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Huang J, Pan X, Yan N. Structural biology and molecular pharmacology of voltage-gated ion channels. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00763-7. [PMID: 39103479 DOI: 10.1038/s41580-024-00763-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2024] [Indexed: 08/07/2024]
Abstract
Voltage-gated ion channels (VGICs), including those for Na+, Ca2+ and K+, selectively permeate ions across the cell membrane in response to changes in membrane potential, thus participating in physiological processes involving electrical signalling, such as neurotransmission, muscle contraction and hormone secretion. Aberrant function or dysregulation of VGICs is associated with a diversity of neurological, psychiatric, cardiovascular and muscular disorders, and approximately 10% of FDA-approved drugs directly target VGICs. Understanding the structure-function relationship of VGICs is crucial for our comprehension of their working mechanisms and role in diseases. In this Review, we discuss how advances in single-particle cryo-electron microscopy have afforded unprecedented structural insights into VGICs, especially on their interactions with clinical and investigational drugs. We present a comprehensive overview of the recent advances in the structural biology of VGICs, with a focus on how prototypical drugs and toxins modulate VGIC activities. We explore how these structures elucidate the molecular basis for drug actions, reveal novel pharmacological sites, and provide critical clues to future drug discovery.
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Affiliation(s)
- Jian Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Xiaojing Pan
- Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, Guangdong, China.
| | - Nieng Yan
- Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, Guangdong, China.
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, China.
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2
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Jegla T, Simonson BT, Spafford JD. A broad survey of choanoflagellates revises the evolutionary history of the Shaker family of voltage-gated K + channels in animals. Proc Natl Acad Sci U S A 2024; 121:e2407461121. [PMID: 39018191 PMCID: PMC11287247 DOI: 10.1073/pnas.2407461121] [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: 04/16/2024] [Accepted: 06/21/2024] [Indexed: 07/19/2024] Open
Abstract
The Shaker family of voltage-gated K+ channels has been thought of as an animal-specific ion channel family that diversified in concert with nervous systems. It comprises four functionally independent gene subfamilies (Kv1-4) that encode diverse neuronal K+ currents. Comparison of animal genomes predicts that only the Kv1 subfamily was present in the animal common ancestor. Here, we show that some choanoflagellates, the closest protozoan sister lineage to animals, also have Shaker family K+ channels. Choanoflagellate Shaker family channels are surprisingly most closely related to the animal Kv2-4 subfamilies which were believed to have evolved only after the divergence of ctenophores and sponges from cnidarians and bilaterians. Structural modeling predicts that the choanoflagellate channels share a T1 Zn2+ binding site with Kv2-4 channels that is absent in Kv1 channels. We functionally expressed three Shakers from Salpingoeca helianthica (SheliKvT1.1-3) in Xenopus oocytes. SheliKvT1.1-3 function only in two heteromultimeric combinations (SheliKvT1.1/1.2 and SheliKvT1.1/1.3) and encode fast N-type inactivating K+ channels with distinct voltage dependence that are most similar to the widespread animal Kv1-encoded A-type Shakers. Structural modeling of the T1 assembly domain supports a preference for heteromeric assembly in a 2:2 stoichiometry. These results push the origin of the Shaker family back into a common ancestor of metazoans and choanoflagellates. They also suggest that the animal common ancestor had at least two distinct molecular lineages of Shaker channels, a Kv1 subfamily lineage predicted from comparison of animal genomes and a Kv2-4 lineage predicted from comparison of animals and choanoflagellates.
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Affiliation(s)
- Timothy Jegla
- Department of Biology, Eberly College of Sciences and Huck Institutes of the Life Sciences, Penn State University, University Park, PA16802
| | - Benjamin T. Simonson
- Department of Biology, Eberly College of Sciences and Huck Institutes of the Life Sciences, Penn State University, University Park, PA16802
| | - J. David Spafford
- Department of Biology, University of Waterloo, Waterloo, ONN2L 3G1, Canada
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3
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Zhou J, Ji X, Wang H, Hsu JC, Hua C, Yang X, Liu Z, Guo H, Huang Y, Li Y, Cai W, Lin X, Ni D. Design of Ultrasound-Driven Charge Interference Therapy for Wound Infection. NANO LETTERS 2024; 24:7868-7878. [PMID: 38912706 PMCID: PMC11334693 DOI: 10.1021/acs.nanolett.4c00930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Wound infections, especially those caused by pathogenic bacteria, present a considerable public health concern due to associated complications and poor therapeutic outcomes. Herein, we developed antibacterial nanoparticles, namely, PGTP, by coordinating guanidine derivatives with a porphyrin-based sonosensitizer. The synthesized PGTP nanoparticles, characterized by their strong positive charge, effectively disrupted the bacterial biosynthesis process through charge interference, demonstrating efficacy against both Gram-negative and Gram-positive bacteria. Additionally, PGTP nanoparticles generated reactive oxygen species under ultrasound stimulation, resulting in the disruption of biofilm integrity and efficient elimination of pathogens. RNA-seq analysis unveiled the detailed mechanism of wound healing, revealing that PGTP nanoparticles, when coupled with ultrasound, impair bacterial metabolism by interfering with the synthesis and transcription of amino acids. This study presents a novel approach to combatting wound infections through ultrasound-driven charge-interfering therapy, facilitated by advanced antibacterial nanomaterials.
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Affiliation(s)
- Jingwei Zhou
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xiuru Ji
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Han Wang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jessica C Hsu
- Departments of Radiology and Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Chen Hua
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xi Yang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Zeyang Liu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Haiyan Guo
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ying Huang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuhan Li
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Weibo Cai
- Departments of Radiology and Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xiaoxi Lin
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Dalong Ni
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou 215163, China
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4
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Biquet-Bisquert A, Carrio B, Meyer N, Fernandes TFD, Abkarian M, Seduk F, Magalon A, Nord AL, Pedaci F. Spatiotemporal dynamics of the proton motive force on single bacterial cells. SCIENCE ADVANCES 2024; 10:eadl5849. [PMID: 38781330 PMCID: PMC11114223 DOI: 10.1126/sciadv.adl5849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Electrochemical gradients across biological membranes are vital for cellular bioenergetics. In bacteria, the proton motive force (PMF) drives essential processes like adenosine triphosphate production and motility. Traditionally viewed as temporally and spatially stable, recent research reveals a dynamic PMF behavior at both single-cell and community levels. Moreover, the observed lateral segregation of respiratory complexes could suggest a spatial heterogeneity of the PMF. Using a light-activated proton pump and detecting the activity of the bacterial flagellar motor, we perturb and probe the PMF of single cells. Spatially homogeneous PMF perturbations reveal millisecond-scale temporal dynamics and an asymmetrical capacitive response. Localized perturbations show a rapid lateral PMF homogenization, faster than proton diffusion, akin to the electrotonic potential spread observed in passive neurons, explained by cable theory. These observations imply a global coupling between PMF sources and consumers along the membrane, precluding sustained PMF spatial heterogeneity but allowing for rapid temporal changes.
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Affiliation(s)
- Anaïs Biquet-Bisquert
- Centre de Biologie Structurale, Université de Montpellier, CNRS, INSERM. Montpellier, France
| | - Baptiste Carrio
- Centre de Biologie Structurale, Université de Montpellier, CNRS, INSERM. Montpellier, France
| | - Nathan Meyer
- Centre de Biologie Structurale, Université de Montpellier, CNRS, INSERM. Montpellier, France
| | - Thales F. D. Fernandes
- Centre de Biologie Structurale, Université de Montpellier, CNRS, INSERM. Montpellier, France
| | - Manouk Abkarian
- Centre de Biologie Structurale, Université de Montpellier, CNRS, INSERM. Montpellier, France
| | - Farida Seduk
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13402 Marseille, France
| | - Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, 13402 Marseille, France
| | - Ashley L. Nord
- Centre de Biologie Structurale, Université de Montpellier, CNRS, INSERM. Montpellier, France
| | - Francesco Pedaci
- Centre de Biologie Structurale, Université de Montpellier, CNRS, INSERM. Montpellier, France
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Gao J, Zhou K, Li H, Li Y, Yang K, Wang W. Intermittent proton bursts of single lactic acid bacteria. Chem Sci 2024; 15:3516-3523. [PMID: 38455010 PMCID: PMC10915832 DOI: 10.1039/d3sc06238d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 03/09/2024] Open
Abstract
Lactic acid bacteria are a kind of probiotic microorganisms that efficiently convert carbohydrates to lactic acids, thus playing essential roles in fermentation and food industry. While conventional wisdom often suggests continuous release of protons from bacteria during acidification, here we developed a methodology to measure the dynamics of proton release at the single bacteria level, and report on the discovery of a proton burst phenomenon, i.e., the intermittent efflux of protons, of single Lactobacillus plantarum bacteria. When placing an individual bacterium in an oil-sealed microwell, efflux and accumulation of protons consequently reduced the pH in the confined extracellular medium, which was monitored with fluorescent pH indicators in a high-throughput and real-time manner. In addition to the slow and continuous proton release behavior (as expected), stochastic and intermittent proton burst events were surprisingly observed with a typical timescale of several seconds. It was attributed to the regulatory response of bacteria by activating H+-ATPase to compensate the stochastic and transient depolarizations of membrane potential. These findings not only revealed an unprecedented proton burst phenomenon in lactic acid bacteria, but also shed new lights on the intrinsic roles of H+-ATPase in membrane potential homeostasis, with implications for both fermentation industry and bacterial electrophysiology.
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Affiliation(s)
- Jia Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Kai Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Haoran Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Yaohua Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Kairong Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University Nanjing 210023 China
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6
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Sarkar D, Bhunia A. Delineating the Role of GxxxG Motif in Amyloidogenesis: A New Perspective in Targeting Amyloid-Beta Mediated AD Pathogenesis. ACS BIO & MED CHEM AU 2024; 4:4-19. [PMID: 38404748 PMCID: PMC10885112 DOI: 10.1021/acsbiomedchemau.3c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 02/27/2024]
Abstract
The pursuit of a novel structural motif that can shed light on the key functional attributes is a primary focus in the study of protein folding disorders. Decades of research on Alzheimer's disease (AD) have centered on the Amyloid β (Aβ) pathway, highlighting its significance in understanding the disorder. The diversity in the Aβ pathway and the possible silent tracks which are yet to discover, makes it exceedingly intimidating to the interdisciplinary scientific community. Over the course of AD research, Aβ has consistently been at the forefront of scientific inquiry and discussion. In this review, we epitomize the role of a potential structural motif (GxxxG motif) that may provide a new horizon to the Aβ conflict. We emphasize on how comprehensive understanding of this motif from a structure-function perspective may pave the way for designing novel therapeutics intervention in AD and related diseases.
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Affiliation(s)
- Dibakar Sarkar
- Department of Chemical Sciences, Bose Institute, Unified Academic Campus, Sector V, Salt Lake EN
80, Kolkata 700 091, India
| | - Anirban Bhunia
- Department of Chemical Sciences, Bose Institute, Unified Academic Campus, Sector V, Salt Lake EN
80, Kolkata 700 091, India
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7
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García-Morales A, Balleza D. Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors. J Mol Evol 2023; 91:819-836. [PMID: 37955698 DOI: 10.1007/s00239-023-10140-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
Abstract
The voltage-sensing domain (VSD) is a module capable of responding to changes in the membrane potential through conformational changes and facilitating electromechanical coupling to open a pore gate, activate proton permeation pathways, or promote enzymatic activity in some membrane-anchored phosphatases. To carry out these functions, this module acts cooperatively through conformational changes. The VSD is formed by four transmembrane segments (S1-S4) but the S4 segment is critical since it carries positively charged residues, mainly Arg or Lys, which require an aqueous environment for its proper function. The discovery of this module in voltage-gated ion channels (VGICs), proton channels (Hv1), and voltage sensor-containing phosphatases (VSPs) has expanded our understanding of the principle of modularity in the voltage-sensing mechanism of these proteins. Here, by sequence comparison and the evaluation of the relationship between sequence composition, intrinsic flexibility, and structural analysis in 14 selected representatives of these three major protein groups, we report five interesting differences in the folding patterns of the VSD both in prokaryotes and eukaryotes. Our main findings indicate that this module is highly conserved throughout the evolutionary scale, however: (1) segments S1 to S3 in eukaryotes are significantly more hydrophobic than those present in prokaryotes; (2) the S4 segment has retained its hydrophilic character; (3) in eukaryotes the extramembranous linkers are significantly larger and more flexible in comparison with those present in prokaryotes; (4) the sensors present in the kHv1 proton channel and the ciVSP phosphatase, both of eukaryotic origin, exhibit relationships of flexibility and folding patterns very close to the typical ones found in prokaryotic voltage sensors; and (5) archaeal channels KvAP and MVP have flexibility profiles which are clearly contrasting in the S3-S4 region, which could explain their divergent activation mechanisms. Finally, to elucidate the obscure origins of this module, we show further evidence for a possible connection between voltage sensors and TolQ proteins.
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Affiliation(s)
- Abigail García-Morales
- Tecnológico Nacional de México, Instituto Tecnológico de Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Calz. Miguel Angel de Quevedo 2779, Col. Formando Hogar, CP. 91897, Veracruz, Ver, Mexico
| | - Daniel Balleza
- Tecnológico Nacional de México, Instituto Tecnológico de Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Calz. Miguel Angel de Quevedo 2779, Col. Formando Hogar, CP. 91897, Veracruz, Ver, Mexico.
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8
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Affiliation(s)
- Pamela Lyon
- Faculty of Arts, Business, Law and Economics, University of Adelaide, Adelaide, SA, 5000, Australia.
| | - Ken Cheng
- School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
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Muñoz-Rodríguez D, Bourqqia-Ramzi M, García-Esteban MT, Murciano-Cespedosa A, Vian A, Lombardo-Hernández J, García-Pérez P, Conejero F, Mateos González Á, Geuna S, Herrera-Rincon C. Bioelectrical State of Bacteria Is Linked to Growth Dynamics and Response to Neurotransmitters: Perspectives for the Investigation of the Microbiota-Brain Axis. Int J Mol Sci 2023; 24:13394. [PMID: 37686197 PMCID: PMC10488255 DOI: 10.3390/ijms241713394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Inter-cellular communication is mediated by a sum of biochemical, biophysical, and bioelectrical signals. This might occur not only between cells belonging to the same tissue and/or animal species but also between cells that are, from an evolutionary point of view, far away. The possibility that bioelectrical communication takes place between bacteria and nerve cells has opened exciting perspectives in the study of the gut microbiota-brain axis. The aim of this paper is (i) to establish a reliable method for the assessment of the bioelectrical state of two bacterial strains: Bacillus subtilis (B. subtilis) and Limosilactobacillus reuteri (L. reuteri); (ii) to monitor the bacterial bioelectrical profile throughout its growth dynamics; and (iii) to evaluate the effects of two neurotransmitters (glutamate and γ-aminobutyric acid-GABA) on the bioelectrical signature of bacteria. Our results show that membrane potential (Vmem) and the proliferative capacity of the population are functionally linked in B. subtilis in each phase of the cell cycle. Remarkably, we demonstrate that bacteria respond to neural signals by changing Vmem properties. Finally, we show that Vmem changes in response to neural stimuli are present also in a microbiota-related strain L. reuteri. Our proof-of-principle data reveal a new methodological approach for the better understanding of the relation between bacteria and the brain, with a special focus on gut microbiota. Likewise, this approach will open exciting perspectives in the study of the inter-cellular mechanisms which regulate the bi-directional communication between bacteria and neurons and, ultimately, for designing gut microbiota-brain axis-targeted treatments for neuropsychiatric diseases.
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Affiliation(s)
- David Muñoz-Rodríguez
- Biomathematics Unit, Data Analysis & Computational Tools for Biology Research Group, Department of Biodiversity, Ecology & Evolution, and Modeling, Complutense University of Madrid, 28040 Madrid, Spain
- Molecular Biotechnology Center, University of Turin, 10126 Turin, Italy
| | - Marwane Bourqqia-Ramzi
- Biomathematics Unit, Data Analysis & Computational Tools for Biology Research Group, Department of Biodiversity, Ecology & Evolution, and Modeling, Complutense University of Madrid, 28040 Madrid, Spain
- Molecular Biotechnology Center, University of Turin, 10126 Turin, Italy
| | - Maria Teresa García-Esteban
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, 28040 Madrid, Spain (A.V.)
| | - Antonio Murciano-Cespedosa
- Biomathematics Unit, Data Analysis & Computational Tools for Biology Research Group, Department of Biodiversity, Ecology & Evolution, and Modeling, Complutense University of Madrid, 28040 Madrid, Spain
- Neuro-Computing and Neuro-Robotics Research Group, Neural Plasticity Research Group Instituto Investigación Sanitaria Hospital Clínico San Carlos (IdISSC), Complutense University of Madrid, 28040 Madrid, Spain
| | - Alejandro Vian
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, 28040 Madrid, Spain (A.V.)
| | - Juan Lombardo-Hernández
- Biomathematics Unit, Data Analysis & Computational Tools for Biology Research Group, Department of Biodiversity, Ecology & Evolution, and Modeling, Complutense University of Madrid, 28040 Madrid, Spain
- Molecular Biotechnology Center, University of Turin, 10126 Turin, Italy
| | - Pablo García-Pérez
- Biomathematics Unit, Data Analysis & Computational Tools for Biology Research Group, Department of Biodiversity, Ecology & Evolution, and Modeling, Complutense University of Madrid, 28040 Madrid, Spain
| | - Francisco Conejero
- Biomathematics Unit, Data Analysis & Computational Tools for Biology Research Group, Department of Biodiversity, Ecology & Evolution, and Modeling, Complutense University of Madrid, 28040 Madrid, Spain
| | - Álvaro Mateos González
- NYU-ECNU Institute of Mathematical Sciences, Shanghai New York University, Shanghai 200122, China;
| | - Stefano Geuna
- Molecular Biotechnology Center, University of Turin, 10126 Turin, Italy
| | - Celia Herrera-Rincon
- Biomathematics Unit, Data Analysis & Computational Tools for Biology Research Group, Department of Biodiversity, Ecology & Evolution, and Modeling, Complutense University of Madrid, 28040 Madrid, Spain
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10
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Silic MR, Zhang G. Bioelectricity in Developmental Patterning and Size Control: Evidence and Genetically Encoded Tools in the Zebrafish Model. Cells 2023; 12:cells12081148. [PMID: 37190057 DOI: 10.3390/cells12081148] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Developmental patterning is essential for regulating cellular events such as axial patterning, segmentation, tissue formation, and organ size determination during embryogenesis. Understanding the patterning mechanisms remains a central challenge and fundamental interest in developmental biology. Ion-channel-regulated bioelectric signals have emerged as a player of the patterning mechanism, which may interact with morphogens. Evidence from multiple model organisms reveals the roles of bioelectricity in embryonic development, regeneration, and cancers. The Zebrafish model is the second most used vertebrate model, next to the mouse model. The zebrafish model has great potential for elucidating the functions of bioelectricity due to many advantages such as external development, transparent early embryogenesis, and tractable genetics. Here, we review genetic evidence from zebrafish mutants with fin-size and pigment changes related to ion channels and bioelectricity. In addition, we review the cell membrane voltage reporting and chemogenetic tools that have already been used or have great potential to be implemented in zebrafish models. Finally, new perspectives and opportunities for bioelectricity research with zebrafish are discussed.
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Affiliation(s)
- Martin R Silic
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - GuangJun Zhang
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Inflammation, Immunology and Infectious Diseases (PI4D), Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, 625 Harrison Street, West Lafayette, IN 47907, USA
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11
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Lane BJ, Pliotas C. Approaches for the modulation of mechanosensitive MscL channel pores. Front Chem 2023; 11:1162412. [PMID: 37021145 PMCID: PMC10069478 DOI: 10.3389/fchem.2023.1162412] [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: 02/09/2023] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
MscL was the first mechanosensitive ion channel identified in bacteria. The channel opens its large pore when the turgor pressure of the cytoplasm increases close to the lytic limit of the cellular membrane. Despite their ubiquity across organisms, their importance in biological processes, and the likelihood that they are one of the oldest mechanisms of sensory activation in cells, the exact molecular mechanism by which these channels sense changes in lateral tension is not fully understood. Modulation of the channel has been key to understanding important aspects of the structure and function of MscL, but a lack of molecular triggers of these channels hindered early developments in the field. Initial attempts to activate mechanosensitive channels and stabilize functionally relevant expanded or open states relied on mutations and associated post-translational modifications that were often cysteine reactive. These sulfhydryl reagents positioned at key residues have allowed the engineering of MscL channels for biotechnological purposes. Other studies have modulated MscL by altering membrane properties, such as lipid composition and physical properties. More recently, a variety of structurally distinct agonists have been shown bind to MscL directly, close to a transmembrane pocket that has been shown to have an important role in channel mechanical gating. These agonists have the potential to be developed further into antimicrobial therapies that target MscL, by considering the structural landscape and properties of these pockets.
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Affiliation(s)
- Benjamin J. Lane
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Christos Pliotas
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester, United Kingdom
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
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12
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Elices I, Kulkarni A, Escoubet N, Pontani LL, Prevost AM, Brette R. An electrophysiological and kinematic model of Paramecium, the "swimming neuron". PLoS Comput Biol 2023; 19:e1010899. [PMID: 36758112 PMCID: PMC9946239 DOI: 10.1371/journal.pcbi.1010899] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 02/22/2023] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
Paramecium is a large unicellular organism that swims in fresh water using cilia. When stimulated by various means (mechanically, chemically, optically, thermally), it often swims backward then turns and swims forward again in a new direction: this is called the avoiding reaction. This reaction is triggered by a calcium-based action potential. For this reason, several authors have called Paramecium the "swimming neuron". Here we present an empirically constrained model of its action potential based on electrophysiology experiments on live immobilized paramecia, together with simultaneous measurement of ciliary beating using particle image velocimetry. Using these measurements and additional behavioral measurements of free swimming, we extend the electrophysiological model by coupling calcium concentration to kinematic parameters, turning it into a swimming model. In this way, we obtain a model of autonomously behaving Paramecium. Finally, we demonstrate how the modeled organism interacts with an environment, can follow gradients and display collective behavior. This work provides a modeling basis for investigating the physiological basis of autonomous behavior of Paramecium in ecological environments.
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Affiliation(s)
- Irene Elices
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Anirudh Kulkarni
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Department of Bioengineering and Centre for Neurotechnology, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Nicolas Escoubet
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris
| | - Léa-Laetitia Pontani
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris
| | - Alexis Michel Prevost
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris
| | - Romain Brette
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- * E-mail:
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13
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Down the membrane hole: Ion channels in protozoan parasites. PLoS Pathog 2022; 18:e1011004. [PMID: 36580479 PMCID: PMC9799330 DOI: 10.1371/journal.ppat.1011004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Parasitic diseases caused by protozoans are highly prevalent around the world, disproportionally affecting developing countries, where coinfection with other microorganisms is common. Control and treatment of parasitic infections are constrained by the lack of specific and effective drugs, plus the rapid emergence of resistance. Ion channels are main drug targets for numerous diseases, but their potential against protozoan parasites is still untapped. Ion channels are membrane proteins expressed in all types of cells, allowing for the flow of ions between compartments, and regulating cellular functions such as membrane potential, excitability, volume, signaling, and death. Channels and transporters reside at the interface between parasites and their hosts, controlling nutrient uptake, viability, replication, and infectivity. To understand how ion channels control protozoan parasites fate and to evaluate their suitability for therapeutics, we must deepen our knowledge of their structure, function, and modulation. However, methodological approaches commonly used in mammalian cells have proven difficult to apply in protozoans. This review focuses on ion channels described in protozoan parasites of clinical relevance, mainly apicomplexans and trypanosomatids, highlighting proteins for which molecular and functional evidence has been correlated with their physiological functions.
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14
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Telesh IV, Skarlato SO. Harmful Blooms of Potentially Toxic Dinoflagellates in the Baltic Sea: Ecological, Cellular, and Molecular Background. RUSS J ECOL+ 2022. [DOI: 10.1134/s1067413622060157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Mineralogy, morphology, and reaction kinetics of ureolytic bio-cementation in the presence of seawater ions and varying soil materials. Sci Rep 2022; 12:17100. [PMID: 36224231 PMCID: PMC9556692 DOI: 10.1038/s41598-022-21268-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/26/2022] [Indexed: 01/04/2023] Open
Abstract
Microbially-induced calcium carbonate precipitation (MICP) is a bio-cementation process that can improve the engineering properties of granular soils through the precipitation of calcium carbonate (CaCO3) minerals on soil particle surfaces and contacts. The technology has advanced rapidly as an environmentally conscious soil improvement method, however, our understanding of the effect of changes in field-representative environmental conditions on the physical and chemical properties of resulting precipitates has remained limited. An improved understanding of the effect of subsurface geochemical and soil conditions on process reaction kinetics and the morphology and mineralogy of bio-cementation may be critical towards enabling successful field-scale deployment of the technology and improving our understanding of the long-term chemical permanence of bio-cemented soils in different environments. In this study, thirty-five batch experiments were performed to specifically investigate the influence of seawater ions and varying soil materials on the mineralogy, morphology, and reaction kinetics of ureolytic bio-cementation. During experiments, differences in reaction kinetics were quantified to identify conditions inhibiting CaCO3 precipitation and ureolysis. Following experiments, scanning electron microscopy, x-ray diffraction, and chemical composition analyses were employed to quantify differences in mineralogical compositions and material morphology. Ions present in seawater and variations in soil materials were shown to significantly influence ureolytic activity and precipitate mineralogy and morphology, however, calcite remained the predominant CaCO3 polymorph in all experiments with relative percentages exceeding 80% by mass in all precipitates.
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16
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Shankar U, Mishra SK, Jain N, Tawani A, Yadav P, Kumar A. Ni +2 permease system of Helicobacter pylori contains highly conserved G-quadruplex motifs. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105298. [PMID: 35526824 DOI: 10.1016/j.meegid.2022.105298] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 03/30/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
The genome of a micro-organism contains all the information required for its survival inside its host cells. The guanine rich regions of the genome can form stable G-quadruplex structures that act as the regulators of gene expression. Herein, the completely sequenced genomes of Helicobacter pylori were explored for the identification and characterization of the conserved G-quadruplex motifs in this gastrointestinal pathogen. Initial in silico analysis revealed the presence of ~8241 GQ motifs in the H. pylori genome. Metal binding proteins of H. pylori are significantly enriched in the GQ motifs. Our study emphasizes the identification and characterization of four highly conserved G-quadruplex forming motifs (HPGQs) in the nickel transporter genes (nixA, niuB1, niuB2, and niuD) of the H. pylori. Nickel is a virulence determinant in H. pylori and is required as a co-factor for the urease and [NiFe] hydrogenase enzymes that are crucial for its survival in the stomach lining of humans. The presence of GQ motifs in these nickel transporter genes can affect their expression and may alter the functioning of Urease and [NiFe] hydrogenase. Similar to human and virus G-quadruplexes, targeting these conserved PGQs with bioactive molecules may represent a novel therapeutic avenue for combating infection of H. pylori. The identified HPGQs were characterized in-vitro by using CD spectroscopy, electrophoresis technique, and NMR spectroscopy at both acidic (4.5) and neutral pH (7.0). ITC revealed the specific interaction of these HPGQs with high affinity to the known G-quadruplex binding ligand, TMPyP4. The mTFP based reporter assay showed decrease in the gene expression of mTFP in the TMPyP4 treated cells as compared to the untreated and further affirmed the formation of stable G-quadruplex structures in the HPGQ motifs in vivo. This is the first report for characterizing G-quadruplex motifs in nickel transport-associated genes in the H. pylori bacterium.
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Affiliation(s)
- Uma Shankar
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Subodh Kumar Mishra
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Neha Jain
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Arpita Tawani
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering Indore, Simrol, Indore, Madhya Pradesh 455235, India.
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17
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Abstract
The noncanonical structures, G-quadruplexes (GQs), formed in the guanine-rich region of nucleic acids regulate various biological and molecular functions in prokaryotes and eukaryotes. Neisseria meningitidis is a commensal residing in a human's upper respiratory tract but occasionally becomes virulent, causing life-threatening septicemia and meningitis. The factors causing these changes in phenotypes are not fully understood. At the molecular level, regulatory components help in a clearer understanding of the pathogen's virulence and pathogenesis. Herein, genome analysis followed by biophysical assays and cell-based experiments revealed the presence of conserved GQ motifs in N. meningitidis. These GQs are linked to the essential genes involved in cell adhesion, pathogenesis, virulence, transport, DNA repair, and recombination. Primer extension stop assay, reporter assays, and quantitative real-time polymerase chain reaction (qRT-PCR) further affirmed the formation of stable GQs in vitro and in vivo. These results support the existence of evolutionarily conserved GQ motifs in N. meningitidis and uphold the usage of GQ-specific ligands as novel antimeningococcal therapeutics.
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18
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Gunina A, Kuzyakov Y. From energy to (soil organic) matter. GLOBAL CHANGE BIOLOGY 2022; 28:2169-2182. [PMID: 34978126 DOI: 10.1111/gcb.16071] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
In this concept paper, we propose a new view on soil organic matter (SOM) formation: microorganisms use most of the organics entering the soil as energy rather than as a source of carbon (C), while SOM accumulates as a residual by-product because the microbial energy investment in its decomposition exceeds the energy gain. During the initial stages of decomposition, the nominal oxidation state of C (NOSC) in remaining litter decreases, and the energy content increases. This reflects the rapid mineralization of available compounds with positive and neutral NOSC (carboxylic acids, sugars, some amino acids). Consequently, the NOSC of the remaining compounds drops to -0.3 units, and the oxidation rate decreases due to the residual relative accumulation of aromatic and aliphatic compounds (which are hydrolized later) and entombment of the necromass. Ultimately, incompletely decomposed plant residues will have 1%-2.5% more energy per C unit than the initial litter. The linear decrease in energy density of a broad range of organic substances by 106 kJ mol-1 C per NOSC unit upon oxidation is supported by experimental data on litter decomposition. Preferential recycling of energy-rich reduced (lipids, aromatics, certain amino acids, amino sugars) and the microbial degradation of oxidized compounds (carboxylic acids) also energetically enrich SOM. Despite the high energy content, the availability of energy stored in SOM is lower than in litter. This explains why SOM is not fully mineralized (thermodynamically unfavorable), especially in the absence of plant C to provide new energy (e.g., in bare soil). Energy from litter activates decomposers to mine nutrients stored in SOM (the main ecological function of priming effects) because the nutrient content in SOM is 2-5 times higher than that of litter. This results in only 0.4%-5% year-1 of litter-derived C being sequestered in SOM, whereas SOM stores 1%-10% year-1 of the total litter-derived energy. Thus, the energy captured by photosynthesis is the main reason why microorganisms utilize organic matter, whereby SOM is merely a residual by-product of nutrient storage and a mediator of energy fluxes.
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Affiliation(s)
- Anna Gunina
- Department of Environmental Chemistry, University of Kassel, Witzenhausen, Germany
- Tyumen State University, Tyumen, Russian Federation
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Göttingen, Germany
- Peoples Friendship University of Russia (RUDN University), Moscow, Russian Federation
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19
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Bavaharan A, Skilbeck C. Electrical signalling in prokaryotes and its convergence with quorum sensing in Bacillus. Bioessays 2022; 44:e2100193. [PMID: 35195292 DOI: 10.1002/bies.202100193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
The importance of electrical signalling in bacteria is an emerging paradigm. Bacillus subtilis biofilms exhibit electrical communication that regulates metabolic activity and biofilm growth. Starving cells initiate oscillatory extracellular potassium signals that help even the distribution of nutrients within the biofilm and thus help regulate biofilm development. Quorum sensing also regulates biofilm growth and crucially there is convergence between electrical and quorum sensing signalling axes. This makes B. subtilis an interesting model for cell signalling research. SpoOF is predicted to act as a logic gate for signalling pathway convergence, raising interesting questions about the functional nature of this gate and the relative importance of these disparate signals on biofilm behaviour. How is an oscillating signal integrated with a quorum signal? The model presented offers rich opportunities for future experimental and theoretical modelling research. The importance of direct cell-to-cell electrical signalling in prokaryotes, so characteristic of multicellular eukaryotes, is also discussed.
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20
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D'Avanzo N, Miles AJ, Powl AM, Nichols CG, Wallace BA, O'Reilly AO. The T1-tetramerisation domain of Kv1.2 rescues expression and preserves function of a truncated NaChBac sodium channel. FEBS Lett 2022; 596:772-783. [PMID: 35015304 PMCID: PMC9303580 DOI: 10.1002/1873-3468.14279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022]
Abstract
Cytoplasmic domains frequently promote functional assembly of multimeric ion channels. To investigate structural determinants of this process, we generated the ‘T1‐chimera’ construct of the NaChBac sodium channel by truncating its C‐terminal domain and splicing the T1‐tetramerisation domain of the Kv1.2 channel to the N terminus. Purified T1‐chimera channels were tetrameric, conducted Na+ when reconstituted into proteoliposomes, and were functionally blocked by the drug mibefradil. Both the T1‐chimera and full‐length NaChBac had comparable expression levels in the membrane, whereas a NaChBac mutant lacking a cytoplasmic domain had greatly reduced membrane expression. Our findings support a model whereby bringing the transmembrane regions into close proximity enables their tetramerisation. This phenomenon is found with other channels, and thus, our findings substantiate this as a common assembly mechanism.
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Affiliation(s)
- Nazzareno D'Avanzo
- Department of Pharmacology and Physiology, Université de Montréal, Canada
| | - Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck, University of London, UK
| | - Andrew M Powl
- Institute of Structural and Molecular Biology, Birkbeck, University of London, UK
| | - Colin G Nichols
- Department of Cell Biology and Physiology, Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, USA
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck, University of London, UK
| | - Andrias O O'Reilly
- School of Biological & Environmental Sciences, Liverpool John Moores University, UK
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21
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Abstract
TRP channels have been heavily pursued as cryo-electron microscopy targets since they rang in the "resolution revolution." Although widespread in eukaryotes, a fungal TRP channel structure was missing. In this issue of Structure, Ahmed et al. (2022) present structural insights into the regulation of yeast TRPY1 by Ca2+ and lipids.
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Affiliation(s)
- Ute A Hellmich
- Friedrich Schiller University Jena, Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence "Balance of the Microverse", 07743 Jena, Germany; Center for Biomolecular Magnetic Resonance, Goethe-University, 60438 Frankfurt, Germany.
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
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22
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Cañas CA, Castaño-Valencia S, Castro-Herrera F. Pharmacological blockade of KV1.3 channel as a promising treatment in autoimmune diseases. J Transl Autoimmun 2022; 5:100146. [PMID: 35146402 PMCID: PMC8818563 DOI: 10.1016/j.jtauto.2022.100146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/20/2022] [Accepted: 01/22/2022] [Indexed: 11/27/2022] Open
Abstract
There are more than 100 autoimmune diseases (AD), which have a high prevalence that ranges between 5% and 8% of the general population. Type I diabetes mellitus, multiple sclerosis, systemic lupus erythematosus and rheumatoid arthritis remain the health problem of highest concern among people worldwide due to its high morbidity and mortality. The development of new treatment strategies has become a research hotspot. In recent years, the study of the ion channels presents in the cells of the immune system, regarding their functional role, the consequences of mutations in their genes and the different ways of blocking them are the subject of intense research. Pharmacological blockade of KV1.3 channel inhibits Ca2+ signaling, T cell proliferation, and pro-inflammatory interleukins production in human CD4+ effector memory T cells. These cells mediated most of the AD and their inhibition is a promising therapeutic target. In this review, we will highlight the biological function of KV1.3 channel in T cells, consequence of the pharmacological inhibition (through anemone and scorpion toxins, synthetic peptides, nanoparticles, or monoclonal antibodies) as well as the possible therapeutical application in AD.
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Affiliation(s)
- Carlos A. Cañas
- Universidad Icesi, CIRAT, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
- Unit of Rheumatology, Fundación Valle del Lili, Cali, Colombia
- Corresponding author. Rheumatology Unit, Fundación Valle del Lili, Cra. 98 18-49, Cali, 760032, Colombia.
| | - Santiago Castaño-Valencia
- Department of Physiological Sciences, Department of Health Sciences, Universidad del Valle, Cali, Colombia
| | - Fernando Castro-Herrera
- Department of Physiological Sciences, Department of Health Sciences, Universidad del Valle, Cali, Colombia
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23
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York JM, Zakon HH. OUP accepted manuscript. Genome Biol Evol 2022; 14:6519823. [PMID: 35106545 PMCID: PMC8857925 DOI: 10.1093/gbe/evac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2022] [Indexed: 11/14/2022] Open
Abstract
Animals rely on their sensory systems to inform them of ecologically relevant environmental variation. In the Southern Ocean, the thermal environment has remained between −1.9 and 5 °C for 15 Myr, yet we have no knowledge of how an Antarctic marine organism might sense their thermal habitat as we have yet to discover a thermosensitive ion channel that gates (opens/closes) below 10 °C. Here, we investigate the evolutionary dynamics of transient receptor potential (TRP) channels, which are the primary thermosensors in animals, within cryonotothenioid fishes—the dominant fish fauna of the Southern Ocean. We found cryonotothenioids have a similar complement of TRP channels as other teleosts (∼28 genes). Previous work has shown that thermosensitive gating in a given channel is species specific, and multiple channels act together to sense the thermal environment. Therefore, we combined evidence of changes in selective pressure, gene gain/loss dynamics, and the first sensory ganglion transcriptome in this clade to identify the best candidate TRP channels that might have a functional dynamic range relevant for frigid Antarctic temperatures. We concluded that TRPV1a, TRPA1b, and TRPM4 are the likeliest putative thermosensors, and found evidence of diversifying selection at sites across these proteins. We also put forward hypotheses for molecular mechanisms of other cryonotothenioid adaptations, such as reduced skeletal calcium deposition, sensing oxidative stress, and unusual magnesium homeostasis. By completing a comprehensive and unbiased survey of these genes, we lay the groundwork for functional characterization and answering long-standing thermodynamic questions of thermosensitive gating and protein adaptation to low temperatures.
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Affiliation(s)
- Julia M York
- Department of Integrative Biology, University of Texas at Austin, USA
- Corresponding author: E-mail:
| | - Harold H Zakon
- Department of Integrative Biology, University of Texas at Austin, USA
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24
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McCuskey SR, Chatsirisupachai J, Zeglio E, Parlak O, Panoy P, Herland A, Bazan GC, Nguyen TQ. Current Progress of Interfacing Organic Semiconducting Materials with Bacteria. Chem Rev 2021; 122:4791-4825. [PMID: 34714064 DOI: 10.1021/acs.chemrev.1c00487] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microbial bioelectronics require interfacing microorganisms with electrodes. The resulting abiotic/biotic platforms provide the basis of a range of technologies, including energy conversion and diagnostic assays. Organic semiconductors (OSCs) provide a unique strategy to modulate the interfaces between microbial systems and external electrodes, thereby improving the performance of these incipient technologies. In this review, we explore recent progress in the field on how OSCs, and related materials capable of charge transport, are being used within the context of microbial systems, and more specifically bacteria. We begin by examining the electrochemical communication modes in bacteria and the biological basis for charge transport. Different types of synthetic organic materials that have been designed and synthesized for interfacing and interrogating bacteria are discussed next, followed by the most commonly used characterization techniques for evaluating transport in microbial, synthetic, and hybrid systems. A range of applications is subsequently examined, including biological sensors and energy conversion systems. The review concludes by summarizing what has been accomplished so far and suggests future design approaches for OSC bioelectronics materials and technologies that hybridize characteristic properties of microbial and OSC systems.
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Affiliation(s)
- Samantha R McCuskey
- Department of Chemistry, National University of Singapore, Singapore 119077, Singapore
| | - Jirat Chatsirisupachai
- Center for Polymers and Organic Solids & Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan, Rayong 21210, Thailand
| | - Erica Zeglio
- Division of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm 17177, Sweden
| | - Onur Parlak
- Dermatology and Venereology Division, Department of Medicine(Solna), Karolinska Institute, Stockholm 17177, Sweden.,AIMES Center of Integrated Medical and Engineering Sciences, Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden
| | - Patchareepond Panoy
- Center for Polymers and Organic Solids & Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Materials Science and Engineering, School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan, Rayong 21210, Thailand
| | - Anna Herland
- Division of Micro and Nanosystems, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, Stockholm 17177, Sweden.,AIMES Center of Integrated Medical and Engineering Sciences, Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden
| | - Guillermo C Bazan
- Department of Chemistry, National University of Singapore, Singapore 119077, Singapore
| | - Thuc-Quyen Nguyen
- Center for Polymers and Organic Solids & Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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25
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Unappreciated Roles for K+ Channels in Bacterial Physiology. Trends Microbiol 2021; 29:942-950. [DOI: 10.1016/j.tim.2020.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 01/03/2023]
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26
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Haschka D, Grander M, Eibensteiner J, Dichtl S, Koppelstätter S, Weiss G. Nifedipine Potentiates Susceptibility of Salmonella Typhimurium to Different Classes of Antibiotics. Antibiotics (Basel) 2021; 10:antibiotics10101200. [PMID: 34680781 PMCID: PMC8532624 DOI: 10.3390/antibiotics10101200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
The calcium channel blocker nifedipine induces cellular iron export, thereby limiting the availability of the essential nutrient iron for intracellular pathogens, resulting in bacteriostatic activity. To study if nifedipine may exert a synergistic anti-microbial activity when combined with antibiotics, we used the mouse macrophage cell line RAW267.4, infected with the intracellular bacterium Salmonella Typhimurium, and exposed the cells to varying concentrations of nifedipine and/or ampicillin, azithromycin and ceftriaxone. We observed a significant additive effect of nifedipine in combination with various antibiotics, which was not observed when using Salmonella, with defects in iron uptake. Of interest, increasing intracellular iron levels increased the bacterial resistance to treatment with antibiotics or nifedipine or their combination. We further showed that nifedipine increases the expression of the siderophore-binding peptide lipocalin-2 and promotes iron storage within ferritin, where the metal is less accessible for bacteria. Our data provide evidence for an additive effect of nifedipine with conventional antibiotics against Salmonella, which is partly linked to reduced bacterial access to iron.
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27
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Native structure of the RhopH complex, a key determinant of malaria parasite nutrient acquisition. Proc Natl Acad Sci U S A 2021; 118:2100514118. [PMID: 34446549 PMCID: PMC8536402 DOI: 10.1073/pnas.2100514118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Malaria parasites invade and replicate within human red blood cells, which lack nuclei and have minimal metabolic activity. To survive, the parasites create new pathways that alter the permeability of the red blood cell membrane, allowing them to import nutrients and export waste. Here, we present the native structure of the three-membered RhopH protein complex, which plays a key role in this process. We determined the structure of this essential complex from a heterogeneous mixture of proteins enriched directly from parasite cell lysate, using a cryo-electron microscopy–enabled endogenous structural proteomics approach. The native structure of the RhopH complex in a soluble, trafficking state helps elucidate the long-standing question of how parasite transmembrane proteins are trafficked to the erythrocyte membrane. The RhopH complex is implicated in malaria parasites’ ability to invade and create new permeability pathways in host erythrocytes, but its mechanisms remain poorly understood. Here, we enrich the endogenous RhopH complex in a native soluble form, comprising RhopH2, CLAG3.1, and RhopH3, directly from parasite cell lysates and determine its atomic structure using cryo–electron microscopy (cryo-EM), mass spectrometry, and the cryoID program. CLAG3.1 is positioned between RhopH2 and RhopH3, which both share substantial binding interfaces with CLAG3.1 but make minimal contacts with each other. The forces stabilizing individual subunits include 13 intramolecular disulfide bonds. Notably, CLAG3.1 residues 1210 to 1223, previously predicted to constitute a transmembrane helix, are embedded within a helical bundle formed by residues 979 to 1289 near the C terminus of CLAG3.1. Buried in the core of the RhopH complex and largely shielded from solvent, insertion of this putative transmembrane helix into the erythrocyte membrane would likely require a large conformational rearrangement. Given the unusually high disulfide content of the complex, it is possible that such a rearrangement could be initiated by the breakage of allosteric disulfide bonds, potentially triggered by interactions at the erythrocyte membrane. This first direct observation of an exported Plasmodium falciparum transmembrane protein—in a soluble, trafficking state and with atomic details of buried putative membrane-insertion helices—offers insights into the assembly and trafficking of RhopH and other parasite-derived complexes to the erythrocyte membrane. Our study demonstrates the potential the endogenous structural proteomics approach holds for elucidating the molecular mechanisms of hard-to-isolate complexes in their native, functional forms.
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28
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Vaud S, Pearcy N, Hanževački M, Van Hagen AMW, Abdelrazig S, Safo L, Ehsaan M, Jonczyk M, Millat T, Craig S, Spence E, Fothergill J, Bommareddy RR, Colin PY, Twycross J, Dalby PA, Minton NP, Jäger CM, Kim DH, Yu J, Maness PC, Lynch S, Eckert CA, Conradie A, Bryan SJ. Engineering improved ethylene production: Leveraging systems biology and adaptive laboratory evolution. Metab Eng 2021; 67:308-320. [PMID: 34245888 DOI: 10.1016/j.ymben.2021.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/26/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Ethylene is a small hydrocarbon gas widely used in the chemical industry. Annual worldwide production currently exceeds 150 million tons, producing considerable amounts of CO2 contributing to climate change. The need for a sustainable alternative is therefore imperative. Ethylene is natively produced by several different microorganisms, including Pseudomonas syringae pv. phaseolicola via a process catalyzed by the ethylene-forming enzyme (EFE), subsequent heterologous expression of EFE has led to ethylene production in non-native bacterial hosts including Escherichia coli and cyanobacteria. However, solubility of EFE and substrate availability remain rate-limiting steps in biological ethylene production. We employed a combination of genome-scale metabolic modelling, continuous fermentation, and protein evolution to enable the accelerated development of a high efficiency ethylene producing E. coli strain, yielding a 49-fold increase in production, the most significant improvement reported to date. Furthermore, we have clearly demonstrated that this increased yield resulted from metabolic adaptations that were uniquely linked to EFE (wild type versus mutant). Our findings provide a novel solution to deregulate metabolic bottlenecks in key pathways, which can be readily applied to address other engineering challenges.
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Affiliation(s)
- Sophie Vaud
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Nicole Pearcy
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Marko Hanževački
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexander M W Van Hagen
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Salah Abdelrazig
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Laudina Safo
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Muhammad Ehsaan
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Magdalene Jonczyk
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Thomas Millat
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Sean Craig
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Edward Spence
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - James Fothergill
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Rajesh Reddy Bommareddy
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Pierre-Yves Colin
- Department of Biochemical Engineering, Bernard Katz Building, University College London, WC1E 6BT, UK
| | - Jamie Twycross
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK; School of Computer Science, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, Bernard Katz Building, University College London, WC1E 6BT, UK
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, The Biodiscovery Institute, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Jianping Yu
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA
| | - Sean Lynch
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, USA; Somalogic, Inc., Boulder, CO, USA
| | - Carrie A Eckert
- Biosciences Center, National Renewable Energy Laboratory (NREL), Golden, CO, USA; Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, USA
| | - Alex Conradie
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Samantha J Bryan
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD, UK.
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29
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Galera-Laporta L, Comerci CJ, Garcia-Ojalvo J, Süel GM. IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria. Cell Syst 2021; 12:497-508. [PMID: 34139162 PMCID: PMC8570674 DOI: 10.1016/j.cels.2021.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022]
Abstract
Metal ions are essential for life and represent the second most abundant constituent (after water) of any living cell. While the biological importance of inorganic ions has been appreciated for over a century, we are far from a comprehensive understanding of the functional roles that ions play in cells and organisms. In particular, recent advances are challenging the traditional view that cells maintain constant levels of ion concentrations (ion homeostasis). In fact, the ionic composition (metallome) of cells appears to be purposefully dynamic. The scientific journey that started over 60 years ago with the seminal work by Hodgkin and Huxley on action potentials in neurons is far from reaching its end. New evidence is uncovering how changes in ionic composition regulate unexpected cellular functions and physiology, especially in bacteria, thereby hinting at the evolutionary origins of the dynamic metallome. It is an exciting time for this field of biology, which we discuss and refer to here as IonoBiology.
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Affiliation(s)
- Leticia Galera-Laporta
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Colin J Comerci
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Gürol M Süel
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California, San Diego, La Jolla, CA 92093- 0380, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093-0380, USA.
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30
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Paternò GM, Bondelli G, Lanzani G. Bringing Microbiology to Light: Toward All-Optical Electrophysiology in Bacteria. Bioelectricity 2021; 3:136-142. [PMID: 34476389 DOI: 10.1089/bioe.2021.0008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The observation of neuron-like behavior in bacteria, such as the occurrence of electric spiking and extended bioelectric signaling, points to the role of membrane dynamics in prokaryotes. Electrophysiology of bacteria, however, has been overlooked for long time, due to the difficulties in monitoring bacterial bioelectric phenomena with those probing techniques that are commonly used for eukaryotes. Optical technologies can allow a paradigm shift in the field of electrophysiology of bacteria, as they would permit to elicit and monitor signaling rapidly, remotely, and with high spatiotemporal precision. In this perspective, we discuss about the potentiality of light interrogation methods in microbiology, encouraging the development of all-optical electrophysiology of bacteria.
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Affiliation(s)
| | - Gaia Bondelli
- Center for Nanoscience and Technology, Istituto Italiano di Tecnologia, Milano, Italy.,Physics Department, Politecnico di Milano, Milano, Italy
| | - Guglielmo Lanzani
- Center for Nanoscience and Technology, Istituto Italiano di Tecnologia, Milano, Italy.,Physics Department, Politecnico di Milano, Milano, Italy
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31
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Abstract
Bacteria are electrically powered organisms; cells maintain an electrical potential across their plasma membrane as a source of free energy to drive essential processes. In recent years, however, bacterial membrane potential has been increasingly recognized as dynamic. Those dynamics have been implicated in diverse physiological functions and behaviors, including cell division and cell-to-cell signaling. In eukaryotic cells, such dynamics play major roles in coupling bioelectrical stimuli to changes in internal cell states. Neuroscientists and physiologists have established detailed molecular pathways that transduce eukaryotic membrane potential dynamics to physiological and gene expression responses. We are only just beginning to explore these intracellular responses to bioelectrical activity in bacteria. In this review, we summarize progress in this area, including evidence of gene expression responses to stimuli from electrodes and mechanically induced membrane potential spikes. We argue that the combination of provocative results, missing molecular detail, and emerging tools makes the investigation of bioelectrically induced long-term intracellular responses an important and rewarding effort in the future of microbiology.
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Affiliation(s)
- Joshua M Jones
- Department of Biology, Boston University, Boston, Massachusetts, USA.,Department of Physics, Boston University, Boston, Massachusetts, USA.,Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Joseph W Larkin
- Department of Biology, Boston University, Boston, Massachusetts, USA.,Department of Physics, Boston University, Boston, Massachusetts, USA.,Biological Design Center, Boston University, Boston, Massachusetts, USA
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32
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Brette R. Integrative Neuroscience of Paramecium, a "Swimming Neuron". eNeuro 2021; 8:ENEURO.0018-21.2021. [PMID: 33952615 PMCID: PMC8208649 DOI: 10.1523/eneuro.0018-21.2021] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/28/2022] Open
Abstract
Paramecium is a unicellular organism that swims in fresh water by beating thousands of cilia. When it is stimulated (mechanically, chemically, optically, thermally…), it often swims backward then turns and swims forward again. This "avoiding reaction" is triggered by a calcium-based action potential. For this reason, some authors have called Paramecium a "swimming neuron." This review summarizes current knowledge about the physiological basis of behavior of Paramecium.
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Affiliation(s)
- Romain Brette
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de la Vision, Paris 75012, France
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33
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Biquet-Bisquert A, Labesse G, Pedaci F, Nord AL. The Dynamic Ion Motive Force Powering the Bacterial Flagellar Motor. Front Microbiol 2021; 12:659464. [PMID: 33927708 PMCID: PMC8076557 DOI: 10.3389/fmicb.2021.659464] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
The bacterial flagellar motor (BFM) is a rotary molecular motor embedded in the cell membrane of numerous bacteria. It turns a flagellum which acts as a propeller, enabling bacterial motility and chemotaxis. The BFM is rotated by stator units, inner membrane protein complexes that stochastically associate to and dissociate from individual motors at a rate which depends on the mechanical and electrochemical environment. Stator units consume the ion motive force (IMF), the electrochemical gradient across the inner membrane that results from cellular respiration, converting the electrochemical energy of translocated ions into mechanical energy, imparted to the rotor. Here, we review some of the main results that form the base of our current understanding of the relationship between the IMF and the functioning of the flagellar motor. We examine a series of studies that establish a linear proportionality between IMF and motor speed, and we discuss more recent evidence that the stator units sense the IMF, altering their rates of dynamic assembly. This, in turn, raises the question of to what degree the classical dependence of motor speed on IMF is due to stator dynamics vs. the rate of ion flow through the stators. Finally, while long assumed to be static and homogeneous, there is mounting evidence that the IMF is dynamic, and that its fluctuations control important phenomena such as cell-to-cell signaling and mechanotransduction. Within the growing toolbox of single cell bacterial electrophysiology, one of the best tools to probe IMF fluctuations may, ironically, be the motor that consumes it. Perfecting our incomplete understanding of how the BFM employs the energy of ion flow will help decipher the dynamical behavior of the bacterial IMF.
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Affiliation(s)
- Anaïs Biquet-Bisquert
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - Gilles Labesse
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - Francesco Pedaci
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - Ashley L Nord
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
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34
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Stautz J, Hellmich Y, Fuss MF, Silberberg JM, Devlin JR, Stockbridge RB, Hänelt I. Molecular Mechanisms for Bacterial Potassium Homeostasis. J Mol Biol 2021; 433:166968. [PMID: 33798529 DOI: 10.1016/j.jmb.2021.166968] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Potassium ion homeostasis is essential for bacterial survival, playing roles in osmoregulation, pH homeostasis, regulation of protein synthesis, enzyme activation, membrane potential adjustment and electrical signaling. To accomplish such diverse physiological tasks, it is not surprising that a single bacterium typically encodes several potassium uptake and release systems. To understand the role each individual protein fulfills and how these proteins work in concert, it is important to identify the molecular details of their function. One needs to understand whether the systems transport ions actively or passively, and what mechanisms or ligands lead to the activation or inactivation of individual systems. Combining mechanistic information with knowledge about the physiology under different stress situations, such as osmostress, pH stress or nutrient limitation, one can identify the task of each system and deduce how they are coordinated with each other. By reviewing the general principles of bacterial membrane physiology and describing the molecular architecture and function of several bacterial K+-transporting systems, we aim to provide a framework for microbiologists studying bacterial potassium homeostasis and the many K+-translocating systems that are still poorly understood.
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Affiliation(s)
- Janina Stautz
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yvonne Hellmich
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michael F Fuss
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jakob M Silberberg
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jason R Devlin
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States.
| | - Inga Hänelt
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
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35
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Hanson A. Spontaneous electrical low-frequency oscillations: a possible role in Hydra and all living systems. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190763. [PMID: 33487108 PMCID: PMC7934974 DOI: 10.1098/rstb.2019.0763] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
As one of the first model systems in biology, the basal metazoan Hydra has been revealing fundamental features of living systems since it was first discovered by Antonie van Leeuwenhoek in the early eighteenth century. While it has become well-established within cell and developmental biology, this tiny freshwater polyp is only now being re-introduced to modern neuroscience where it has already produced a curious finding: the presence of low-frequency spontaneous neural oscillations at the same frequency as those found in the default mode network in the human brain. Surprisingly, increasing evidence suggests such spontaneous electrical low-frequency oscillations (SELFOs) are found across the wide diversity of life on Earth, from bacteria to humans. This paper reviews the evidence for SELFOs in diverse phyla, beginning with the importance of their discovery in Hydra, and hypothesizes a potential role as electrical organism organizers, which supports a growing literature on the role of bioelectricity as a 'template' for developmental memory in organism regeneration. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.
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Affiliation(s)
- Alison Hanson
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Psychiatry, New York State Psychiatric Institute, Columbia University, New York, NY, USA
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36
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Abstract
All living cells interact dynamically with a constantly changing world. Eukaryotes, in particular, evolved radically new ways to sense and react to their environment. These advances enabled new and more complex forms of cellular behaviour in eukaryotes, including directional movement, active feeding, mating, and responses to predation. But what are the key events and innovations during eukaryogenesis that made all of this possible? Here we describe the ancestral repertoire of eukaryotic excitability and discuss five major cellular innovations that enabled its evolutionary origin. The innovations include a vastly expanded repertoire of ion channels, the emergence of cilia and pseudopodia, endomembranes as intracellular capacitors, a flexible plasma membrane and the relocation of chemiosmotic ATP synthesis to mitochondria, which liberated the plasma membrane for more complex electrical signalling involved in sensing and reacting. We conjecture that together with an increase in cell size, these new forms of excitability greatly amplified the degrees of freedom associated with cellular responses, allowing eukaryotes to vastly outperform prokaryotes in terms of both speed and accuracy. This comprehensive new perspective on the evolution of excitability enriches our view of eukaryogenesis and emphasizes behaviour and sensing as major contributors to the success of eukaryotes. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.
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Affiliation(s)
- Kirsty Y. Wan
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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37
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Saraf M, Tavakkoli Yaraki M, Prateek, Tan YN, Gupta RK. Insights and Perspectives Regarding Nanostructured Fluorescent Materials toward Tackling COVID-19 and Future Pandemics. ACS APPLIED NANO MATERIALS 2021; 4:911-948. [PMID: 37556236 PMCID: PMC7885806 DOI: 10.1021/acsanm.0c02945] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/26/2021] [Indexed: 07/28/2023]
Abstract
The COVID-19 outbreak has exposed the world's preparation to fight against unknown/unexplored infectious and life-threatening pathogens. The unavailability of vaccines, slow or sometimes unreliable real-time virus/bacteria detection techniques, insufficient personal protective equipment (PPE), and a shortage of ventilators and many other transportation equipments have further raised serious concerns. Material research has been playing a pivotal role in developing antimicrobial agents for water treatment and photodynamic therapy, fast and ultrasensitive biosensors for virus/biomarkers detection, as well as for relevant biomedical and environmental applications. It has been noticed that these research efforts nowadays primarily focus on the nanomaterials-based platforms owing to their simplicity, reliability, and feasibility. In particular, nanostructured fluorescent materials have shown key potential due to their fascinating optical and unique properties at the nanoscale to combat against a COVID-19 kind of pandemic. Keeping these points in mind, this review attempts to give a perspective on the four key fluorescent materials of different families, including carbon dots, metal nanoclusters, aggregation-induced-emission luminogens, and MXenes, which possess great potential for the development of ultrasensitive biosensors and infective antimicrobial agents to fight against various infections/diseases. Particular emphasis has been given to the biomedical and environmental applications that are linked directly or indirectly to the efforts in combating COVID-19 pandemics. This review also aims to raise the awareness of researchers and scientists across the world to utilize such powerful materials in tackling similar pandemics in future.
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Affiliation(s)
- Mohit Saraf
- Department of Chemical Engineering,
Indian Institute of Technology Kanpur, Kanpur 208016, Uttar
Pradesh, India
| | - Mohammad Tavakkoli Yaraki
- Department of Chemical and Biomolecular Engineering,
National University of Singapore, 4 Engineering Drive 4,
117585, Singapore
- Research and Development Department,
Nanofy Technologies Pte. Ltd., 048580,
Singapore
| | - Prateek
- Department of Chemical Engineering,
Indian Institute of Technology Kanpur, Kanpur 208016, Uttar
Pradesh, India
| | - Yen Nee Tan
- Faculty of Science, Agriculture & Engineering,
Newcastle University, Newcastle upon Tyne NE1 7RU,
U.K.
- Newcastle Research & Innovation Institute,
Devan Nair Institute for Employment & Employability, 80
Jurong East Street 21, 609607, Singapore
| | - Raju Kumar Gupta
- Department of Chemical Engineering,
Indian Institute of Technology Kanpur, Kanpur 208016, Uttar
Pradesh, India
- Centre for Environmental Science and Engineering,
Indian Institute of Technology Kanpur, Kanpur 208016, Uttar
Pradesh, India
- Department of Sustanable Energy Engineering,
Indian Institute of Technology Kanpur, Kanpur 208016, Uttar
Pradesh, India
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38
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Badari JC, Díaz-Roa A, Teixeira Rocha MM, Mendonça RZ, da Silva Junior PI. Patagonin-CRISP: Antimicrobial Activity and Source of Antimicrobial Molecules in Duvernoy's Gland Secretion ( Philodryas patagoniensis Snake). Front Pharmacol 2021; 11:586705. [PMID: 33603660 PMCID: PMC7884886 DOI: 10.3389/fphar.2020.586705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
Snake venom contains a variety of toxins with a range of biological activity, among these toxins cysteine-rich secreted proteins (CRISPs) can be found. The proteins of this family have masses of 20-30 kDa and display homologous amino acid sequences containing 16 cysteine residues, forming eight disulfide bonds. Some of these proteins have been explored, characterized, and described in terms of their activity; however, little is known about their range of activities. A search for new antimicrobial molecules is ongoing, as the number of microbial strains resistant to available antibiotics is increasing. We identified antimicrobial activity in the secretion of Duvernoy's gland of the rear-fanged Philodryas patagoniensis. Fractions of this venom were subjected to reverse-phase high performance liquid chromatography and analyzed to determine their antimicrobial activity with a liquid broth inhibition assay. One of the fractions presented activity against a Gram-negative bacterium and a filamentous fungus. This fraction was analyzed with LC-MS/MS, and a protein of 24,848.8 Da was identified. Database searches allowed us to identify it as a CRISP due to the presence of some unique fragments in the molecule. We called it patagonin-CRISP, as the same protein in the venom of P. patagoniensis had previously been characterized as having a different biological activity. Patagonin-CRISP presented activity at very low concentrations and showed no cytotoxic activity. This is the first time that antimicrobial activity has been identified for P. patagoniensis venom or for a CRISP family protein.
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Affiliation(s)
| | - Andrea Díaz-Roa
- Laboratory for Applied Toxinology (LETA) - Center of Toxins, Immune-Response and Cell Signaling - CeTICS/CEPID Butantan Institute, São Paulo, Brazil.,Escuela de Ciencias Agrícolas, Pecuarias y del Medio Ambiente (ECAPMA), Universidad Nacional Abierta y a Distancia (UNAD), Bogotá, Colombia
| | | | | | - Pedro Ismael da Silva Junior
- Laboratory for Applied Toxinology (LETA) - Center of Toxins, Immune-Response and Cell Signaling - CeTICS/CEPID Butantan Institute, São Paulo, Brazil
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39
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Du W, Li G, Ho N, Jenkins L, Hockaday D, Tan J, Cao H. CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms. Brief Bioinform 2020; 22:6035272. [PMID: 33320930 DOI: 10.1093/bib/bbaa375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 11/14/2022] Open
Abstract
CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarizes four types of information: common biological functions (pathways) driving CyanoHABs, customized pathway maps, classification of blooming type based on databases and the genomes of cyanobacteria. A total of 19 pathways are reconstructed, which are involved in the utilization of macronutrients (e.g. carbon, nitrogen, phosphorus and sulfur), micronutrients (e.g. zinc, magnesium, iron, etc.) and other resources (e.g. light and vitamins) and in stress resistance (e.g. lead and copper). These pathways, comprised of both transport and biochemical reactions, are reconstructed with proteins from NCBI and reactions from KEGG and visualized with self-created transport/reaction maps. The pathways are hierarchical and consist of subpathways, protein/enzyme complexes and constituent proteins. New cyanobacterial genomes can be annotated and visualized for these pathways and compared with existing species. This set of genomic functional repertoire is useful in analyzing aquatic metagenomes and metatranscriptomes in CyanoHAB research. Most importantly, it establishes a link between genome and ecology. All these reference proteins, pathways and maps and genomes are free to download at http://www.csbg-jlu.info/CyanoPATH.
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Affiliation(s)
| | | | - Nicholas Ho
- Biodesign Center for Fundamental and Applied Microbiomics at Arizona State University
| | - Landon Jenkins
- Biodesign Center for Fundamental and Applied Microbiomics at Arizona State University
| | - Drew Hockaday
- Biodesign Center for Fundamental and Applied Microbiomics at Arizona State University
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40
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Are antibacterial effects of non-antibiotic drugs random or purposeful because of a common evolutionary origin of bacterial and mammalian targets? Infection 2020; 49:569-589. [PMID: 33325009 PMCID: PMC7737717 DOI: 10.1007/s15010-020-01547-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/28/2020] [Indexed: 01/09/2023]
Abstract
Purpose Advances in structural biology, genetics, bioinformatics, etc. resulted in the availability of an enormous pool of information enabling the analysis of the ancestry of pro- and eukaryotic genes and proteins. Methods This review summarizes findings of structural and/or functional homologies of pro- and eukaryotic enzymes catalysing analogous biological reactions because of their highly conserved active centres so that non-antibiotics interacted with bacterial targets. Results Protease inhibitors such as staurosporine or camostat inhibited bacterial serine/threonine or serine/tyrosine protein kinases, serine/threonine phosphatases, and serine/threonine kinases, to which penicillin-binding-proteins are linked, so that these drugs synergized with β-lactams, reverted aminoglycoside-resistance and attenuated bacterial virulence. Calcium antagonists such as nitrendipine or verapamil blocked not only prokaryotic ion channels but interacted with negatively charged bacterial cell membranes thus disrupting membrane energetics and inducing membrane stress response resulting in inhibition of P-glycoprotein such as bacterial pumps thus improving anti-mycobacterial activities of rifampicin, tetracycline, fluoroquinolones, bedaquilin and imipenem-activity against Acinetobacter spp. Ciclosporine and tacrolimus attenuated bacterial virulence. ACE-inhibitors like captopril interacted with metallo-β-lactamases thus reverting carbapenem-resistance; prokaryotic carbonic anhydrases were inhibited as well resulting in growth impairment. In general, non-antibiotics exerted weak antibacterial activities on their own but synergized with antibiotics, and/or reverted resistance and/or attenuated virulence. Conclusions Data summarized in this review support the theory that prokaryotic proteins represent targets for non-antibiotics because of a common evolutionary origin of bacterial- and mammalian targets resulting in highly conserved active centres of both, pro- and eukaryotic proteins with which the non-antibiotics interact and exert antibacterial actions.
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41
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Cremin K, Jones BA, Teahan J, Meloni GN, Perry D, Zerfass C, Asally M, Soyer OS, Unwin PR. Scanning Ion Conductance Microscopy Reveals Differences in the Ionic Environments of Gram-Positive and Negative Bacteria. Anal Chem 2020; 92:16024-16032. [PMID: 33241929 DOI: 10.1021/acs.analchem.0c03653] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This paper reports on the use of scanning ion conductance microscopy (SICM) to locally map the ionic properties and charge environment of two live bacterial strains: the Gram-negative Escherichia coli and the Gram-positive Bacillus subtilis. SICM results find heterogeneities across the bacterial surface and significant differences among the Gram-positive and Gram-negative bacteria. The bioelectrical environment of the B. subtilis was found to be considerably more negatively charged compared to E. coli. SICM measurements, fitted to a simplified finite element method (FEM) model, revealed surface charge values of -80 to -140 mC m-2 for the Gram-negative E. coli. The Gram-positive B. subtilis show a much higher conductivity around the cell wall, and surface charge values between -350 and -450 mC m-2 were found using the same simplified model. SICM was also able to detect regions of high negative charge near B. subtilis, not detected in the topographical SICM response and attributed to the extracellular polymeric substance. To further explore how the B. subtilis cell wall structure can influence the SICM current response, a more comprehensive FEM model, accounting for the physical properties of the Gram-positive cell wall, was developed. The new model provides a more realistic description of the cell wall and allows investigation of the relation between its key properties and SICM currents, building foundations to further investigate and improve understanding of the Gram-positive cellular microenvironment.
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Affiliation(s)
- Kelsey Cremin
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.,Molecular Analytical Science Centre for Doctoral Training (MAS CDT), University of Warwick, Coventry CV4 7AL, U.K.,School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
| | - Bryn A Jones
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - James Teahan
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.,Molecular Analytical Science Centre for Doctoral Training (MAS CDT), University of Warwick, Coventry CV4 7AL, U.K
| | - Gabriel N Meloni
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - David Perry
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Christian Zerfass
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
| | - Munehiro Asally
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
| | - Orkun S Soyer
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
| | - Patrick R Unwin
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry CV4 7AL, U.K.,Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
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42
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Bekmukhametova A, Ruprai H, Hook JM, Mawad D, Houang J, Lauto A. Photodynamic therapy with nanoparticles to combat microbial infection and resistance. NANOSCALE 2020; 12:21034-21059. [PMID: 33078823 DOI: 10.1039/d0nr04540c] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Infections caused by drug-resistant pathogens are rapidly increasing in incidence and pose an urgent global health concern. New treatments are needed to address this critical situation while preventing further resistance acquired by the pathogens. One promising approach is antimicrobial photodynamic therapy (PDT), a technique that selectively damages pathogenic cells through reactive oxygen species (ROS) that have been deliberately produced by light-activated chemical reactions via a photosensitiser. There are currently some limitations to its wider deployment, including aggregation, hydrophobicity, and sub-optimal penetration capabilities of the photosensitiser, all of which decrease the production of ROS and lead to reduced therapeutic performance. In combination with nanoparticles, however, these challenges may be overcome. Their small size, functionalisable structure, and large contact surface allow a high degree of internalization by cellular membranes and tissue barriers. In this review, we first summarise the mechanism of PDT action and the interaction between nanoparticles and the cell membrane. We then introduce the categorisation of nanoparticles in PDT, acting as nanocarriers, photosensitising molecules, and transducers, in which we highlight their use against a range of bacterial and fungal pathogens. We also compare the antimicrobial efficiency of nanoparticles to unbound photosensitisers and examine the relevant safety considerations. Finally, we discuss the use of nanoparticulate drug delivery systems in clinical applications of antimicrobial PDT.
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Affiliation(s)
| | - Herleen Ruprai
- School of Science, Western Sydney University, Penrith, NSW 2750, Australia.
| | - James M Hook
- School of Chemistry, University of New South Wales, Kensington, NSW 2052, Australia
| | - Damia Mawad
- School of Materials Science and Engineering, University of New South Wales, Kensington, NSW 2052, Australia and Centre for Advanced Macromolecular Design, Australian Centre for NanoMedicine and ARC Centre of Excellence in Convergent BioNano Science and Technology, UNSW Australia, Sydney, NSW 2052, Australia
| | - Jessica Houang
- Biomedical Engineering, School of Aerospace, Mechanical and Mechatronic Engineering, University of Sydney, Sydney, NSW 2006, Australia and Biomedical Engineering & Neuroscience Research Group, The MARCS Institute, Western Sydney University, Penrith, NSW 2750, Australia
| | - Antonio Lauto
- School of Science, Western Sydney University, Penrith, NSW 2750, Australia. and Biomedical Engineering & Neuroscience Research Group, The MARCS Institute, Western Sydney University, Penrith, NSW 2750, Australia
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43
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Pozdnyakov I, Safonov P, Skarlato S. Diversity of voltage-gated potassium channels and cyclic nucleotide-binding domain-containing channels in eukaryotes. Sci Rep 2020; 10:17758. [PMID: 33082475 PMCID: PMC7576140 DOI: 10.1038/s41598-020-74971-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 10/06/2020] [Indexed: 12/04/2022] Open
Abstract
Voltage-gated potassium channels (Kv) and cyclic nucleotide-binding domain-containing cation channels HCN, CNG, and KCNH are the evolutionarily related families of ion channels in animals. Their homologues were found in several lineages of eukaryotes and prokaryotes; however, the actual phylogenetic and structural diversity of these ion channels remains unclear. In this work, we present a taxonomically broad investigation of evolutionary relationships and structural diversity of Kv, HCN, CNG, and KCNH and their homologues in eukaryotes focusing on channels from different protistan groups. We demonstrate that both groups of channels consist of a more significant number of lineages than it was shown before, and these lineages can be grouped in two clusters termed Kv-like channels and CNBD-channels. Moreover, we, for the first time, report the unusual two-repeat tandem Kv-like channels and CNBD-channels in several eukaryotic groups, i.e. dinoflagellates, oomycetes, and chlorarachniophytes. Our findings reveal still underappreciated phylogenetic and structural diversity of eukaryotic ion channel lineages.
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Affiliation(s)
- Ilya Pozdnyakov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia.
| | - Pavel Safonov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
| | - Sergei Skarlato
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
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44
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Sen CK, Mathew-Steiner SS, Das A, Sundaresan VB, Roy S. Electroceutical Management of Bacterial Biofilms and Surgical Infection. Antioxid Redox Signal 2020; 33:713-724. [PMID: 32466673 PMCID: PMC7475090 DOI: 10.1089/ars.2020.8086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 01/04/2023]
Abstract
Significance: In the host-microbe microenvironment, bioelectrical factors influence microbes and hosts as well as host-microbe interactions. This article discusses relevant mechanistic underpinnings of this novel paradigm. It also addresses how such knowledge may be leveraged to develop novel electroceutical solutions to manage biofilm infection. Recent Advances: Systematic review and meta-analysis of several hundred wound studies reported a 78.2% prevalence of biofilms in chronic wounds. Biofilm infection is a major cause of delayed wound healing. In the host-microbe microenvironment, bioelectrical factors influence interactions between microbes and hosts. Critical Issues: Rapid biological responses are driven by electrical signals generated by ion currents moving across cell membranes. Bacterial life, growth, and function rely on a bioelectrical milieu, which when perturbed impairs their ability to form a biofilm, a major threat to health care. Electrokinetic stability of several viral particles depend on electrostatic forces. Weak electrical field strength, otherwise safe for humans, can be anti-microbial in this context. In the host, the electric field enhanced keratinocyte migration, bolstered immune defenses, improved mitochondrial function, and demonstrated multiple other effects consistent with supporting wound healing. A deeper mechanistic understanding of bioelectrical principles will inform the design of next-generation electroceuticals. Future Directions: This is an opportune moment in time as there is a surge of interest in electroceuticals in medicine. Projected to reach $35.5 billion by 2025, electroceuticals are becoming a cynosure in the global market. The World Health Organization reports that more than 50% of surgical site infections can be antibiotic resistant. Electroceuticals offer a serious alternative.
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Affiliation(s)
- Chandan K. Sen
- Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Shomita S. Mathew-Steiner
- Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Amitava Das
- Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Vishnu Baba Sundaresan
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Sashwati Roy
- Indiana Center for Regenerative Medicine and Engineering, Indiana University School of Medicine, Indianapolis, Indiana, USA
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45
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Kholina EG, Kovalenko IB, Bozdaganyan ME, Strakhovskaya MG, Orekhov PS. Cationic Antiseptics Facilitate Pore Formation in Model Bacterial Membranes. J Phys Chem B 2020; 124:8593-8600. [PMID: 32896131 DOI: 10.1021/acs.jpcb.0c07212] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Antiseptics are an essential line of defense against bacterial and viral infections in modern medical practice. Many of them are supposed to act on microbial membranes. However, the detailed mechanisms of their action are still elusive. Here, we utilized coarse-grained molecular dynamics simulations to investigate interactions of different types of cationic antiseptics (CAs) with a model bacterial membrane. The simulations revealed qualitatively distinct patterns of dynamic and structural alterations of membrane induced by different types of antiseptics although none of them caused disintegration or solubilization of the bilayer even at the highest explored concentration. At the same time, the adsorption of antiseptics rendered membranes more vulnerable to poration under exposure to the external electric field. We further discuss the possible relation of the enhanced pore formation induced by CAs to their cytotoxic action.
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Affiliation(s)
- E G Kholina
- Department of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - I B Kovalenko
- Department of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sechenov University, Moscow 119991, Russia.,Astrakhan State University, Astrakhan 414056, Russia.,Peoples' Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - M E Bozdaganyan
- Department of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119991, Russia.,Moscow Polytechnic University, Moscow 107023, Russia
| | - M G Strakhovskaya
- Department of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Federal Medical and Biological Agency of Russia, Moscow 115682, Russia
| | - P S Orekhov
- Department of Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sechenov University, Moscow 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
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46
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Tawfik H, Puza S, Seemann R, Fleury JB. Transport Properties of Gramicidin A Ion Channel in a Free-Standing Lipid Bilayer Filled With Oil Inclusions. Front Cell Dev Biol 2020; 8:531229. [PMID: 33015051 PMCID: PMC7498540 DOI: 10.3389/fcell.2020.531229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/14/2020] [Indexed: 11/13/2022] Open
Abstract
Ion channels are key proteins in mammalian cell membranes. They have a central role in the physiology of excitable cells such as neurons, muscle, and heart cells. They also play a crucial role in kidney physiology. The gramicidin ion channel is one of the most studied ion channels, in particular it was intensively employed to investigate the lipid–protein interactions in model cell membranes. For example, even though the sequence of gramicidin is extremely hydrophobic, its motion is impaired in membrane bilayer, i.e., it does not rapidly flip to the other membrane leaflet, and low channel activity were observed when gramicidin is added asymmetrically to only one leaflet of a model cell membrane. In this article, we study the transport properties of gramicidin channel in a heterogeneous model membrane. Using microfluidics, we are forming freestanding bilayers as model cell membranes including heterogeneous domains that are created by oil inclusions. The presence of oil inclusions is then demonstrated by measuring the bilayer capacity via a patch-clamp amplifier and fluorescent confocal inspection. Based on electrophysiological and optical measurements Gramicidin A (gA) ion channels are dispersed into the buffer phases on both side of the formed lipid bilayer and insert spontaneously into the bilayer upon formation. The presence of functional Gramicidin A is then demonstrated by measuring conductivity signals. Based on electrophysiological and optical measurements, we explore the consequence of the presence of these oil inclusions on the functionality of incorporated gA ion channels. For low oil concentration, we measure a decrease of gA transport properties due to the reduction of the bilayer tension. For large oil concentration, we measure a saturation of gA transport properties due to an increase of the bilayer thickness.
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Affiliation(s)
- Harvey Tawfik
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
| | - Sevde Puza
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
| | - Ralf Seemann
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
| | - Jean-Baptiste Fleury
- Experimental Physics and Center for Biophysics, Universität des Saarlandes, Saarbrücken, Germany
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47
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Lezhnina MM, Rochowiak W, Göhde W, Kuczius R, Kynast U. The microbial threat: Can rare earths help? JOURNAL OF BIOPHOTONICS 2020; 13:e202000068. [PMID: 32500670 DOI: 10.1002/jbio.202000068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/15/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
Despite an ever increasing demand for reliable and cheap methods in the detection and quantification of microbes, surprisingly few investigations have explored or utilized the luminescence of rare earths in the microbial context, neither in conventional, that is, plating and microscopic imaging techniques, nor in advanced methods like fluorescence flow cytometry. We have thus investigated the potential of some rare earth complexes and hybrid materials for microbiological analysis. We found fairly simple procedures for internal staining (dyes inside the bacterial cell) and external staining (dyes on the cell surface). The present paper is predominantly relying on microscopic imaging and luminescence spectroscopies (excitation, emission, decay times), but also evaluates model rare earth microspheres to estimate an eventual rare earth based stain for a fast and sensitive bacteria enumeration with luminescence flow cytometry.
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Affiliation(s)
- Marina M Lezhnina
- Quantum Analysis GmbH, Münster, Germany
- Institute for Optical Technologies, Münster University of Applied Sciences, Steinfurt, Germany
| | - Weronika Rochowiak
- Institute for Optical Technologies, Münster University of Applied Sciences, Steinfurt, Germany
| | | | - Rauni Kuczius
- Mikrobiologisches Labor Dr. Michael Lohmeyer GmbH, Münster, Germany
| | - Ulrich Kynast
- Institute for Optical Technologies, Münster University of Applied Sciences, Steinfurt, Germany
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48
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Majumder R, De Coster T, Kudryashova N, Verkerk AO, Kazbanov IV, Ördög B, Harlaar N, Wilders R, de Vries AA, Ypey DL, Panfilov AV, Pijnappels DA. Self-restoration of cardiac excitation rhythm by anti-arrhythmic ion channel gating. eLife 2020; 9:55921. [PMID: 32510321 PMCID: PMC7316504 DOI: 10.7554/elife.55921] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/02/2020] [Indexed: 12/21/2022] Open
Abstract
Homeostatic regulation protects organisms against hazardous physiological changes. However, such regulation is limited in certain organs and associated biological processes. For example, the heart fails to self-restore its normal electrical activity once disturbed, as with sustained arrhythmias. Here we present proof-of-concept of a biological self-restoring system that allows automatic detection and correction of such abnormal excitation rhythms. For the heart, its realization involves the integration of ion channels with newly designed gating properties into cardiomyocytes. This allows cardiac tissue to i) discriminate between normal rhythm and arrhythmia based on frequency-dependent gating and ii) generate an ionic current for termination of the detected arrhythmia. We show in silico, that for both human atrial and ventricular arrhythmias, activation of these channels leads to rapid and repeated restoration of normal excitation rhythm. Experimental validation is provided by injecting the designed channel current for arrhythmia termination in human atrial myocytes using dynamic clamp.
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Affiliation(s)
- Rupamanjari Majumder
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Tim De Coster
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands.,Department of Physics and Astronomy, Ghent University, Ghent, Belgium.,Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Nina Kudryashova
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands.,Department of Physics and Astronomy, Ghent University, Ghent, Belgium
| | - Arie O Verkerk
- Department of Medical Biology, Amsterdam UMC, Amsterdam, Netherlands.,Department of Experimental Cardiology, Amsterdam UMC, Amsterdam, Netherlands
| | - Ivan V Kazbanov
- Department of Physics and Astronomy, Ghent University, Ghent, Belgium
| | - Balázs Ördög
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Niels Harlaar
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ronald Wilders
- Department of Medical Biology, Amsterdam UMC, Amsterdam, Netherlands
| | - Antoine Af de Vries
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Dirk L Ypey
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
| | - Alexander V Panfilov
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands.,Department of Physics and Astronomy, Ghent University, Ghent, Belgium.,Laboratory of Computational Biology and Medicine, Ural Federal University, Ekaterinburg, Russian Federation
| | - Daniël A Pijnappels
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, Netherlands
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49
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Lin M, Grandinetti G, Hartnell LM, Bliss D, Subramaniam S, Rikihisa Y. Host membrane lipids are trafficked to membranes of intravacuolar bacterium Ehrlichia chaffeensis. Proc Natl Acad Sci U S A 2020; 117:8032-8043. [PMID: 32193339 PMCID: PMC7149431 DOI: 10.1073/pnas.1921619117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Ehrlichia chaffeensis, a cholesterol-rich and cholesterol-dependent obligate intracellular bacterium, partially lacks genes for glycerophospholipid biosynthesis. We found here that E. chaffeensis is dependent on host glycerolipid biosynthesis, as an inhibitor of host long-chain acyl CoA synthetases, key enzymes for glycerolipid biosynthesis, significantly reduced bacterial proliferation. E. chaffeensis cannot synthesize phosphatidylcholine or cholesterol but encodes enzymes for phosphatidylethanolamine (PE) biosynthesis; however, exogenous NBD-phosphatidylcholine, Bodipy-PE, and TopFluor-cholesterol were rapidly trafficked to ehrlichiae in infected cells. DiI (3,3'-dioctadecylindocarbocyanine)-prelabeled host-cell membranes were unidirectionally trafficked to Ehrlichia inclusion and bacterial membranes, but DiI-prelabeled Ehrlichia membranes were not trafficked to host-cell membranes. The trafficking of host-cell membranes to Ehrlichia inclusions was dependent on both host endocytic and autophagic pathways, and bacterial protein synthesis, as the respective inhibitors blocked both infection and trafficking of DiI-labeled host membranes to Ehrlichia In addition, DiI-labeled host-cell membranes were trafficked to autophagosomes induced by the E. chaffeensis type IV secretion system effector Etf-1, which traffic to and fuse with Ehrlichia inclusions. Cryosections of infected cells revealed numerous membranous vesicles inside inclusions, as well as multivesicular bodies docked on the inclusion surface, both of which were immunogold-labeled by a GFP-tagged 2×FYVE protein that binds to phosphatidylinositol 3-phosphate. Focused ion-beam scanning electron microscopy of infected cells validated numerous membranous structures inside bacteria-containing inclusions. Our results support the notion that Ehrlichia inclusions are amphisomes formed through fusion of early endosomes, multivesicular bodies, and early autophagosomes induced by Etf-1, and they provide host-cell glycerophospholipids and cholesterol that are necessary for bacterial proliferation.
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Affiliation(s)
- Mingqun Lin
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
| | - Giovanna Grandinetti
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lisa M Hartnell
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Donald Bliss
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Yasuko Rikihisa
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210;
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50
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Benarroch JM, Asally M. The Microbiologist’s Guide to Membrane Potential Dynamics. Trends Microbiol 2020; 28:304-314. [DOI: 10.1016/j.tim.2019.12.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 10/25/2022]
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