Cc-5, which is present in only one amongst 34 known and sequenced myxobacterial genomes, Corallococcus coralloides. In addition, we propose that this energy taxis cluster is involved in oxygen sensing, suggesting that C. coralloides can sense (either directly or indirectly) and then respond to changing concentrations of molecular oxygen. Conclusions This hypothesis is based on the presence of a unique MCP encoded in this gene cluster that contains two different oxygen-binding sensor domains, PAS and globin. In addition, the two monooxygenases encoded in this cluster may contribute to aerobic respiration via ubiquinone biosynthesis, which is part of the cytochrome bc1 complex. Finally, we suggest that this cluster was acquired from Actinobacteria, Gammaproteobacteria or Cyanobacteria. Overall, this in silico study has identified a potentially innovative and evolved mechanism of energy taxis in only one of the myxobacteria, C. coralloides. Electronic supplementary material The online version of this article (10.1186/s12864-018-5151-6) contains supplementary material, which is available to authorized users.
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Bastos-Arrieta J, Revilla-Guarinos A, Uspal WE, Simmchen J. Bacterial Biohybrid Microswimmers. Front Robot AI 2018; 5:97. [PMID: 33500976 PMCID: PMC7805739 DOI: 10.3389/frobt.2018.00097] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
Over millions of years, Nature has optimized the motion of biological systems at the micro and nanoscales. Motor proteins to motile single cells have managed to overcome Brownian motion and solve several challenges that arise at low Reynolds numbers. In this review, we will briefly describe naturally motile systems and their strategies to move, starting with a general introduction that surveys a broad range of developments, followed by an overview about the physical laws and parameters that govern and limit motion at the microscale. We characterize some of the classes of biological microswimmers that have arisen in the course of evolution, as well as the hybrid structures that have been constructed based on these, ranging from Montemagno's ATPase motor to the SpermBot. Thereafter, we maintain our focus on bacteria and their biohybrids. We introduce the inherent properties of bacteria as a natural microswimmer and explain the different principles bacteria use for their motion. We then elucidate different strategies that have been employed for the coupling of a variety of artificial microobjects to the bacterial surface, and evaluate the different effects the coupled objects have on the motion of the "biohybrid." Concluding, we give a short overview and a realistic evaluation of proposed applications in the field.
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Affiliation(s)
| | - Ainhoa Revilla-Guarinos
- Department of General Microbiology, Institute of Microbiology, Technische Universität Dresden, Dresden, Germany
| | - William E Uspal
- Department of Theory of Inhomogeneous Condensed Matter, Max-Planck-Institut für Intelligente Systeme, Stuttgart, Germany.,IV. Institut für Theoretische Physik, Universität Stuttgart, Stuttgart, Germany
| | - Juliane Simmchen
- Physikalische Chemie, Technische Universität Dresden, Dresden, Germany
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Karbalaei A, Cho HJ. Microfluidic Devices Developed for and Inspired by Thermotaxis and Chemotaxis. MICROMACHINES 2018; 9:E149. [PMID: 30424083 PMCID: PMC6187570 DOI: 10.3390/mi9040149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/07/2018] [Accepted: 03/22/2018] [Indexed: 01/08/2023]
Abstract
Taxis has been reported in many cells and microorganisms, due to their tendency to migrate toward favorable physical situations and avoid damage and death. Thermotaxis and chemotaxis are two of the major types of taxis that naturally occur on a daily basis. Understanding the details of the thermo- and chemotactic behavioral response of cells and microorganisms is necessary to reveal the body function, diagnosing diseases and developing therapeutic treatments. Considering the length-scale and range of effectiveness of these phenomena, advances in microfluidics have facilitated taxis experiments and enhanced the precision of controlling and capturing microscale samples. Microfabrication of fluidic chips could bridge the gap between in vitro and in situ biological assays, specifically in taxis experiments. Numerous efforts have been made to develop, fabricate and implement novel microchips to conduct taxis experiments and increase the accuracy of the results. The concepts originated from thermo- and chemotaxis, inspired novel ideas applicable to microfluidics as well, more specifically, thermocapillarity and chemocapillarity (or solutocapillarity) for the manipulation of single- and multi-phase fluid flows in microscale and fluidic control elements such as valves, pumps, mixers, traps, etc. This paper starts with a brief biological overview of the concept of thermo- and chemotaxis followed by the most recent developments in microchips used for thermo- and chemotaxis experiments. The last section of this review focuses on the microfluidic devices inspired by the concept of thermo- and chemotaxis. Various microfluidic devices that have either been used for, or inspired by thermo- and chemotaxis are reviewed categorically.
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Affiliation(s)
- Alireza Karbalaei
- Department of Mechanical and Aerospace Engineering, University of Central Florida, Orlando, FL 32816, USA.
| | - Hyoung Jin Cho
- Department of Mechanical and Aerospace Engineering, University of Central Florida, Orlando, FL 32816, USA.
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31
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Sagawa T, Mashiko R, Yokota Y, Naruse Y, Okada M, Kojima H. Logistic Regression of Ligands of Chemotaxis Receptors Offers Clues about Their Recognition by Bacteria. Front Bioeng Biotechnol 2018; 5:88. [PMID: 29404321 PMCID: PMC5786873 DOI: 10.3389/fbioe.2017.00088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/26/2017] [Indexed: 11/13/2022] Open
Abstract
Because of relative simplicity of signal transduction pathway, bacterial chemotaxis sensory systems have been expected to be applied to biosensor. Tar and Tsr receptors mediate chemotaxis of Escherichia coli and have been studied extensively as models of chemoreception by bacterial two-transmembrane receptors. Such studies are typically conducted using two canonical ligands: l-aspartate for Tar and l-serine for Tsr. However, Tar and Tsr also recognize various analogs of aspartate and serine; it remains unknown whether the mechanism by which the canonical ligands are recognized is also common to the analogs. Moreover, in terms of engineering, it is important to know a single species of receptor can recognize various ligands to utilize bacterial receptor as the sensor for wide range of substances. To answer these questions, we tried to extract the features that are common to the recognition of the different analogs by constructing classification models based on machine-learning. We computed 20 physicochemical parameters for each of 38 well-known attractants that act as chemoreception ligands, and 15 known non-attractants. The classification models were generated by utilizing one or more of the seven physicochemical properties as descriptors. From the classification models, we identified the most effective physicochemical parameter for classification: the minimum electron potential. This descriptor that occurred repeatedly in classification models with the highest accuracies, This descriptor used alone could accurately classify 42/53 of compounds. Among the 11 misclassified compounds, eight contained two carboxyl groups, which is analogous to the structure of characteristic of aspartate analog. When considered separately, 16 of the 17 aspartate analogs could be classified accurately based on the distance between their two carboxyl groups. As shown in these results, we succeed to predict the ligands for bacterial chemoreceptors using only a few descriptors; single descriptor for single receptor. This result might be due to the relatively simple topology of bacterial two-transmembrane receptors compared to the G-protein-coupled receptors of seven-transmembrane receptors. Moreover, this distance between carboxyl groups correlated with the receptor binding affinity of the aspartate analogs. In view of this correlation, we propose a common mechanism underlying ligand recognition by Tar of compounds with two carboxyl groups.
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Affiliation(s)
- Takashi Sagawa
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
| | - Ryota Mashiko
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan.,Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yusuke Yokota
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
| | - Yasushi Naruse
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
| | - Masato Okada
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan.,Department of Complexity Science and Engineering, The University of Tokyo, Kashiwa, Japan
| | - Hiroaki Kojima
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
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32
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Abstract
Although the mechanism of bacterial chemotaxis has been extensively studied in enteric bacteria, the hunt for novel and atypical chemoeffectors (in enterics and distantly-related species alike) has necessitated the modification of classic chemotaxis assays to deal with recalcitrant and potentially toxic chemicals. Here, we describe detailed protocols for the quantitative and qualitative assessment of chemotaxis responses that are categorized into short-term direct population response assays and long-term metabolism-based assays that can be used to identify novel chemoeffector molecules and the specific chemoreceptors involved. We emphasize the importance of behavior-based assays to verify the biochemical and physiological relevance of newly identified chemoeffector-receptor pairs.
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Affiliation(s)
- Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Jayna L Ditty
- Department of Biology, College of Arts and Sciences, University of St. Thomas, St. Paul, MN, USA.
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33
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Varuni P, Menon SN, Menon GI. Phototaxis as a Collective Phenomenon in Cyanobacterial Colonies. Sci Rep 2017; 7:17799. [PMID: 29259320 PMCID: PMC5736714 DOI: 10.1038/s41598-017-18160-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/05/2017] [Indexed: 01/16/2023] Open
Abstract
Cyanobacteria are a diverse group of photosynthetic bacteria that exhibit phototaxis, or motion in response to light. Cyanobacteria such as Synechocystis sp. secrete a mixture of complex polysaccharides that facilitate cell motion, while their type 4 pili allow them to physically attach to each other. Even though cells can respond individually to light, colonies are observed to move collectively towards the light source in dense finger-like projections. We present an agent-based model for cyanobacterial phototaxis that accounts for slime deposition as well as for direct physical links between bacteria, mediated through their type 4 pili. We reproduce the experimentally observed aggregation of cells at the colony boundary as a precursor to finger formation. Our model also describes the changes in colony morphology that occur when the location of the light source is abruptly changed. We find that the overall motion of cells toward light remains relatively unimpaired even if a fraction of them do not sense light, allowing heterogeneous populations to continue to mount a robust collective response to stimuli. Our work suggests that in addition to bio-chemical signalling via diffusible molecules in the context of bacterial quorum-sensing, short-ranged physical interactions may also contribute to collective effects in bacterial motility.
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Affiliation(s)
- P Varuni
- The Institute of Mathematical Sciences, C.I.T Campus, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Shakti N Menon
- The Institute of Mathematical Sciences, C.I.T Campus, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Gautam I Menon
- The Institute of Mathematical Sciences, C.I.T Campus, Taramani, Chennai, 600113, Tamil Nadu, India.
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, Maharashtra, India.
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34
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Matilla MA. Novel pressure sensors and bioreporters in the synthetic biology era. Environ Microbiol 2017; 20:141-144. [PMID: 29230925 DOI: 10.1111/1462-2920.14019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 12/02/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, Granada 18008, Spain
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35
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Nesper J, Hug I, Kato S, Hee CS, Habazettl JM, Manfredi P, Grzesiek S, Schirmer T, Emonet T, Jenal U. Cyclic di-GMP differentially tunes a bacterial flagellar motor through a novel class of CheY-like regulators. eLife 2017; 6:28842. [PMID: 29091032 PMCID: PMC5677366 DOI: 10.7554/elife.28842] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/28/2017] [Indexed: 12/22/2022] Open
Abstract
The flagellar motor is a sophisticated rotary machine facilitating locomotion and signal transduction. Owing to its important role in bacterial behavior, its assembly and activity are tightly regulated. For example, chemotaxis relies on a sensory pathway coupling chemical information to rotational bias of the motor through phosphorylation of the motor switch protein CheY. Using a chemical proteomics approach, we identified a novel family of CheY-like (Cle) proteins in Caulobacter crescentus, which tune flagellar activity in response to binding of the second messenger c-di-GMP to a C-terminal extension. In their c-di-GMP bound conformation Cle proteins interact with the flagellar switch to control motor activity. We show that individual Cle proteins have adopted discrete cellular functions by interfering with chemotaxis and by promoting rapid surface attachment of motile cells. This study broadens the regulatory versatility of bacterial motors and unfolds mechanisms that tie motor activity to mechanical cues and bacterial surface adaptation.
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Affiliation(s)
- Jutta Nesper
- Focal Area of Infection Biology, Biozentrum of the University of Basel, Basel, Switzerland
| | - Isabelle Hug
- Focal Area of Infection Biology, Biozentrum of the University of Basel, Basel, Switzerland
| | - Setsu Kato
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Chee-Seng Hee
- Focal Area of Structural Biology and Biophysics, Biozentrum of the University of Basel, Basel, Switzerland
| | - Judith Maria Habazettl
- Focal Area of Structural Biology and Biophysics, Biozentrum of the University of Basel, Basel, Switzerland
| | - Pablo Manfredi
- Focal Area of Infection Biology, Biozentrum of the University of Basel, Basel, Switzerland
| | - Stephan Grzesiek
- Focal Area of Structural Biology and Biophysics, Biozentrum of the University of Basel, Basel, Switzerland
| | - Tilman Schirmer
- Focal Area of Structural Biology and Biophysics, Biozentrum of the University of Basel, Basel, Switzerland
| | - Thierry Emonet
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,Department of Physics, Yale University, New Haven, United States
| | - Urs Jenal
- Focal Area of Infection Biology, Biozentrum of the University of Basel, Basel, Switzerland
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Abstract
Bacterial motility, and in particular repulsion or attraction toward specific chemicals, has been a subject of investigation for over 100 years, resulting in detailed understanding of bacterial chemotaxis and the corresponding sensory network in many bacterial species. For Escherichia coli most of the current understanding comes from the experiments with low levels of chemotactically active ligands. However, chemotactically inactive chemical species at concentrations found in the human gastrointestinal tract produce significant changes in E. coli's osmotic pressure and have been shown to lead to taxis. To understand how these nonspecific physical signals influence motility, we look at the response of individual bacterial flagellar motors under stepwise changes in external osmolarity. We combine these measurements with a population swimming assay under the same conditions. Unlike for chemotactic response, a long-term increase in swimming/motor speeds is observed, and in the motor rotational bias, both of which scale with the osmotic shock magnitude. We discuss how the speed changes we observe can lead to steady-state bacterial accumulation.
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37
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Salah Ud-Din AIM, Roujeinikova A. Methyl-accepting chemotaxis proteins: a core sensing element in prokaryotes and archaea. Cell Mol Life Sci 2017; 74:3293-3303. [PMID: 28409190 PMCID: PMC11107704 DOI: 10.1007/s00018-017-2514-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/06/2017] [Accepted: 03/24/2017] [Indexed: 11/29/2022]
Abstract
Chemotaxis is the directed motility by means of which microbes sense chemical cues and relocate towards more favorable environments. Methyl-accepting chemotaxis proteins (MCPs) are the most common receptors in bacteria and archaea. They are arranged as trimers of dimers that, in turn, form hexagonal arrays in the cytoplasmic membrane or in the cytoplasm. Several different classes of MCPs have been identified according to their ligand binding region and membrane topology. MCPs have been further classified based on the length and sequence conservation of their cytoplasmic domains. Clusters of membrane-embedded MCPs often localize to the poles of the cell, whereas cytoplasmic MCPs can be targeted to the poles or distributed throughout the cell body. MCPs play an important role in cell survival, pathogenesis, and biodegradation. Bacterial adaptation to diverse environmental conditions promotes diversity among the MCPs. This review summarizes structure, classification, and structure-activity relationship of the known MCP receptors, with a brief overview of the signal transduction mechanisms in bacteria and archaea.
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Affiliation(s)
- Abu Iftiaf Md Salah Ud-Din
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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38
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Colin R, Sourjik V. Emergent properties of bacterial chemotaxis pathway. Curr Opin Microbiol 2017; 39:24-33. [PMID: 28822274 DOI: 10.1016/j.mib.2017.07.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 07/27/2017] [Indexed: 11/17/2022]
Abstract
The chemotaxis pathway of Escherichia coli is the most studied sensory system in prokaryotes. The highly conserved general architecture of this pathway consists of two modules which mediate signal transduction and adaptation. The signal transduction module detects and amplifies changes in environmental conditions and rapidly transmits these signals to control bacterial swimming behavior. The adaptation module gradually resets the activity and sensitivity of the first module after initial stimulation and thereby enables the temporal comparisons necessary for bacterial chemotaxis. Recent experimental and theoretical work has unraveled multiple quantitative features emerging from the interplay between these two modules. This has laid the groundwork for rationalization of these emerging properties in the context of the evolutionary optimization of the chemotactic behavior.
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Affiliation(s)
- Remy Colin
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology, Karl-von-Frisch-strasse 16, 35043 Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology, Karl-von-Frisch-strasse 16, 35043 Marburg, Germany.
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Distinct Domains of CheA Confer Unique Functions in Chemotaxis and Cell Length in Azospirillum brasilense Sp7. J Bacteriol 2017; 199:JB.00189-17. [PMID: 28416707 DOI: 10.1128/jb.00189-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/11/2017] [Indexed: 01/15/2023] Open
Abstract
Chemotaxis is the movement of cells in response to gradients of diverse chemical cues. Motile bacteria utilize a conserved chemotaxis signal transduction system to bias their motility and navigate through a gradient. A central regulator of chemotaxis is the histidine kinase CheA. This cytoplasmic protein interacts with membrane-bound receptors, which assemble into large polar arrays, to propagate the signal. In the alphaproteobacterium Azospirillum brasilense, Che1 controls transient increases in swimming speed during chemotaxis, but it also biases the cell length at division. However, the exact underlying molecular mechanisms for Che1-dependent control of multiple cellular behaviors are not known. Here, we identify specific domains of the CheA1 histidine kinase implicated in modulating each of these functions. We show that CheA1 is produced in two isoforms: a membrane-anchored isoform produced as a fusion with a conserved seven-transmembrane domain of unknown function (TMX) at the N terminus and a soluble isoform similar to prototypical CheA. Site-directed and deletion mutagenesis combined with behavioral assays confirm the role of CheA1 in chemotaxis and implicate the TMX domain in mediating changes in cell length. Fluorescence microscopy further reveals that the membrane-anchored isoform is distributed around the cell surface while the soluble isoform localizes at the cell poles. Together, the data provide a mechanism for the role of Che1 in controlling multiple unrelated cellular behaviors via acquisition of a new domain in CheA1 and production of distinct functional isoforms.IMPORTANCE Chemotaxis provides a significant competitive advantage to bacteria in the environment, and this function has been transferred laterally multiple times, with evidence of functional divergence in different genomic contexts. The molecular principles that underlie functional diversification of chemotaxis in various genomic contexts are unknown. Here, we provide a molecular mechanism by which a single CheA protein controls two unrelated functions: chemotaxis and cell length. Acquisition of this multifunctionality is seemingly a recent evolutionary event. The findings illustrate a mechanism by which chemotaxis function may be co-opted to regulate additional cellular functions.
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Pohl O, Hintsche M, Alirezaeizanjani Z, Seyrich M, Beta C, Stark H. Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients. PLoS Comput Biol 2017; 13:e1005329. [PMID: 28114420 PMCID: PMC5293273 DOI: 10.1371/journal.pcbi.1005329] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 02/06/2017] [Accepted: 12/21/2016] [Indexed: 11/19/2022] Open
Abstract
Many bacteria perform a run-and-tumble random walk to explore their surrounding and to perform chemotaxis. In this article we present a novel method to infer the relevant parameters of bacterial motion from experimental trajectories including the tumbling events. We introduce a stochastic model for the orientation angle, where a shot-noise process initiates tumbles, and analytically calculate conditional moments, reminiscent of Kramers-Moyal coefficients. Matching them with the moments calculated from experimental trajectories of the bacteria E. coli and Pseudomonas putida, we are able to infer their respective tumble rates, the rotational diffusion constants, and the distributions of tumble angles in good agreement with results from conventional tumble recognizers. We also define a novel tumble recognizer, which explicitly quantifies the error in recognizing tumbles. In the presence of a chemical gradient we condition the moments on the bacterial direction of motion and thereby explore the chemotaxis strategy. For both bacteria we recover and quantify the classical chemotactic strategy, where the tumble rate is smallest along the chemical gradient. In addition, for E. coli we detect some cells, which bias their mean tumble angle towards smaller values. Our findings are supported by a scaling analysis of appropriate ratios of conditional moments, which are directly calculated from experimental data. The movement strategies of bacteria have received increasing attention over the past decade, in particular with respect to the tracking of individual cells and the mathematical description of the resulting trajectories. Bacteria typically move in almost straight runs interrupted by sharp turning events (run-and-tumble). In order to characterize their motion on a single cell level, the tumble events in individual trajectories have to be identified. Traditionally, tumble recognition relies on threshold values that are applied to the swimming speed and the reorientation angle. They are chosen in an ad hoc fashion and introduce a certain degree of arbitrariness to the results of statistical motion analyses. Here, we propose a new stochastic model for the orientation angle of a bacterium and formulate conditonal moments, which we determine both in theory and from experimental trajectories. This provides an alternative way of quantifying the bacterial run-and-tumble strategy and of recognizing tumble events. Our approach no longer relies on arbitrarily chosen segmentation thresholds and rigorously quantifies the uncertainty in tumble recognition. We successfully apply our method not only to the paradigmatic case of E. coli but also to trajectories of the soil bacterium Pseudomonas putida, demonstrating that our approach provides a novel way to reliably characterize the tumbling statistics and chemotaxis strategies of bacterial swimmers across different species.
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Affiliation(s)
- Oliver Pohl
- Institute of Theoretical Physics, Technical University Berlin, Berlin, Germany
- * E-mail:
| | - Marius Hintsche
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
| | | | - Maximilian Seyrich
- Institute of Theoretical Physics, Technical University Berlin, Berlin, Germany
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany
| | - Holger Stark
- Institute of Theoretical Physics, Technical University Berlin, Berlin, Germany
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Bacillus subtilis Early Colonization of Arabidopsis thaliana Roots Involves Multiple Chemotaxis Receptors. mBio 2016; 7:mBio.01664-16. [PMID: 27899502 PMCID: PMC5137498 DOI: 10.1128/mbio.01664-16] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Colonization of plant roots by Bacillus subtilis is mutually beneficial to plants and bacteria. Plants can secrete up to 30% of their fixed carbon via root exudates, thereby feeding the bacteria, and in return the associated B. subtilis bacteria provide the plant with many growth-promoting traits. Formation of a biofilm on the root by matrix-producing B. subtilis is a well-established requirement for long-term colonization. However, we observed that cells start forming a biofilm only several hours after motile cells first settle on the plant. We also found that intact chemotaxis machinery is required for early root colonization by B. subtilis and for plant protection. Arabidopsis thaliana root exudates attract B. subtilis in vitro, an activity mediated by the two characterized chemoreceptors, McpB and McpC, as well as by the orphan receptor TlpC. Nonetheless, bacteria lacking these chemoreceptors are still able to colonize the root, suggesting that other chemoreceptors might also play a role in this process. These observations suggest that A. thaliana actively recruits B. subtilis through root-secreted molecules, and our results stress the important roles of B. subtilis chemoreceptors for efficient colonization of plants in natural environments. These results demonstrate a remarkable strategy adapted by beneficial rhizobacteria to utilize carbon-rich root exudates, which may facilitate rhizobacterial colonization and a mutualistic association with the host. Bacillus subtilis is a plant growth-promoting rhizobacterium that establishes robust interactions with roots. Many studies have now demonstrated that biofilm formation is required for long-term colonization. However, we observed that motile B. subtilis mediates the first contact with the roots. These cells differentiate into biofilm-producing cells only several hours after the bacteria first contact the root. Our study reveals that intact chemotaxis machinery is required for the bacteria to reach the root. Many, if not all, of the B. subtilis 10 chemoreceptors are involved in the interaction with the plant. These observations stress the importance of root-bacterium interactions in the B. subtilis lifestyle.
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Gkorezis P, Daghio M, Franzetti A, Van Hamme JD, Sillen W, Vangronsveld J. The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective. Front Microbiol 2016; 7:1836. [PMID: 27917161 PMCID: PMC5116465 DOI: 10.3389/fmicb.2016.01836] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/01/2016] [Indexed: 11/24/2022] Open
Abstract
Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.
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Affiliation(s)
- Panagiotis Gkorezis
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Matteo Daghio
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
- Department of Biological Sciences, Thompson Rivers University, KamloopsBC, Canada
| | - Andrea Franzetti
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
| | | | - Wouter Sillen
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
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43
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Brewster JL, McKellar JLO, Finn TJ, Newman J, Peat TS, Gerth ML. Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringae. Sci Rep 2016; 6:35198. [PMID: 27734909 PMCID: PMC5062169 DOI: 10.1038/srep35198] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/26/2016] [Indexed: 01/26/2023] Open
Abstract
Chemoreceptors enable bacteria to detect chemical signals in the environment and navigate towards niches that are favourable for survival. The sensor domains of chemoreceptors function as the input modules for chemotaxis systems, and provide sensory specificity by binding specific ligands. Cache-like domains are the most common extracellular sensor module in prokaryotes, however only a handful have been functionally or structurally characterised. Here, we have characterised a chemoreceptor Cache-like sensor domain (PscD-SD) from the plant pathogen Pseudomonas syringae pv. actinidiae (Psa). High-throughput fluorescence thermal shift assays, combined with isothermal thermal titration calorimetry, revealed that PscD-SD binds specifically to C2 (glycolate and acetate) and C3 (propionate and pyruvate) carboxylates. We solved the structure of PscD-SD in complex with propionate using X-ray crystallography. The structure reveals the key residues that comprise the ligand binding pocket and dictate the specificity of this sensor domain for C2 and C3 carboxylates. We also demonstrate that all four carboxylate ligands are chemoattractants for Psa, but only two of these (acetate and pyruvate) are utilisable carbon sources. This result suggests that in addition to guiding the bacteria towards nutrients, another possible role for carboxylate sensing is in locating potential sites of entry into the host plant.
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Affiliation(s)
- Jodi L Brewster
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - James L O McKellar
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Thomas J Finn
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Janet Newman
- Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, 3052, Australia
| | - Thomas S Peat
- Biomedical Manufacturing Program, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, 3052, Australia
| | - Monica L Gerth
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
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A Chemotaxis Receptor Modulates Nodulation during the Azorhizobium caulinodans-Sesbania rostrata Symbiosis. Appl Environ Microbiol 2016; 82:3174-84. [PMID: 26994081 DOI: 10.1128/aem.00230-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/14/2016] [Indexed: 01/02/2023] Open
Abstract
UNLABELLED Azorhizobium caulinodans ORS571 is a free-living nitrogen-fixing bacterium which can induce nitrogen-fixing nodules both on the root and the stem of its legume host Sesbania rostrata This bacterium, which is an obligate aerobe that moves by means of a polar flagellum, possesses a single chemotaxis signal transduction pathway. The objective of this work was to examine the role that chemotaxis and aerotaxis play in the lifestyle of the bacterium in free-living and symbiotic conditions. In bacterial chemotaxis, chemoreceptors sense environmental changes and transmit this information to the chemotactic machinery to guide motile bacteria to preferred niches. Here, we characterized a chemoreceptor of A. caulinodans containing an N-terminal PAS domain, named IcpB. IcpB is a soluble heme-binding protein that localized at the cell poles. An icpB mutant strain was impaired in sensing oxygen gradients and in chemotaxis response to organic acids. Compared to the wild-type strain, the icpB mutant strain was also affected in the production of extracellular polysaccharides and impaired in flocculation. When inoculated alone, the icpB mutant induced nodules on S. rostrata, but the nodules formed were smaller and had reduced N2-fixing activity. The icpB mutant failed to nodulate its host when inoculated competitively with the wild-type strain. Together, the results identify chemotaxis and sensing of oxygen by IcpB as key regulators of the A. caulinodans-S. rostrata symbiosis. IMPORTANCE Bacterial chemotaxis has been implicated in the establishment of various plant-microbe associations, including that of rhizobial symbionts with their legume host. The exact signal(s) detected by the motile bacteria that guide them to their plant hosts remain poorly characterized. Azorhizobium caulinodans ORS571 is a diazotroph that is a motile and chemotactic rhizobial symbiont of Sesbania rostrata, where it forms nitrogen-fixing nodules on both the roots and the stems of the legume host. We identify here a chemotaxis receptor sensing oxygen in A. caulinodans that is critical for nodulation and nitrogen fixation on the stems and roots of S. rostrata These results identify oxygen sensing and chemotaxis as key regulators of the A. caulinodans-S. rostrata symbiosis.
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45
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Pal S, Banat F, Almansoori A, Abu Haija M. Review of technologies for biotreatment of refinery wastewaters: progress, challenges and future opportunities. ACTA ACUST UNITED AC 2016. [DOI: 10.1080/21622515.2016.1164252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sreela Pal
- Department of Chemical Engineering, The Petroleum Institute, Abu Dhabi, UAE
| | - Fawzi Banat
- Department of Chemical Engineering, The Petroleum Institute, Abu Dhabi, UAE
| | - Ali Almansoori
- Department of Chemical Engineering, The Petroleum Institute, Abu Dhabi, UAE
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46
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Garcia D, Watts KJ, Johnson MS, Taylor BL. Delineating PAS-HAMP interaction surfaces and signalling-associated changes in the aerotaxis receptor Aer. Mol Microbiol 2016; 100:156-72. [PMID: 26713609 DOI: 10.1111/mmi.13308] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2015] [Indexed: 11/27/2022]
Abstract
The Escherichia coli aerotaxis receptor, Aer, monitors cellular oxygen and redox potential via FAD bound to a cytosolic PAS domain. Here, we show that Aer-PAS controls aerotaxis through direct, lateral interactions with a HAMP domain. This contrasts with most chemoreceptors where signals propagate along the protein backbone from an N-terminal sensor to HAMP. We mapped the interaction surfaces of the Aer PAS, HAMP and proximal signalling domains in the kinase-off state by probing the solvent accessibility of 129 cysteine substitutions. Inaccessible PAS-HAMP surfaces overlapped with a cluster of PAS kinase-on lesions and with cysteine substitutions that crosslinked the PAS β-scaffold to the HAMP AS-2 helix. A refined Aer PAS-HAMP interaction model is presented. Compared to the kinase-off state, the kinase-on state increased the accessibility of HAMP residues (apparently relaxing PAS-HAMP interactions), but decreased the accessibility of proximal signalling domain residues. These data are consistent with an alternating static-dynamic model in which oxidized Aer-PAS interacts directly with HAMP AS-2, enforcing a static HAMP domain that in turn promotes a dynamic proximal signalling domain, resulting in a kinase-off output. When PAS-FAD is reduced, PAS interaction with HAMP is relaxed and a dynamic HAMP and static proximal signalling domain convey a kinase-on output.
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Affiliation(s)
- Darysbel Garcia
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Kylie J Watts
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Mark S Johnson
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Barry L Taylor
- Division of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
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Black WP, Wang L, Davis MY, Yang Z. The orphan response regulator EpsW is a substrate of the DifE kinase and it regulates exopolysaccharide in Myxococcus xanthus. Sci Rep 2015; 5:17831. [PMID: 26639551 PMCID: PMC4671073 DOI: 10.1038/srep17831] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 11/06/2015] [Indexed: 11/17/2022] Open
Abstract
Here we attempted to identify the downstream target of the DifE histidine kinase in the regulation of exopolysaccharide (EPS) production in the Gram-negative bacterium Myxococcus xanthus. This bacterium is an important model system for the studies of Type IV pilus (T4P) because it is motile by social (S) motility which is powered by T4P retraction. EPS is critical for S motility because it is the preferred anchor for T4P retraction in this bacterium. Previous studies identified the Dif chemosensory pathway as crucial for the regulation of EPS production. However, the downstream target of the DifE kinase in this pathway was unknown. In this study, EpsW, an orphan and single-domain response regulator (RR), was identified as a potential DifE target first by bioinformatics. Subsequent experiments demonstrated that epsW is essential for EPS biosynthesis in vivo and that EpsW is directly phosphorylated by DifE in vitro. Targted mutagenesis of epsW suggests that EpsW is unlikely the terminal RR of the Dif pathway. We propose instead that EpsW is an intermediary in a multistep phosphorelay that regulates EPS in M. xanthus.
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Affiliation(s)
- Wesley P Black
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Lingling Wang
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.,College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Manli Y Davis
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Zhaomin Yang
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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48
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Characterization of the Vibrio fischeri Fatty Acid Chemoreceptors, VfcB and VfcB2. Appl Environ Microbiol 2015; 82:696-704. [PMID: 26567312 DOI: 10.1128/aem.02856-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/09/2015] [Indexed: 11/20/2022] Open
Abstract
Bacteria use a wide variety of methyl-accepting chemotaxis proteins (MCPs) to mediate their attraction to or repulsion from different chemical signals in their environment. The bioluminescent marine bacterium Vibrio fischeri is the monospecific symbiont of the Hawaiian bobtail squid, Euprymna scolopes, and encodes a large repertoire of MCPs that are hypothesized to be used during different parts of its complex, multistage lifestyle. Here, we report the initial characterization of two such MCPs from V. fischeri that are responsible for mediating migration toward short- and medium-chain aliphatic (or fatty) acids. These receptors appear to be distributed among only members of the family Vibrionaceae and are likely descended from a receptor that has been lost by the majority of the members of this family. While chemotaxis greatly enhances the efficiency of host colonization by V. fischeri, fatty acids do not appear to be used as a chemical cue during this stage of the symbiosis. This study presents an example of straight-chain fatty acid chemoattraction and contributes to the growing body of characterized MCP-ligand interactions.
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49
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Liu YC, Machuca MA, Beckham SA, Gunzburg MJ, Roujeinikova A. Structural basis for amino-acid recognition and transmembrane signalling by tandem Per-Arnt-Sim (tandem PAS) chemoreceptor sensory domains. ACTA ACUST UNITED AC 2015; 71:2127-36. [PMID: 26457436 DOI: 10.1107/s139900471501384x] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/21/2015] [Indexed: 11/10/2022]
Abstract
Chemotaxis, mediated by methyl-accepting chemotaxis protein (MCP) receptors, plays an important role in the ecology of bacterial populations. This paper presents the first crystallographic analysis of the structure and ligand-induced conformational changes of the periplasmic tandem Per-Arnt-Sim (PAS) sensing domain (PTPSD) of a characterized MCP chemoreceptor. Analysis of the complex of the Campylobacter jejuni Tlp3 PTPSD with isoleucine (a chemoattractant) revealed that the PTPSD is a dimer in the crystal. The two ligand-binding sites are located in the membrane-distal PAS domains on the faces opposite to the dimer interface. Mutagenesis experiments show that the five strongly conserved residues that stabilize the main-chain moiety of isoleucine are essential for binding, suggesting that the mechanism by which this family of chemoreceptors recognizes amino acids is highly conserved. Although the fold and mode of ligand binding of the PTPSD are different from the aspartic acid receptor Tar, the structural analysis suggests that the PTPSDs of amino-acid chemoreceptors are also likely to signal by a piston displacement mechanism. The PTPSD fluctuates between piston (C-terminal helix) `up' and piston `down' states. Binding of an attractant to the distal PAS domain locks it in the closed form, weakening its association with the proximal domain and resulting in the transition of the latter into an open form, concomitant with a downward (towards the membrane) 4 Å piston displacement of the C-terminal helix. In vivo, this movement would generate a transmembrane signal by driving a downward displacement of the transmembrane helix 2 towards the cytoplasm.
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Affiliation(s)
- Yu C Liu
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Mayra A Machuca
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Simone A Beckham
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Menachem J Gunzburg
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Anna Roujeinikova
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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50
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Río-Álvarez I, Muñoz-Gómez C, Navas-Vásquez M, Martínez-García PM, Antúnez-Lamas M, Rodríguez-Palenzuela P, López-Solanilla E. Role of Dickeya dadantii 3937 chemoreceptors in the entry to Arabidopsis leaves through wounds. MOLECULAR PLANT PATHOLOGY 2015; 16:685-98. [PMID: 25487519 PMCID: PMC6638404 DOI: 10.1111/mpp.12227] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Chemotaxis enables bacteria to move towards an optimal environment in response to chemical signals. In the case of plant-pathogenic bacteria, chemotaxis allows pathogens to explore the plant surface for potential entry sites with the ultimate aim to prosper inside plant tissues and to cause disease. Chemoreceptors, which constitute the sensory core of the chemotaxis system, are usually transmembrane proteins which change their conformation when sensing chemicals in the periplasm and transduce the signal through a kinase pathway to the flagellar motor. In the particular case of the soft-rot pathogen Dickeya dadantii 3937, jasmonic acid released in a plant wound has been found to be a strong chemoattractant which drives pathogen entry into the plant apoplast. In order to identify candidate chemoreceptors sensing wound-derived plant compounds, we carried out a bioinformatics search of candidate chemoreceptors in the genome of Dickeya dadantii 3937. The study of the chemotactic response to several compounds and the analysis of the entry process to Arabidopsis leaves of 10 selected mutants in chemoreceptors allowed us to determine the implications of at least two of them (ABF-0020167 and ABF-0046680) in the chemotaxis-driven entry process through plant wounds. Our data suggest that ABF-0020167 and ABF-0046680 may be candidate receptors of jasmonic acid and xylose, respectively.
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Affiliation(s)
- Isabel Río-Álvarez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Parque Científico y Tecnológico de la UPM, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, UPM, Avda, Complutense S/N, 28040, Madrid, Spain
| | - Cristina Muñoz-Gómez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Parque Científico y Tecnológico de la UPM, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, UPM, Avda, Complutense S/N, 28040, Madrid, Spain
| | - Mariela Navas-Vásquez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Parque Científico y Tecnológico de la UPM, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, UPM, Avda, Complutense S/N, 28040, Madrid, Spain
| | - Pedro M Martínez-García
- Área de Genética, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM-UMA-CSIC), Universidad de Málaga, E-29071, Málaga, Spain
| | - María Antúnez-Lamas
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, UPM, Avda, Complutense S/N, 28040, Madrid, Spain
| | - Pablo Rodríguez-Palenzuela
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Parque Científico y Tecnológico de la UPM, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, UPM, Avda, Complutense S/N, 28040, Madrid, Spain
| | - Emilia López-Solanilla
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Parque Científico y Tecnológico de la UPM, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, UPM, Avda, Complutense S/N, 28040, Madrid, Spain
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