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Takekawa N, Nishikino T, Kishikawa JI, Hirose M, Kinoshita M, Kojima S, Minamino T, Uchihashi T, Kato T, Imada K, Homma M. Structural analysis of S-ring composed of FliFG fusion proteins in marine Vibrio polar flagellar motor. mBio 2024:e0126124. [PMID: 39240115 DOI: 10.1128/mbio.01261-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024] Open
Abstract
The marine bacterium Vibrio alginolyticus possesses a polar flagellum driven by a sodium ion flow. The main components of the flagellar motor are the stator and rotor. The C-ring and MS-ring, which are composed of FliG and FliF, respectively, are parts of the rotor. Here, we purified an MS-ring composed of FliF-FliG fusion proteins and solved the near-atomic resolution structure of the S-ring-the upper part of the MS-ring-using cryo-electron microscopy. This is the first report of an S-ring structure from Vibrio, whereas, previously, only those from Salmonella have been reported. The Vibrio S-ring structure reveals novel features compared with that of Salmonella, such as tilt angle differences of the RBM3 domain and the β-collar region, which contribute to the vertical arrangement of the upper part of the β-collar region despite the diversity in the RBM3 domain angles. Additionally, there is a decrease of the inter-subunit interaction between RBM3 domains, which influences the efficiency of the MS-ring formation in different bacterial species. Furthermore, although the inner-surface electrostatic properties of Vibrio and Salmonella S-rings are altered, the residues potentially interacting with other flagellar components, such as FliE and FlgB, are well structurally conserved in the Vibrio S-ring. These comparisons clarified the conserved and non-conserved structural features of the MS-ring across different species.IMPORTANCEUnderstanding the structure and function of the flagellar motor in bacterial species is essential for uncovering the mechanisms underlying bacterial motility and pathogenesis. Our study revealed the structure of the Vibrio S-ring, a part of its polar flagellar motor, and highlighted its unique features compared with the well-studied Salmonella S-ring. The observed differences in the inter-subunit interactions and in the tilt angles between the Vibrio and Salmonella S-rings highlighted the species-specific variations and the mechanism for the optimization of MS-ring formation in the flagellar assembly. By concentrating on the region where the S-ring and the rod proteins interact, we uncovered conserved residues essential for the interaction. Our research contributes to the advancement of bacterial flagellar biology.
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Affiliation(s)
- Norihiro Takekawa
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Tatsuro Nishikino
- Institute for protein research, Osaka University, Suita, Osaka, Japan
| | | | - Mika Hirose
- Institute for protein research, Osaka University, Suita, Osaka, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Seiji Kojima
- Department of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Takayuki Uchihashi
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Takayuki Kato
- Institute for protein research, Osaka University, Suita, Osaka, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Michio Homma
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
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Li M, Xiong L, Chen W, Li Y, Khan A, Powell CA, Chen B, Zhang M. VirB11, a traffic ATPase, mediated flagella assembly and type IV pilus morphogenesis to control the motility and virulence of Xanthomonas albilineans. MOLECULAR PLANT PATHOLOGY 2024; 25:e70001. [PMID: 39223938 PMCID: PMC11369208 DOI: 10.1111/mpp.70001] [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] [Received: 02/17/2024] [Revised: 07/29/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Xanthomonas albilineans (Xal) is a gram-negative bacterial pathogen responsible for developing sugarcane leaf scald disease, which engenders significant economic losses within the sugarcane industry. In the current study, homologous recombination exchange was carried out to induce mutations within the virB/D4-like type IV secretion system (T4SS) genes of Xal. The results revealed that the virB11-deletion mutant (ΔvirB11) exhibited a loss in swimming and twitching motility. Application of transmission electron microscopy analysis further demonstrated that the ΔvirB11 failed to develop flagella formation and type IV pilus morphology and exhibited reduced swarming behaviour and virulence. However, these alterations had no discernible impact on bacterial growth. Comparative transcriptome analysis between the wild-type Xal JG43 and the deletion-mutant ΔvirB11 revealed 123 differentially expressed genes (DEGs), of which 28 and 10 DEGs were notably associated with flagellar assembly and chemotaxis, respectively. In light of these findings, we postulate that virB11 plays an indispensable role in regulating the processes related to motility and chemotaxis in Xal.
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Affiliation(s)
- Meilin Li
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | - Liya Xiong
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | - Wenhan Chen
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | - YiSha Li
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | - Abdullah Khan
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | | | - Baoshan Chen
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
| | - Muqing Zhang
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory of Conservation and Utilization for Subtropical Agri‐Biological ResourcesGuangxi UniversityNanningGuangxiChina
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3
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Deng J, Zhang W, Zhang L, Qin C, Wang H, Ling W. Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review. ENVIRONMENT INTERNATIONAL 2024; 191:108972. [PMID: 39180776 DOI: 10.1016/j.envint.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/11/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.
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Affiliation(s)
- Jibao Deng
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenkang Zhang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lingyu Zhang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hefei Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Tan J, Zhang L, Zhou X, Han S, Zhou Y, Zhu Y. Structural basis of the bacterial flagellar motor rotational switching. Cell Res 2024:10.1038/s41422-024-01017-z. [PMID: 39179739 DOI: 10.1038/s41422-024-01017-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/08/2024] [Indexed: 08/26/2024] Open
Abstract
The bacterial flagellar motor is a huge bidirectional rotary nanomachine that drives rotation of the flagellum for bacterial motility. The cytoplasmic C ring of the flagellar motor functions as the switch complex for the rotational direction switching from counterclockwise to clockwise. However, the structural basis of the rotational switching and how the C ring is assembled have long remained elusive. Here, we present two high-resolution cryo-electron microscopy structures of the C ring-containing flagellar basal body-hook complex from Salmonella Typhimurium, which are in the default counterclockwise state and in a constitutively active CheY mutant-induced clockwise state, respectively. In both complexes, the C ring consists of four subrings, but is in two different conformations. The CheY proteins are bound into an open groove between two adjacent protomers on the surface of the middle subring of the C ring and interact with the FliG and FliM subunits. The binding of the CheY protein induces a significant upward shift of the C ring towards the MS ring and inward movements of its protomers towards the motor center, which eventually remodels the structures of the FliG subunits and reverses the orientations and surface electrostatic potential of the αtorque helices to trigger the counterclockwise-to-clockwise rotational switching. The conformational changes of the FliG subunits reveal that the stator units on the motor require a relocation process in the inner membrane during the rotational switching. This study provides unprecedented molecular insights into the rotational switching mechanism and a detailed overall structural view of the bacterial flagellar motors.
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Affiliation(s)
- Jiaxing Tan
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ling Zhang
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xingtong Zhou
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Siyu Han
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Zhou
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Yongqun Zhu
- Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and College of Animal Sciences, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
- Center for Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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5
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Unay J, Kint N, Viollier PH. Evolution of paralogous multicomponent systems for site-specific O-sialylation of flagellin in Gram-negative and Gram-positive bacteria. Curr Biol 2024; 34:2932-2947.e7. [PMID: 38897200 DOI: 10.1016/j.cub.2024.05.058] [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: 12/14/2023] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
Many bacteria glycosylate flagellin on serine or threonine residues using pseudaminic acid (Pse) or other sialic acid-like donor sugars. Successful reconstitution of Pse-dependent sialylation by the conserved Maf-type flagellin glycosyltransferase (fGT) may require (a) missing component(s). Here, we characterize both Maf paralogs in the Gram-negative bacterium Shewanella oneidensis MR-1 and reconstitute Pse-dependent glycosylation in heterologous hosts. Remarkably, we uncovered distinct acceptor determinants and target specificities for each Maf. Whereas Maf-1 uses its C-terminal tetratricopeptide repeat (TPR) domain to confer flagellin acceptor and O-glycosylation specificity, Maf-2 requires the newly identified conserved specificity factor, glycosylation factor for Maf (GlfM), to form a ternary complex with flagellin. GlfM orthologs are co-encoded with Maf-2 in Gram-negative and Gram-positive bacteria and require an invariant aspartate in their four-helix bundle to function with Maf-2. Thus, convergent fGT evolution underlies distinct flagellin-binding modes in tripartite versus bipartite systems and, consequently, distinct O-glycosylation preferences of acceptor serine residues with Pse.
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Affiliation(s)
- Jovelyn Unay
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Nicolas Kint
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université Paris Cité, 75006 Paris, France
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland.
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6
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An L, Yang L, Yan T, Yi M, Liu S, Li H, Bao X. Synthesis and agricultural antimicrobial evaluation of new quinazoline derivatives containing both a piperazine linker and the N-acetyl moiety. PEST MANAGEMENT SCIENCE 2024. [PMID: 38899477 DOI: 10.1002/ps.8256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/23/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND To discover more efficient agricultural antimicrobial agents, a series of new quinazoline derivatives containing both a piperazine linker and the N-acetyl moiety were prepared and assessed for their antibacterial and antifungal activities. RESULTS All the target compounds were characterized by 1H and 13C NMR as well as high-resolution mass spectrometry (HRMS), and the chemical structure of the most potent compound E19 incorporating a 4-trifluoromethoxy substituent was clearly confirmed via single crystal X-ray diffraction measurements. The bioassay results indicated that some compounds possessed notable inhibitory effects in vitro against the bacterium Xanthomonas oryzae pv. oryzicola (Xoc). For example, compound E19 had an EC50 (effective concentration for 50% activity) value of 7.1 μg/mL towards this pathogen, approximately 15- and 10-fold more effective than the commercial bactericides thiodiazole copper and bismerthiazol (EC50 = 110.2 and 72.4 μg/mL, respectively). Subsequently, the mechanistic studies showed that compound E19 likely exerted its antibacterial efficacies by altering the cell morphology, increasing the permeability of bacterial cytoplasmic membrane, suppressing the production of bacterial extracellular polysaccharides and the extracellular enzyme activities (amylase and cellulase), and blocking the swimming motility of Xoc. Moreover, the proteomic analysis revealed that compound E19 could reduce the bacterial flagellar biosynthesis and decrease the flagellar motility by down-regulating the expression of the related differential proteins. CONCLUSION Compound E19 exhibited good potential for further development as a bactericide candidate for control of Xoc. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Lian An
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang, People's Republic of China
| | - Lan Yang
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
| | - Taisen Yan
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang, People's Republic of China
| | - Mingyan Yi
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang, People's Republic of China
| | - Songsong Liu
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang, People's Republic of China
| | - Hong Li
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang, People's Republic of China
| | - Xiaoping Bao
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Centre for Research and Development of Fine Chemicals, Guizhou University, Guiyang, People's Republic of China
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7
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Kou B, Wang Z, Mousavi S, Wang P, Ke Y. Dynamic Gold Nanostructures Based on DNA Self Assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308862. [PMID: 38143287 DOI: 10.1002/smll.202308862] [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] [Received: 10/04/2023] [Revised: 12/10/2023] [Indexed: 12/26/2023]
Abstract
The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10 nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.
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Affiliation(s)
- Bo Kou
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Zhichao Wang
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Shikufa Mousavi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
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8
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Singh PK, Sharma P, Afanzar O, Goldfarb MH, Maklashina E, Eisenbach M, Cecchini G, Iverson TM. CryoEM structures reveal how the bacterial flagellum rotates and switches direction. Nat Microbiol 2024; 9:1271-1281. [PMID: 38632342 PMCID: PMC11087270 DOI: 10.1038/s41564-024-01674-1] [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: 08/19/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024]
Abstract
Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural uncertainty regarding the cytoplasmic C-ring, or 'switch', limits our understanding of how the motor transmits torque and direction to the flagellar rod. Here we report cryogenic electron microscopy structures for Salmonella enterica serovar typhimurium inner membrane MS-ring and C-ring in a counterclockwise pose (4.0 Å) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å). Conformational differences between rotational poses include a 180° shift in FliF/FliG domains that rotates the outward-facing MotA/B binding site to inward facing. The regulator has specificity for the clockwise pose by bridging elements unique to this conformation. We used these structures to propose how the switch reverses rotation and transmits torque to the flagellum, which advances the understanding of bacterial chemotaxis and bidirectional motor rotation.
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Affiliation(s)
- Prashant K Singh
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Oshri Afanzar
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Margo H Goldfarb
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
| | - Michael Eisenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.
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9
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Vélez-González F, Marcos-Vilchis A, Vega-Baray B, Dreyfus G, Poggio S, Camarena L. Rotation of the Fla2 flagella of Cereibacter sphaeroides requires the periplasmic proteins MotK and MotE that interact with the flagellar stator protein MotB2. PLoS One 2024; 19:e0298028. [PMID: 38507361 PMCID: PMC10954123 DOI: 10.1371/journal.pone.0298028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/16/2024] [Indexed: 03/22/2024] Open
Abstract
The bacterial flagellum is a complex structure formed by more than 25 different proteins, this appendage comprises three conserved structures: the basal body, the hook and filament. The basal body, embedded in the cell envelope, is the most complex structure and houses the export apparatus and the motor. In situ images of the flagellar motor in different species have revealed a huge diversity of structures that surround the well-conserved periplasmic components of the basal body. The identity of the proteins that form these novel structures in many cases has been elucidated genetically and biochemically, but in others they remain to be identified or characterized. In this work, we report that in the alpha proteobacteria Cereibacter sphaeroides the novel protein MotK along with MotE are essential for flagellar rotation. We show evidence that these periplasmic proteins interact with each other and with MotB2. Moreover, these proteins localize to the flagellated pole and MotK localization is dependent on MotB2 and MotA2. These results together suggest that the role of MotK and MotE is to activate or recruit the flagellar stators to the flagellar structure.
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Affiliation(s)
- Fernanda Vélez-González
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Arely Marcos-Vilchis
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Benjamín Vega-Baray
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Georges Dreyfus
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sebastian Poggio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura Camarena
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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10
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Liu W, Zhang C, Zhang H, Ma S, Deng J, Wang D, Chang Z, Yang J. Molecular basis for curvature formation in SepF polymerization. Proc Natl Acad Sci U S A 2024; 121:e2316922121. [PMID: 38381790 PMCID: PMC10907229 DOI: 10.1073/pnas.2316922121] [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: 10/08/2023] [Accepted: 11/20/2023] [Indexed: 02/23/2024] Open
Abstract
The self-assembly of proteins into curved structures plays an important role in many cellular processes. One good example of this phenomenon is observed in the septum-forming protein (SepF), which forms polymerized structures with uniform curvatures. SepF is essential for regulating the thickness of the septum during bacteria cell division. In Bacillus subtilis, SepF polymerization involves two distinct interfaces, the β-β and α-α interfaces, which define the assembly unit and contact interfaces, respectively. However, the mechanism of curvature formation in this step is not yet fully understood. In this study, we employed solid-state NMR (SSNMR) to compare the structures of cyclic wild-type SepF assemblies with linear assemblies resulting from a mutation of G137 on the β-β interface. Our results demonstrate that while the sequence differences arise from the internal assembly unit, the dramatic changes in the shape of the assemblies depend on the α-α interface between the units. We further provide atomic-level insights into how the angular variation of the α2 helix on the α-α interface affects the curvature of the assemblies, using a combination of SSNMR, cryo-electron microscopy, and simulation methods. Our findings shed light on the shape control of protein assemblies and emphasize the importance of interhelical contacts in retaining curvature.
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Affiliation(s)
- Wenjing Liu
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Chang Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
| | - Huawei Zhang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen518055, People’s Republic of China
- Southern University of Science and Technology, Shenzhen518055, People’s Republic of China
| | - Shaojie Ma
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
| | - Jing Deng
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
| | - Daping Wang
- Southern University of Science and Technology, Shenzhen518055, People’s Republic of China
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen518000, People’s Republic of China
| | - Ziwei Chang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
- Interdisciplinary Institute of NMR and Molecular Sciences, School of Chemistry and Chemical Engineering, The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan430081, People’s Republic of China
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11
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Xu L, Liu X, Wu Q, Hua ZL, Yang F, Zhang JF. Phylogenetic analysis of pathogenic genes in Helicobacter species. Shijie Huaren Xiaohua Zazhi 2024; 32:58-70. [DOI: 10.11569/wcjd.v32.i1.58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/01/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Helicobacter bacteria are associated with gastrointestinal diseases, especially Helicobacter pylori (H. pylori). With the isolation of many non-Helicobacter pylori Helicobacters (NHPH) from the liver, intestines, and gallbladder of natural animal reservoirs, NHPH have been potential zoonotic pathogens, but their infection and pathogenic mechanisms are still unclear.
AIM To explore the phylogenetic relationship of Helicobacter species based on their pathogenic genes.
METHODS The present study collected the genomic sequences of 50 strains in genus Helicobacter, including 12 strains of H. pylori and 38 strains of NHPH. Based on 16S rRNA gene and several pathogenic genes (flagella, urease, and virulence factors), MAGA software (Version 11.0) was used to align their sequences and construct phylogenetic trees.
RESULTS The phylogenetic tree of 16S rRNA gene showed that gastric Helicobacter (GH) and enterohepatic Helicobacter species (EHS) were clustered into two large branches, respectively. All of the GH's hosts were mammals, while the hosts of EHS were many wild poultry and mammals. Based on the flagella motility-related genes (flaA, flaB, fliP, fliQ, fliR, fliG, fliM, and fliN), the phylogenetic trees were divided into two major branches (GH and EHS). Similarly, the phylogenetic trees of lipopolysaccharide (LPS) biosynthesis-related genes (lptA, waaC, and waaF) presented two major branches (GH and EHS), too. The urease genes existed in all of the 12 strains of H. pylori, 13 strains of gastric NHPH, and 4 strains of EHS (H. hepaticus, H. muridarum, H. bilis, and H. anseris). However, no significant phylogenetic patterns of GH and EHS were observed in the seven urease genes (ureA, ureB, ureE, ureF, ureG, ureH, and ureI).
CONCLUSION The phylogenetic relationship of Helicobacter species' pathogenic genes is dominated distinctly by the special colonization areas including gastric and enterohepatic niches.
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Affiliation(s)
- Le Xu
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Xing Liu
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province, China
| | - Qi Wu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhao-Lai Hua
- Institute of Tumor Prevention and Control, People's Hospital of Yangzhong City, Zhenjiang 212299, Jiangsu Province, China
| | - Fei Yang
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province, China
| | - Jun-Feng Zhang
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
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12
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Armitage JP. Microbial Primer: The bacterial flagellum - how bacteria swim. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001406. [PMID: 38226962 PMCID: PMC10866024 DOI: 10.1099/mic.0.001406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/11/2023] [Indexed: 01/17/2024]
Abstract
Bacteria swim using membrane-spanning, electrochemical gradient-powered motors that rotate semi-rigid helical filaments. This primer provides a brief overview of the basic synthesis, structure and operation of these nanomachines. Details and variations on the basic system can be found in suggested further reading.
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Affiliation(s)
- Judith P. Armitage
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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13
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Zhu S, Sun X, Li Y, Feng X, Gao B. The common origin and degenerative evolution of flagella in Actinobacteria. mBio 2023; 14:e0252623. [PMID: 38019005 PMCID: PMC10746217 DOI: 10.1128/mbio.02526-23] [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: 09/20/2023] [Accepted: 10/19/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Flagellar motility plays an important role in the environmental adaptation of bacteria and is found in more than 50% of known bacterial species. However, this important characteristic is sparsely distributed within members of the phylum Actinobacteria, which constitutes one of the largest bacterial groups. It is unclear why this important fitness organelle is absent in most actinobacterial species and the origin of flagellar genes in other species. Here, we present detailed analyses of the evolution of flagellar genes in Actinobacteria, in conjunction with the ecological distribution and cell biological features of major actinobacterial lineages, and the co-evolution of signal transduction systems. The results presented in addition to clarifying the puzzle of sporadic distribution of flagellar motility in Actinobacteria, also provide important insights into the evolution of major lineages within this phylum.
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Affiliation(s)
- Siqi Zhu
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian Sun
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
| | - Yuqian Li
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
| | - Xueyin Feng
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences and Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya, Hainan, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
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14
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Minamino T, Kinoshita M. Structure, Assembly, and Function of Flagella Responsible for Bacterial Locomotion. EcoSal Plus 2023; 11:eesp00112023. [PMID: 37260402 PMCID: PMC10729930 DOI: 10.1128/ecosalplus.esp-0011-2023] [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: 01/18/2023] [Accepted: 04/14/2023] [Indexed: 01/28/2024]
Abstract
Many motile bacteria use flagella for locomotion under a variety of environmental conditions. Because bacterial flagella are under the control of sensory signal transduction pathways, each cell is able to autonomously control its flagellum-driven locomotion and move to an environment favorable for survival. The flagellum of Salmonella enterica serovar Typhimurium is a supramolecular assembly consisting of at least three distinct functional parts: a basal body that acts as a bidirectional rotary motor together with multiple force generators, each of which serves as a transmembrane proton channel to couple the proton flow through the channel with torque generation; a filament that functions as a helical propeller that produces propulsion; and a hook that works as a universal joint that transmits the torque produced by the rotary motor to the helical propeller. At the base of the flagellum is a type III secretion system that transports flagellar structural subunits from the cytoplasm to the distal end of the growing flagellar structure, where assembly takes place. In recent years, high-resolution cryo-electron microscopy (cryoEM) image analysis has revealed the overall structure of the flagellum, and this structural information has made it possible to discuss flagellar assembly and function at the atomic level. In this article, we describe what is known about the structure, assembly, and function of Salmonella flagella.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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15
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Tao F, Ye Q, Chen Y, Luo L, Xu H, Xu J, Feng Z, Wang C, Li T, Wen Y, Hu Y, Dong H, Zhao X, Wu J. Antigen-loaded flagellate bacteria for enhanced adaptive immune response by intradermal injection. J Control Release 2023; 364:562-575. [PMID: 37926245 DOI: 10.1016/j.jconrel.2023.10.055] [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: 07/16/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Since the skin limits the distribution of intradermal vaccines, a large number of dendritic cells in the skin cannot be fully utilized to elicit a more effective immune response. Here, we loaded the antigen to the surface of the flagellate bacteria that was modified by cationic polymer, thus creating antigen-loaded flagellate bacteria (denoted as 'FB-Ag') to overcome the skin barrier and perform the active delivery of antigen in the skin. The FB-Ag showed fast speed (∼0.2 μm s-1) and strong dendritic cell activation capabilities in the skin model in vitro. In vivo, the FB-Ag promoted the spread of antigen in the skin through active movement, increased the contact between Intradermal dendritic cells and antigen, and effectively activated the internal dendritic cells in the skin. In a mouse of pulmonary metastatic melanoma and in mice bearing subcutaneous melanoma tumor, the FB-Ag effectively increased antigen-specific therapeutic efficacy and produced long-lasting immune memory. More importantly, the FB-Ag also enhanced the level of COVID-19 specific antibodies in the serum and the number of memory B cells in the spleen of mice. The movement of antigen-loaded flagellate bacteria to overcome intradermal constraints may enhance the activation of intradermal dendritic cells, providing new ideas for developing intradermal vaccines.
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Affiliation(s)
- Feng Tao
- Department of Andrology, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing 210093, China; State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China
| | - Qingsong Ye
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China
| | - Yimiao Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China
| | - Lifeng Luo
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China
| | - Haiheng Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China
| | - Jialong Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China
| | - Zhuo Feng
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China
| | - Chao Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China
| | - Tao Li
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China
| | - Yuxuan Wen
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China
| | - Yiqiao Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China; Jiangsu Provincial Key Laboratory for Nano Technology, Nanjing University, Nanjing 210093, China
| | - Hong Dong
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China.
| | - Xiaozhi Zhao
- Department of Andrology, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing 210093, China.
| | - Jinhui Wu
- Department of Andrology, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Nanjing 210093, China; State Key Laboratory of Pharmaceutical Biotechnology, Medical School of Nanjing University, Nanjing University, Nanjing 210093, China; Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China; Jiangsu Provincial Key Laboratory for Nano Technology, Nanjing University, Nanjing 210093, China.
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16
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Carter EW, Peraza OG, Wang N. The protein interactome of the citrus Huanglongbing pathogen Candidatus Liberibacter asiaticus. Nat Commun 2023; 14:7838. [PMID: 38030598 PMCID: PMC10687234 DOI: 10.1038/s41467-023-43648-7] [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: 07/04/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023] Open
Abstract
The bacterium Candidatus Liberibacter asiaticus (CLas) causes citrus Huanglongbing disease. Our understanding of the pathogenicity and biology of this microorganism remains limited because CLas has not yet been cultivated in artificial media. Its genome is relatively small and encodes approximately 1136 proteins, of which 415 have unknown functions. Here, we use a high-throughput yeast-two-hybrid (Y2H) screen to identify interactions between CLas proteins, thus providing insights into their potential functions. We identify 4245 interactions between 542 proteins, after screening 916 bait and 936 prey proteins. The false positive rate of the Y2H assay is estimated to be 2.9%. Pull-down assays for nine protein-protein interactions (PPIs) likely involved in flagellar function support the robustness of the Y2H results. The average number of PPIs per node in the CLas interactome is 15.6, which is higher than the numbers previously reported for interactomes of free-living bacteria, suggesting that CLas genome reduction has been accompanied by increased protein multi-functionality. We propose potential functions for 171 uncharacterized proteins, based on the PPI results, guilt-by-association analyses, and comparison with data from other bacterial species. We identify 40 hub-node proteins, including quinone oxidoreductase and LysR, which are known to protect other bacteria against oxidative stress and might be important for CLas survival in the phloem. We expect our PPI database to facilitate research on CLas biology and pathogenicity mechanisms.
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Affiliation(s)
- Erica W Carter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Orlene Guerra Peraza
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Nian Wang
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA.
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, US.
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17
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Botting JM, Tachiyama S, Gibson KH, Liu J, Starai VJ, Hoover TR. FlgV forms a flagellar motor ring that is required for optimal motility of Helicobacter pylori. PLoS One 2023; 18:e0287514. [PMID: 37976320 PMCID: PMC10655999 DOI: 10.1371/journal.pone.0287514] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 11/19/2023] Open
Abstract
Flagella-driven motility is essential for Helicobacter pylori to colonize the human stomach, where it causes a variety of diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. H. pylori has evolved a high-torque-generating flagellar motor that possesses several accessories not found in the archetypical Escherichia coli motor. FlgV was one of the first flagellar accessory proteins identified in Campylobacter jejuni, but its structure and function remain poorly understood. Here, we confirm that deletion of flgV in H. pylori B128 and a highly motile variant of H. pylori G27 (G27M) results in reduced motility in soft agar medium. Comparative analyses of in-situ flagellar motor structures of wild-type, ΔflgV, and a strain expressing FlgV-YFP showed that FlgV forms a ring-like structure closely associated with the junction of two highly conserved flagellar components: the MS and C rings. The results of our studies suggest that the FlgV ring has adapted specifically in Campylobacterota to support the assembly and efficient function of the high-torque-generating motors.
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Affiliation(s)
- Jack M. Botting
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Shoichi Tachiyama
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Katherine H. Gibson
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Vincent J. Starai
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Timothy R. Hoover
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
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18
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Partridge JD, Dufour Y, Hwang Y, Harshey RM. Flagellar motor remodeling during swarming requires FliL. Mol Microbiol 2023; 120:670-683. [PMID: 37675594 PMCID: PMC10942728 DOI: 10.1111/mmi.15148] [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: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/08/2023]
Abstract
FliL is an essential component of the flagellar machinery in some bacteria, but a conditional one in others. The conditional role is for optimal swarming in some bacteria. During swarming, physical forces associated with movement on a surface are expected to exert a higher load on the flagellum, requiring more motor torque to move. FliL was reported to enhance motor output in several bacteria and observed to assemble as a ring around ion-conducting stators that power the motor. In this study we identify a common new function for FliL in diverse bacteria-Escherichia coli, Bacillus subtilis, and Proteus mirabilis. During swarming, all these bacteria show increased cell speed and a skewed motor bias that suppresses cell tumbling. We demonstrate that these altered motor parameters, or "motor remodeling," require FliL. Both swarming and motor remodeling can be restored in an E. coli fliL mutant by complementation with fliL genes from P. mirabilis and B. subtilis, showing conservation of a swarming-associated FliL function across phyla. In addition, we demonstrate that the strong interaction we reported earlier between FliL and the flagellar MS-ring protein FliF is confined to the RBM-3 domain of FliF that links the periplasmic rod to the cytoplasmic C-ring. This interaction may explain several phenotypes associated with the absence of FliL.
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Affiliation(s)
- Jonathan D. Partridge
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
| | - Yann Dufour
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - YuneSahng Hwang
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
| | - Rasika M. Harshey
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
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19
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Sun Q, Yuan C, Zhou S, Lu J, Zeng M, Cai X, Song H. Helicobacter pylori infection: a dynamic process from diagnosis to treatment. Front Cell Infect Microbiol 2023; 13:1257817. [PMID: 37928189 PMCID: PMC10621068 DOI: 10.3389/fcimb.2023.1257817] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023] Open
Abstract
Helicobacter pylori, a gram-negative microaerophilic pathogen, causes several upper gastrointestinal diseases, such as chronic gastritis, peptic ulcer disease, and gastric cancer. For the diseases listed above, H. pylori has different pathogenic mechanisms, including colonization and virulence factor expression. It is essential to make accurate diagnoses and provide patients with effective treatment to achieve positive clinical outcomes. Detection of H. pylori can be accomplished invasively and noninvasively, with both having advantages and limitations. To enhance therapeutic outcomes, novel therapeutic regimens, as well as adjunctive therapies with probiotics and traditional Chinese medicine, have been attempted along with traditional empiric treatments, such as triple and bismuth quadruple therapies. An H. pylori infection, however, is difficult to eradicate during treatment owing to bacterial resistance, and there is no commonly available preventive vaccine. The purpose of this review is to provide an overview of our understanding of H. pylori infections and to highlight current treatment and diagnostic options.
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Affiliation(s)
- Qifang Sun
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Traditional Chinese Medicine (TCM) Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Chengzhi Yuan
- Hunan Provincial Key Laboratory of Traditional Chinese Medicine (TCM) Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan, China
- School of Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Sainan Zhou
- The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Jing Lu
- School of Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Meiyan Zeng
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Xiong Cai
- School of International Education, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Houpan Song
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of Traditional Chinese Medicine (TCM) Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan, China
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20
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Yao T, Huang Y, Huai Z, Liu X, Liu X, Liu Y, Sun H, Pang Y. Response mechanisms to acid stress promote LF82 replication in macrophages. Front Cell Infect Microbiol 2023; 13:1255083. [PMID: 37881369 PMCID: PMC10595154 DOI: 10.3389/fcimb.2023.1255083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
Background Adherent-invasive E. coli (AIEC) LF82 is capable of adhering to and invading intestinal epithelial cells, as well as replicating within macrophages without inducing host cell death. Methods We compared the transcriptomics of LF82 at pH=7.5 and pH=5.8 by RNA-sequencing, and qRT-PCR verified differentially expressed genes (DEGs). The deletion mutants of DEGs in the treatment group (pH=5.8) compared to the control group (pH=7.5) were constructed by λ recombinant. The replication differences between the mutants and WT infected Raw 264.7 at 24 h.p.i were analyzed by combining LB solid plate count and confocal observation. NH4Cl and chloroquine diphosphate (CQ) were used for acid neutralization to study the effect of pH on the replication of LF82 in macrophages. Na2NO3 was added to RPMI 1640 to study the effect of nitrate on the replication of LF82 in macrophages. 0.3% solid LB was used for flagellar motility assay and Hela was used to study flagellar gene deletion mutants and WT adhesion and invasion ability. Results In this study, we found that infection with LF82 results in acidification of macrophages. Subsequent experiments demonstrated that an intracellular acidic environment is necessary for LF82 replication. Transcriptome and phenotypic analysis showed that high expression of acid shock genes and acid fitness genes promotes LF82 replication in macrophages. Further, we found that the replication of LF82 in macrophages was increased under nitrate treatment, and nitrogen metabolism genes of LF82 were upregulated in acid treatment. The replication in macrophages of ΔnarK, ΔnarXL, ΔnarP, and Δhmp were decreased. In addition, we found that the expression of flagellar genes was downregulated in acidic pH and after LF82 invading macrophages. Motility assay shows that the movement of LF82 on an acidic semisolid agar plate was limited. Further results showed that ΔfliC and ΔfliD decreased in motility, adhesion ability, and invasion of host cells, but no significant effect on replication in macrophages was observed. Conclusion In this study, we simulated the acidic environment in macrophages, combined with transcriptome technology, and explained from the genetic level that LF82 promotes replication by activating its acid shock and fitness system, enhancing nitrate utilization, and inhibiting flagellar function.
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Affiliation(s)
- Ting Yao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Yu Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Zimeng Huai
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Xingmei Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Xiaowen Liu
- Academy of Psychology and Behavior, Faculty of Psychology, Tianjin Normal University, Tianjin, China
| | - Yutao Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Hao Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Yu Pang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
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21
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Zhang Y, Zhang D, Geng Y, He Y, Song P, Wang R. Construction of self-propelled micromotor for "hunting bacteria". Biomater Sci 2023; 11:6775-6780. [PMID: 37695067 DOI: 10.1039/d3bm01175e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The inherent migration behavior of bacteria has inevitably impacted the advancement of the antibacterial treatment technology. Hunting bacteria, especially those with flagellates, requires self-propelled materials, which could kill bacteria autonomously. Herein, we designed and synthesized a self-propelled micromotor (SPM) tailed with poly(thiazole) to yield bimetallic organic frameworks (BiOFs), in which the assembly of BiOFs are similar to the "Newman projection". The moving speed of the obtained SPM was 238.6 μm s-1 and presented excellent antibacterial activity; more than 90% bacteria were hunted and killed in flowing water. Its minimum inhibitory concentration (MIC) against E. coli and S. aureus was 3.2 and 0.4 mg mL-1, respectively, and its antibacterial activity was still retained after recycling for 5 times. Its antibacterial mechanism along with the contribution of the active units and flow rate was investigated. In summary, a novel self-propelled material for hunting bacteria was synthesized by an unprecedented and efficient strategy. This approach is anticipated to create huge possibilities for its applications in the fields of antibacterial, disinfection, and microdevices.
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Affiliation(s)
- Yaping Zhang
- Key Lab Eco-Functional Polymer Materials of MOE, Institute of Polymer, College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Duoxin Zhang
- Key Lab Eco-Functional Polymer Materials of MOE, Institute of Polymer, College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Yuanze Geng
- Key Lab Eco-Functional Polymer Materials of MOE, Institute of Polymer, College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Yufeng He
- Key Lab Eco-Functional Polymer Materials of MOE, Institute of Polymer, College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Pengfei Song
- Key Lab Eco-Functional Polymer Materials of MOE, Institute of Polymer, College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Rongmin Wang
- Key Lab Eco-Functional Polymer Materials of MOE, Institute of Polymer, College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
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22
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Gibson KH, Botting JM, Al-Otaibi N, Maitre K, Bergeron J, Starai VJ, Hoover TR. Control of the flagellation pattern in Helicobacter pylori by FlhF and FlhG. J Bacteriol 2023; 205:e0011023. [PMID: 37655916 PMCID: PMC10521351 DOI: 10.1128/jb.00110-23] [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: 03/24/2023] [Accepted: 07/06/2023] [Indexed: 09/02/2023] Open
Abstract
FlhF and FlhG control the location and number of flagella, respectively, in many polar-flagellated bacteria. The roles of FlhF and FlhG are not well characterized in bacteria that have multiple polar flagella, such as Helicobacter pylori. Deleting flhG in H. pylori shifted the flagellation pattern where most cells had approximately four flagella to a wider and more even distribution in flagellar number. As reported in other bacteria, deleting flhF in H. pylori resulted in reduced motility, hypoflagellation, and the improper localization of flagella to nonpolar sites. Motile variants of H. pylori ∆flhF mutants that had a higher proportion of flagella localizing correctly to the cell pole were isolated, but we were unable to identify the genetic determinants responsible for the increased localization of flagella to the cell pole. One motile variant though produced more flagella than the ΔflhF parental strain, which apparently resulted from a missense mutation in fliF (encodes the MS ring protein), which changed Asn-255 to aspartate. Recombinant FliFN255D, but not recombinant wild-type FliF, formed ordered ring-like assemblies in vitro that were ~50 nm wide and displayed the MS ring architecture. We infer from these findings that the FliFN225D variant forms the MS ring more effectively in vivo in the absence of FlhF than wild-type FliF. IMPORTANCE Helicobacter pylori colonizes the human stomach where it can cause a variety of diseases, including peptic ulcer disease and gastric cancer. H. pylori uses flagella for motility, which is required for host colonization. FlhG and FlhF control the flagellation patterns in many bacteria. We found that in H. pylori, FlhG ensures that cells have approximately equal number of flagella and FlhF is needed for flagellum assembly and localization. FlhF is proposed to facilitate the assembly of FliF into the MS ring, which is one of the earliest structures formed in flagellum assembly. We identified a FliF variant that assembles the MS ring in the absence of FlhF, which supports the proposed role of FlhF in facilitating MS ring assembly.
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Affiliation(s)
| | - Jack M. Botting
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Natalie Al-Otaibi
- Randall Division of Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Kriti Maitre
- Randall Division of Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Julien Bergeron
- Randall Division of Cell and Molecular Biophysics, King’s College London, London, United Kingdom
| | - Vincent J. Starai
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Timothy R. Hoover
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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23
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Worrall LJ, Majewski DD, Strynadka NCJ. Structural Insights into Type III Secretion Systems of the Bacterial Flagellum and Injectisome. Annu Rev Microbiol 2023; 77:669-698. [PMID: 37713458 DOI: 10.1146/annurev-micro-032521-025503] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
Two of the most fascinating bacterial nanomachines-the broadly disseminated rotary flagellum at the heart of cellular motility and the eukaryotic cell-puncturing injectisome essential to specific pathogenic species-utilize at their core a conserved export machinery called the type III secretion system (T3SS). The T3SS not only secretes the components that self-assemble into their extracellular appendages but also, in the case of the injectisome, subsequently directly translocates modulating effector proteins from the bacterial cell into the infected host. The injectisome is thought to have evolved from the flagellum as a minimal secretory system lacking motility, with the subsequent acquisition of additional components tailored to its specialized role in manipulating eukaryotic hosts for pathogenic advantage. Both nanomachines have long been the focus of intense interest, but advances in structural and functional understanding have taken a significant step forward since 2015, facilitated by the revolutionary advances in cryo-electron microscopy technologies. With several seminal structures of each nanomachine now captured, we review here the molecular similarities and differences that underlie their diverse functions.
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Affiliation(s)
- Liam J Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
| | - Dorothy D Majewski
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
- Current affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
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24
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Genthe E, Miletic S, Tekkali I, Hennell James R, Marlovits TC, Heuser P. PickYOLO: Fast deep learning particle detector for annotation of cryo electron tomograms. J Struct Biol 2023; 215:107990. [PMID: 37364763 DOI: 10.1016/j.jsb.2023.107990] [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: 12/31/2022] [Revised: 05/31/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Particle localization (picking) in digital tomograms is a laborious and time-intensive step in cryogenic electron tomography (cryoET) analysis often requiring considerable user involvement, thus becoming a bottleneck for automated cryoET subtomogram averaging (STA) pipelines. In this paper, we introduce a deep learning framework called PickYOLO to tackle this problem. PickYOLO is a super-fast, universal particle detector based on the deep-learning real-time object recognition system YOLO (You Only Look Once), and tested on single particles, filamentous structures, and membrane-embedded particles. After training with the centre coordinates of a few hundred representative particles, the network automatically detects additional particles with high yield and reliability at a rate of 0.24-3.75 s per tomogram. PickYOLO can automatically detect number of particles comparable to those manually selected by experienced microscopists. This makes PickYOLO a valuable tool to substantially reduce the time and manual effort needed to analyse cryoET data for STA, greatly aiding in high-resolution cryoET structure determination.
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Affiliation(s)
- Erik Genthe
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sean Miletic
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; CSSB Centre for Structural Systems Biology, Notkestr. 85, 22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
| | - Indira Tekkali
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; Helmholtz Imaging, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Rory Hennell James
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; CSSB Centre for Structural Systems Biology, Notkestr. 85, 22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
| | - Thomas C Marlovits
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; CSSB Centre for Structural Systems Biology, Notkestr. 85, 22607 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.
| | - Philipp Heuser
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany; Helmholtz Imaging, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
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25
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Xu H, Xiong S, Chen Y, Ye Q, Guan N, Hu Y, Wu J. Flagella of Tumor-Targeting Bacteria Trigger Local Hemorrhage to Reprogram Tumor-Associated Macrophages for Improved Antitumor Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303357. [PMID: 37310893 DOI: 10.1002/adma.202303357] [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] [Received: 04/11/2023] [Revised: 06/12/2023] [Indexed: 06/15/2023]
Abstract
Tumor-associated macrophages (TAMs) exhibit an immunosuppressive M2 phenotype and lead to failure of antitumor therapy. Infiltrated erythrocytes during hemorrhage are recognized as a promising strategy for polarizing TAMs. However, novel materials that precisely induce tumor hemorrhage without affecting normal coagulation still face challenges. Here, tumor-targeting bacteria (flhDC VNP) are genetically constructed to realize precise tumor hemorrhage. FlhDC VNP colonizes the tumor and overexpresses flagella during proliferation. The flagella promote the expression of tumor necrosis factor α, which induces local tumor hemorrhage. Infiltrated erythrocytes during the hemorrhage temporarily polarize macrophages to the M1 subtype. In the presence of artesunate, this short-lived polarization is transformed into a sustained polarization because artesunate and heme form a complex that continuously produces reactive oxygen species. Therefore, the flagella of active tumor-targeting bacteria may open up new strategies for reprogramming TAMs and improving antitumor therapy.
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Affiliation(s)
- Haiheng Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, 210093, China
- Department of Andrology, Medical School of Nanjing University, Nanjing, 210093, China
- Jiangsu Provincial Key Laboratory for Nano Technology, Nanjing University, Nanjing, 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
- Wuxi Xishan NJU Institute of Applied Biotechnology, Anzhen Street, Xishan District, Wuxi, 214101, China
| | - Shuqin Xiong
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, 210093, China
- Department of Andrology, Medical School of Nanjing University, Nanjing, 210093, China
- Jiangsu Provincial Key Laboratory for Nano Technology, Nanjing University, Nanjing, 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
- Wuxi Xishan NJU Institute of Applied Biotechnology, Anzhen Street, Xishan District, Wuxi, 214101, China
| | - Yiyun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, 210093, China
- Department of Andrology, Medical School of Nanjing University, Nanjing, 210093, China
- Jiangsu Provincial Key Laboratory for Nano Technology, Nanjing University, Nanjing, 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
- Wuxi Xishan NJU Institute of Applied Biotechnology, Anzhen Street, Xishan District, Wuxi, 214101, China
| | - Qingsong Ye
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, 210093, China
- Department of Andrology, Medical School of Nanjing University, Nanjing, 210093, China
- Jiangsu Provincial Key Laboratory for Nano Technology, Nanjing University, Nanjing, 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
- Wuxi Xishan NJU Institute of Applied Biotechnology, Anzhen Street, Xishan District, Wuxi, 214101, China
| | - Nan Guan
- Molecular, Cellular and Development Biology Department, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yiqiao Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, 210093, China
- Jiangsu Provincial Key Laboratory for Nano Technology, Nanjing University, Nanjing, 210093, China
| | - Jinhui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, 210093, China
- Department of Andrology, Medical School of Nanjing University, Nanjing, 210093, China
- Jiangsu Provincial Key Laboratory for Nano Technology, Nanjing University, Nanjing, 210093, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
- Wuxi Xishan NJU Institute of Applied Biotechnology, Anzhen Street, Xishan District, Wuxi, 214101, China
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26
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Kint N, Viollier PH. Extracellular transfer of a conserved polymerization factor for multi-flagellin filament assembly in Caulobacter. Cell Rep 2023; 42:112890. [PMID: 37515768 DOI: 10.1016/j.celrep.2023.112890] [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: 12/12/2022] [Revised: 06/15/2023] [Accepted: 07/12/2023] [Indexed: 07/31/2023] Open
Abstract
Unidirectional growth of filamentous protein assemblies including the bacterial flagellum relies on dedicated polymerization factors (PFs). The molecular determinants and structural transitions imposed by PFs on multi-subunit assembly are poorly understood. Here, we unveil FlaY from the polarized α-proteobacterium Caulobacter crescentus as a defining member of an alternative class of specialized flagellin PFs. Unlike the paradigmatic FliD capping protein, FlaY relies on a funnel-like β-propeller fold for flagellin polymerization. FlaY binds flagellin and is secreted by the flagellar secretion apparatus, yet it can also promote flagellin polymerization exogenously when donated from flagellin-deficient cells, serving as a transferable, extracellular public good. While the surge in FlaY abundance precedes bulk flagellin synthesis, FlaY-independent filament assembly is enhanced by mutation of a conserved region in multiple flagellin paralogs. We suggest that FlaYs are (multi-)flagellin PFs that evolved convergently to FliDs yet appropriated the versatile β-propeller fold implicated in human diseases for chaperone-assisted filament assembly.
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Affiliation(s)
- Nicolas Kint
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Genève, Switzerland.
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine and Geneva Center for Inflammation Research (GCIR), Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Genève, Switzerland.
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27
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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28
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Partridge JD, Dufour Y, Hwang Y, Harshey RM. Flagellar motor remodeling during swarming requires FliL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549092. [PMID: 37503052 PMCID: PMC10370021 DOI: 10.1101/2023.07.14.549092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
FliL is an essential component of the flagellar machinery in some bacteria, but a conditional one in others. The conditional role is for optimal swarming in some bacteria. During swarming, physical forces associated with movement on a surface are expected to exert a higher load on the flagellum, requiring more motor torque to move. Bacterial physiology and morphology are also altered during swarming to cope with the challenges of surface navigation. FliL was reported to enhance motor output in several bacteria and observed to assemble as a ring around ion-conducting stators that power the motor. In this study we identify a common new function for FliL in diverse bacteria - Escherichia coli, Bacillus subtilis and Proteus mirabilis . During swarming, all these bacteria show increased cell speed and a skewed motor bias that suppresses cell tumbling. We demonstrate that these altered motor parameters, or 'motor remodeling', require FliL. Both swarming and motor remodeling can be restored in an E. coli fliL mutant by complementation with fliL genes from P. mirabilis and B. subtilis , showing conservation of swarming-associated FliL function across phyla. In addition, we demonstrate that the strong interaction we reported earlier between FliL and the flagellar MS-ring protein FliF is confined to the RBM-3 domain of FliF that links the periplasmic rod to the cytoplasmic C-ring. This interaction may explain several phenotypes associated with the absence of FliL.
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Affiliation(s)
- Jonathan D Partridge
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Yann Dufour
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - YuneSahng Hwang
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Rasika M Harshey
- Department of Molecular Biosciences and the LaMontagne Center for Infectious Diseases The University of Texas at Austin, Austin, Texas, 78712, USA
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29
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Ye C, Liu Z, Yu S, Fan Z, Wang Y. Design and Motion Analysis of a Soft-Limb Robot Inspired by Bacterial Flagella. Biomimetics (Basel) 2023; 8:271. [PMID: 37504159 PMCID: PMC10377722 DOI: 10.3390/biomimetics8030271] [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: 05/18/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/29/2023] Open
Abstract
Soft robots demonstrate an impressive ability to adapt to objects and environments. However, current soft mobile robots often use a single mode of movement. This gives soft robots good locomotion performance in specific environments but poor performance in others. In this paper, we propose a leg-wheel mechanism inspired by bacterial flagella and use it to design a leg-wheel robot. This mechanism employs a tendon-driven continuum structure to replicate the bacterial flagellar filaments, while servo and gear components mimic the action of bacterial flagellar motors. By utilizing twisting and swinging motions of the continuum structure, the robot achieves both wheeled and legged locomotion. The paper provides comprehensive descriptions and detailed kinematic analysis of the mechanism and the robot. To verify the feasibility of the robot, a prototype was implemented, and experiments were performed on legged mode, wheeled mode, and post-overturning motion. The experimental results demonstrate that the robot can achieve legged and wheeled motions. Moreover, it is also demonstrated that the robot still has mobility after overturning. This expands the applicability scenarios of the current soft mobile robot.
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Affiliation(s)
- Changlong Ye
- School of Mechatronics Engineering, Shenyang Aerospace University, Shenyang 110136, China
| | - Zhanpeng Liu
- School of Mechatronics Engineering, Shenyang Aerospace University, Shenyang 110136, China
| | - Suyang Yu
- School of Mechatronics Engineering, Shenyang Aerospace University, Shenyang 110136, China
| | - Zifu Fan
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 569830, Singapore
| | - Yinchao Wang
- School of Mechatronics Engineering, Shenyang Aerospace University, Shenyang 110136, China
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30
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Liang C, Zhong Q, Pan L, Liu F, Li X, Yang J, Ma Y, Zhou J, Yang ST. Organic ligands regulate the environmental impacts of metal-organic frameworks on nitrogen-fixing bacterium Azotobacter vinelandii. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131373. [PMID: 37031673 DOI: 10.1016/j.jhazmat.2023.131373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/08/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
Metal-organic frameworks (MOFs) are rapidly developed materials with fantastic properties and wide applications. The increasing studies highlighted the potential threats of MOF materials to the environment. Comparing to the limited species of metal elements, the organic ligands have much higher diversity, but the influence of organic ligands on the environmental impacts of MOFs has not been revealed. Herein, we synthesized three Cu-MOFs with different organic ligands, namely Cu-BDC (1,4-terephthalic acid), Cu-IM (imidazole) and Cu-TATB (2,4,6-tris(4-carboxyphenyl)- 1,3,5-triazine), and evaluated their environmental toxicity to the nitrogen-fixing bacterium Azotobacter vinelandii. Cu-BDC inhibited the bacterial growth at lower concentrations than Cu-IM and Cu-TATB. The transcriptomes suggested the changes of membrane components by Cu-MOFs, consistent with the membrane leakage and cell wall damages. Cu-MOFs inhibited the nitrogen fixation activity through energy metabolism disturbance according to Gene Ontology functional annotation of ATP binding, Ca2+Mg2+-ATPase activity and ATP content. Only Cu-IM lowered the nitrogen fixation related nif genes, and affected the ribosome, purine metabolism and oxidative phosphorylation pathways. Otherwise, Cu-BDC and Cu-TATB mainly affected the flagellar assemblies and bacterial chemotaxis pathways. Our results collectively indicated that organic ligands regulated the environmental toxicity of MOFs through different metabolism pathways.
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Affiliation(s)
- Chengzhuang Liang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Qinmei Zhong
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Lejie Pan
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Fangshi Liu
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Xin Li
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Jinwei Yang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Yusen Ma
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Junrou Zhou
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Sheng-Tao Yang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China.
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31
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Takahashi K, Nishikino T, Kajino H, Kojima S, Uchihashi T, Homma M. Ring formation by Vibrio fusion protein composed of FliF and FliG, MS-ring and C-ring component of bacterial flagellar motor in membrane. Biophys Physicobiol 2023; 20:e200028. [PMID: 38496245 PMCID: PMC10941966 DOI: 10.2142/biophysico.bppb-v20.0028] [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: 03/22/2023] [Accepted: 06/05/2023] [Indexed: 03/19/2024] Open
Abstract
The marine bacterium Vibrio alginolyticus has a single flagellum as a locomotory organ at the cell pole, which is rotated by the Na+-motive force to swim in a liquid. The base of the flagella has a motor composed of a stator and rotor, which serves as a power engine to generate torque through the rotor-stator interaction coupled to Na+ influx through the stator channel. The MS-ring, which is embedded in the membrane at the base of the flagella as part of the rotor, is the initial structure required for flagellum assembly. It comprises 34 molecules of the two-transmembrane protein FliF. FliG, FliM, and FliN form a C-ring just below the MS-ring. FliG is an important rotor protein that interacts with the stator PomA and directly contributes to force generation. We previously found that FliG promotes MS-ring formation in E. coli. In the present study, we constructed a fliF-fliG fusion gene, which encodes an approximately 100 kDa protein, and the successful production of this protein effectively formed the MS-ring in E. coli cells. We observed fuzzy structures around the ring using either electron microscopy or high-speed atomic force microscopy (HS-AFM), suggesting that FliM and FliN are necessary for the formation of a stable ring structure. The HS-AFM movies revealed flexible movements at the FliG region.
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Affiliation(s)
- Kanji Takahashi
- Department of Physics, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Tatsuro Nishikino
- Institute for protein research, Osaka University, Suita, Osaka 565-0871, Japan
- Present address: Department of Materials Science and Engineering, Nagoya Institute of Technology, Nagoya Aichi 466-8555, Japan
| | - Hiroki Kajino
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi 464-0814, Japan
- Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Michio Homma
- Department of Physics, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
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Liwo A, Pyrka M, Czaplewski C, Peng X, Niemi AJ. Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach. Biomolecules 2023; 13:941. [PMID: 37371521 PMCID: PMC10296118 DOI: 10.3390/biom13060941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Molecular motors are essential for the movement and transportation of macromolecules in living organisms. Among them, rotatory motors are particularly efficient. In this study, we investigated the long-term dynamics of the designed left-handed alpha/alpha toroid (PDB: 4YY2), the RBM2 flagellum protein ring from Salmonella (PDB: 6SD5), and the V-type Na+-ATPase rotor in Enterococcus hirae (PDB: 2BL2) using microcanonical and canonical molecular dynamics simulations with the coarse-grained UNRES force field, including a lipid-membrane model, on a millisecond laboratory time scale. Our results demonstrate that rotational motion can occur with zero total angular momentum in the microcanonical regime and that thermal motions can be converted into net rotation in the canonical regime, as previously observed in simulations of smaller cyclic molecules. For 6SD5 and 2BL2, net rotation (with a ratcheting pattern) occurring only about the pivot of the respective system was observed in canonical simulations. The extent and direction of the rotation depended on the initial conditions. This result suggests that rotatory molecular motors can convert thermal oscillations into net rotational motion. The energy from ATP hydrolysis is required probably to set the direction and extent of rotation. Our findings highlight the importance of molecular-motor structures in facilitating movement and transportation within living organisms.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland; (M.P.); (C.C.)
| | - Maciej Pyrka
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland; (M.P.); (C.C.)
- Department of Physics and Biophysics, University of Warmia and Mazury, ul. Oczapowskiego 4, 10-719 Olsztyn, Poland
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland; (M.P.); (C.C.)
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China;
| | - Antti J. Niemi
- Nordita, Stockholm University and Uppsala University, Roslagstullsbacken 23, SE-106 91 Stockholm, Sweden;
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Wang X, Jiang C, Wang D, Yang Y, Fan L, Xu S, Zhuang X. Quorum sensing responses of activated sludge to free nitrous acid: Zoogloea deformation, AHL redistribution, and microbiota acclimatization. WATER RESEARCH 2023; 238:119993. [PMID: 37146395 DOI: 10.1016/j.watres.2023.119993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/03/2023] [Accepted: 04/22/2023] [Indexed: 05/07/2023]
Abstract
Free nitrous acid (FNA) has been widely employed for improvement of wastewater management by altering sludge characteristic and function based on its polymer lysing and biocidal capacity. Sludge characteristic and function are commonly considered as the joint consequence of microbial individual behaviors and quorum sensing (QS) involved collective behaviours, but the role of the latter in FNA treatment was still as-yet-unidentified and addressed in this research. The results of sludge morphology and component characterized FNA-induced zoogloea deformation, including inner cell exposure, half of extracellular polymeric substances (EPS) reduction and adsorption site depletion. During zoogloea deformation, four acyl-homoserine lactones (AHLs), including C4-HSL, C8-HSL, C10-HSL and C12-HSL, transferred inward of microbiota, and their total contents reduced by 66% because of depressed signal production, augmented decomposer and recognition. Transcriptome analysis revealed that differentially expressed QS driven by AHL redistribution facilitated microbiota acclimatization including cellular motility and hydrolase synthesis for EPS consumption. Boosted motility may favor escaping from stress spot and moderating intercellular acidity based on cell motility test. Feasible EPS consumption provided nutrition for heterotrophic metabolisms testified by pure culture with EPS as sole nutrition. Our work thus comprehensively revealed QS behaviours responding to FNA and deepened the understanding to FNA treatment performance in wastewater management.
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Affiliation(s)
- Xu Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cancan Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Danhua Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yang Yang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450000, China
| | - Lijing Fan
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450000, China
| | - Shengjun Xu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
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Chu PL, Feng YM, Long ZQ, Xiao WL, Ji J, Zhou X, Qi PY, Zhang TH, Zhang H, Liu LW, Yang S. Novel Benzothiazole Derivatives as Potential Anti-Quorum Sensing Agents for Managing Plant Bacterial Diseases: Synthesis, Antibacterial Activity Assessment, and SAR Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6525-6540. [PMID: 37073686 DOI: 10.1021/acs.jafc.2c07810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
As quorum sensing (QS) regulates bacterial pathogenicity, antiquorum sensing agents have powerful application potential for controlling bacterial infections and overcoming pesticide/drug resistance. Identifying anti-QS agents thus represents a promising approach in agrochemical development. In this study, the anti-QS potency of 53 newly prepared benzothiazole derivatives containing an isopropanolamine moiety was analyzed, and structure-activity relationships were examined. Compound D3 exhibited the strongest antibacterial activity, with an in vitro EC50 of 1.54 μg mL-1 against Xanthomonas oryzae pv oryzae (Xoo). Compound D3 suppressed QS-regulated virulence factors (e.g., biofilm, extracellular polysaccharides, extracellular enzymes, and flagella) to inhibit bacterial infection. In vivo anti-Xoo assays indicated good control efficiency (curative activity, 47.8%; protective activity, 48.7%) at 200 μg mL-1. Greater control efficiency was achieved with addition of 0.1% organic silicone or orange peel essential oil. The remarkable anti-QS potency of these benzothiazole derivatives could facilitate further novel bactericidal compound development.
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Affiliation(s)
- Pan-Long Chu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Yu-Mei Feng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zhou-Qing Long
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Wan-Lin Xiao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jin Ji
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Pu-Ying Qi
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Tai-Hong Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Heng Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Li-Wei Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Song Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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Zhang X, Zhang C, Zhang R, Yuan J. Differential Bending Stiffness of the Bacterial Flagellar Hook under Counterclockwise and Clockwise Rotations. PHYSICAL REVIEW LETTERS 2023; 130:138401. [PMID: 37067319 DOI: 10.1103/physrevlett.130.138401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
The bacterial hook, as a universal joint coupling rotation of the flagellar motor and the filament, is an important component of the flagellum that propels the bacteria to swim. The mechanical properties of the hook are essential for the flagellum to achieve normal functions. In multiflagellated bacteria such as Escherichia coli, the hook must be compliant so that it can bend for the filaments to form a coherently rotating bundle to generate the thrust when the motor rotates counterclockwise (CCW), yet it also must be rigid so that the bundle can disrupt for the bacteria to tumble to change swimming direction when the motor rotates clockwise (CW). Here, by combining an elastic rod model with high-resolution bead assay to accurately measure the bending stiffness of the hook under CCW or CW rotation in vivo, we elucidate how the hook accomplishes this dual functionality: the hook stiffens under CW rotation, with bending stiffness under CW rotation twice as large as that under CCW rotation. This enables a robust run-and-tumble swimming motility for multiflagellated bacteria.
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Affiliation(s)
- Xinwen Zhang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chi Zhang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rongjing Zhang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Junhua Yuan
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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Manoj KM, Jacob VD, Kavdia M, Tamagawa H, Jaeken L, Soman V. Questioning rotary functionality in the bacterial flagellar system and proposing a murburn model for motility. J Biomol Struct Dyn 2023; 41:15691-15714. [PMID: 36970840 DOI: 10.1080/07391102.2023.2191146] [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: 11/29/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023]
Abstract
Bacterial flagellar system (BFS) was the primary example of a purported 'rotary-motor' functionality in a natural assembly. This mandates the translation of a circular motion of components inside into a linear displacement of the cell body outside, which is supposedly orchestrated with the following features of the BFS: (i) A chemical/electrical differential generates proton motive force (pmf, including a trans-membrane potential, TMP), which is electro-mechanically transduced by inward movement of protons via BFS. (ii) Membrane-bound proteins of BFS serve as stators and the slender filament acts as an external propeller, culminating into a hook-rod that pierces the membrane to connect to a 'broader assembly of deterministically movable rotor'. We had disclaimed the purported pmf/TMP-based respiratory/photosynthetic physiology involving Complex V, which was also perceived as a 'rotary machine' earlier. We pointed out that the murburn redox logic was operative therein. We pursue the following similar perspectives in BFS-context: (i) Low probability for the evolutionary attainment of an ordered/synchronized teaming of about two dozen types of proteins (assembled across five-seven distinct phases) towards the singular agendum of rotary motility. (ii) Vital redox activity (not the gambit of pmf/TMP!) powers the molecular and macroscopic activities of cells, including flagella. (iii) Flagellar movement is noted even in ambiances lacking/countering the directionality mandates sought by pmf/TMP. (iv) Structural features of BFS lack component(s) capable of harnessing/achieving pmf/TMP and functional rotation. A viable murburn model for conversion of molecular/biochemical activity into macroscopic/mechanical outcomes is proposed herein for understanding BFS-assisted motility. HIGHLIGHTSThe motor-like functionalism of bacterial flagellar system (BFS) is analyzedProton/Ion-differential based powering of BFS is unviable in bacteriaUncouplers-sponsored effects were misinterpreted, resulting in a detour in BFS researchThese findings mandate new explanation for nano-bio-mechanical movements in BFSA minimalist murburn model for the bacterial flagella-aided movement is proposedCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu, The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Vivian David Jacob
- Satyamjayatu, The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Mahendra Kavdia
- Department of Biomedical Engineering, Wayne State University, Detroit, Michigan, USA
| | - Hirohisa Tamagawa
- Department of Mechanical Engineering, Gifu University, Gifu City, Japan
| | - Laurent Jaeken
- Department of Industrial Sciences and Technology, Karel de Grote-Hogeschool, Antwerp University Association, Belgium
| | - Vidhu Soman
- Department of Bioscience & Bioengineering, IIT Bombay (& DSS Imagetech Pvt. Ltd), Mumbai, Maharashtra, India
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You Y, Ye F, Mao W, Yang H, Lai J, Deng S. An overview of the structure and function of the flagellar hook FlgE protein. World J Microbiol Biotechnol 2023; 39:126. [PMID: 36941455 DOI: 10.1007/s11274-023-03568-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/04/2023] [Indexed: 03/23/2023]
Abstract
The flagellum is an important organelle for the survival of bacteria and consists of a basal body, hook, and filament. The FlgE protein is the subunit of the hook that connects the basal body and the filament and determines the motility of bacteria. Also, flgE gene plays an essential role in flagellar biosynthesis, swimming ability and biofilm formation. Although the intact flagella and the major component filament have been extensively studied, so far, little is known about the comprehensive understanding of flagellar hook and FlgE. Here in this review, we summarize the structures of flagellar hook and its subunit FlgE in various species and physiological functions of FlgE, including the hook assembly, the structural characteristics of flagellar hook, the mechanical properties of hook, and the similarities and differences between FlgE (hook) and FlgG (distal rod), with special attention on the interaction of FlgE with other molecules, the antigenicity and pro-inflammatory effect of FlgE, and cross-linking of FlgE in spirochetes. We hope our summary of this review could provide a better understanding of the FlgE protein and provide some useful information for developing new effective antibacterial drugs in the future work.
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Affiliation(s)
- Yu You
- Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Fei Ye
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wei Mao
- Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hong Yang
- Biopharmaceutical Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jijia Lai
- Department of Laboratory Medicine, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, 610041, China
| | - Shun Deng
- Sichuan Province Orthopedic Hospital, 132 West First Section First Ring Road, Chengdu, 610041, China
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Diving into the complexity of the spirochetal endoflagellum. Trends Microbiol 2023; 31:294-307. [PMID: 36244923 DOI: 10.1016/j.tim.2022.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/27/2022]
Abstract
Spirochaetes, a phylum that includes medically important pathogens such as the causative agents of Lyme disease, syphilis, and leptospirosis, are in many ways highly unique bacteria. Their cell morphology, subcellular organization, and metabolism reveal atypical features. Spirochetal motility is also singular, dependent on the presence of periplasmic flagella or endoflagella, inserted subterminally at cell poles and not penetrating the outer membrane and elongating outside the cell as in enterobacteria. In this review we present a comprehensive comparative genomics analysis of endoflagellar systems in spirochetes, highlighting recent findings on the flagellar basal body and filament. Continued progress in understanding the function and architecture of spirochetal flagella is uncovering paradigm-shifting mechanisms of bacterial motility.
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Sun M, Liu M, Shan H, Li K, Wang P, Guo H, Zhao Y, Wang R, Tao Y, Yang L, Zhang Y, Su X, Liu Y, Li C, Lin J, Chen XL, Zhang YZ, Shen QT. Ring-stacked capsids of white spot syndrome virus and structural transitions with genome ejection. SCIENCE ADVANCES 2023; 9:eadd2796. [PMID: 36812312 PMCID: PMC9946344 DOI: 10.1126/sciadv.add2796] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
White spot syndrome virus (WSSV) is one of the largest DNA viruses and the major pathogen responsible for white spot syndrome in crustaceans. The WSSV capsid is critical for genome encapsulation and ejection and exhibits the rod-shaped and oval-shaped structures during the viral life cycle. However, the detailed architecture of the capsid and the structural transition mechanism remain unclear. Here, using cryo-electron microscopy (cryo-EM), we obtained a cryo-EM model of the rod-shaped WSSV capsid and were able to characterize its ring-stacked assembly mechanism. Furthermore, we identified an oval-shaped WSSV capsid from intact WSSV virions and analyzed the structural transition mechanism from the oval-shaped to rod-shaped capsids induced by high salinity. These transitions, which decrease internal capsid pressure, always accompany DNA release and mostly eliminate the infection of the host cells. Our results demonstrate an unusual assembly mechanism of the WSSV capsid and offer structural insights into the pressure-driven genome release.
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Affiliation(s)
- Meiling Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Mingdong Liu
- School of Life Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Hong Shan
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Kang Li
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
| | - Peng Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Huarong Guo
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yaqi Zhao
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Rui Wang
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yiwen Tao
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Liuyan Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
| | - Ying Zhang
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaoming Su
- High Performance Computing Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yunhui Liu
- School of Life Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Chunyang Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - James Lin
- High Performance Computing Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
| | - Yu-Zhong Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China
- Corresponding author. (Q.-T.S.); (Y.-Z.Z.)
| | - Qing-Tao Shen
- School of Life Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Corresponding author. (Q.-T.S.); (Y.-Z.Z.)
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Xiong D, Yang Z, He X, He W, Shen D, Wang L, Lin L, Murero A, Minamino T, Shao X, Qian G. Loss of Flagella-Related Genes Enables a Nonflagellated, Fungal-Predating Bacterium To Strengthen the Synthesis of an Antifungal Weapon. Microbiol Spectr 2023; 11:e0414922. [PMID: 36629418 PMCID: PMC9927559 DOI: 10.1128/spectrum.04149-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/17/2022] [Indexed: 01/12/2023] Open
Abstract
Loss of flagellar genes causes a nonmotile phenotype. The genus Lysobacter consists of numerous environmentally ubiquitous, nonflagellated bacteria, including Lysobacter enzymogenes, an antifungal bacterium that is beneficial to plants. L. enzymogenes still has many flagellar genes on its genome, although this bacterium does not engage in flagella-driven motility. Here, we report that loss of certain flagellar genes allows L. enzymogenes to strengthen its evolutionarily gained capacity in fungal killing. To clarify why this bacterium loses flagellar genes during the evolutionary process, we cloned several representative flagellar genes from Xanthomonas oryzae, a flagellated, phylogenetically related species of Lysobacter, and introduced them individually into L. enzymogenes to mimic genomic reacquisition of lost flagellar genes. Heterogeneous expression of the three X. oryzae flagellar structural genes (Xo-motA, Xo-motB, Xo-fliE) and one flagellar regulatory gene (Xo-fleQ) remarkably weakened the bacterial capacity to kill fungal pathogens by impairing the synthesis of an antifungal weapon, known as the heat-stable antifungal factor (HSAF). We further investigated the underlying mechanism by selecting Xo-FleQ as the representative because it is a master transcription factor responsible for flagellar gene expression. Xo-FleQ inhibited the transcription of operon genes responsible for HSAF synthesis via direct binding of Xo-FleQ to the promoter region, thereby decreasing HSAF biosynthesis by L. enzymogenes. These observations suggest a possible genome and function coevolution event, in which an antifungal bacterium deletes certain flagellar genes in order to enhance its ability to kill fungi. IMPORTANCE It is generally recognized that flagellar genes are commonly responsible for the flagella-driven bacterial motility. Thus, finding nonflagellated bacteria partially or fully lost flagellar genes is not a surprise. However, the present study provides new insights into this common idea. We found that loss of either certain flagellar structural or regulatory genes (such as motA, motB, fliE, and fleQ) allows a nonflagellated, antifungal bacterium (L. enzymogenes) to stimulate its fungal-killing capacity, outlining a genome-function coevolution event, where an antifungal bacterium "smartly" designed its genome to "delete" crucial flagellar genes to coordinate flagellar loss and fungal predation. This unusual finding might trigger bacteriologists to reconsider previously ignored functions of the lost flagellar genes in any nonflagellated, pathogenic, or beneficial bacteria.
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Affiliation(s)
- Dan Xiong
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Zixiang Yang
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xueting He
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Weimei He
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Danyu Shen
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Lu Wang
- Medical College, China Three Gorges University, Yichang, China
| | - Long Lin
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Aprodisia Murero
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Xiaolong Shao
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
| | - Guoliang Qian
- College of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, P. R. China
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Lv X, Wang L, Mei A, Xu Y, Ruan X, Wang W, Shao J, Yang D, Dong X. Recent Nanotechnologies to Overcome the Bacterial Biofilm Matrix Barriers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206220. [PMID: 36470671 DOI: 10.1002/smll.202206220] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Bacterial biofilm-related infectious diseases severely influence human health. Under typical situations, pathogens can colonize inert or biological surfaces and form biofilms. Biofilms are functional aggregates that coat bacteria with extracellular polymeric substances (EPS). The main reason for the failure of biofilm infection treatment is the low permeability and enrichment of therapeutic agents within the biofilm, which results from the particular features of biofilm matrix barriers such as negatively charged biofilm components and highly viscous compact EPS structures. Hence, developing novel therapeutic strategies with enhanced biofilm penetrability is crucial. Herein, the current progress of nanotechnology methods to improve therapeutic agents' penetrability against biofilm matrix, such as regulating material morphology and surface properties, utilizing the physical penetration of nano/micromotors or microneedle patches, and equipping nanoparticles with EPS degradation enzymes or signal molecules, is first summarized. Finally, the challenges, perspectives, and future implementations of engineered delivery systems to manage biofilm infections are presented in detail.
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Affiliation(s)
- Xinyi Lv
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, 211816, China
| | - Leichen Wang
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, 211816, China
| | - Anqing Mei
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, 211816, China
| | - Yan Xu
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, 211816, China
| | - Xiaohong Ruan
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, 211816, China
| | - Wenjun Wang
- School of Physical Science and Information Technology, Liaocheng University, Liaocheng, 252059, China
| | - Jinjun Shao
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, 211816, China
| | - Dongliang Yang
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, 211816, China
| | - Xiaochen Dong
- Key Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced Materials (IAM), School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, 211816, China
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
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42
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Lai L, Cheung YW, Martinez M, Kixmoeller K, Palao L, Steimle S, Ho MC, Black BE, Lai EM, Chang YW. In Situ Structure Determination of Bacterial Surface Nanomachines Using Cryo-Electron Tomography. Methods Mol Biol 2023; 2646:211-248. [PMID: 36842118 DOI: 10.1007/978-1-0716-3060-0_18] [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] [Indexed: 04/13/2023]
Abstract
Bacterial surface nanomachines are often refractory to structural determination in their intact form due to their extensive association with the cell envelope preventing them from being properly purified for traditional structural biology methods. Cryo-electron tomography (cryo-ET) is an emerging branch of cryo-electron microscopy that can visualize supramolecular complexes directly inside frozen-hydrated cells in 3D at nanometer resolution, therefore posing a unique capability to study the intact structures of bacterial surface nanomachines in situ and reveal their molecular association with other cellular components. Furthermore, the resolution of cryo-ET is continually improving alongside methodological advancement. Here, using the type IV pilus machine in Myxococcus xanthus as an example, we describe a step-by-step workflow for in situ structure determination including sample preparation and screening, microscope and camera tuning, tilt series acquisition, data processing and tomogram reconstruction, subtomogram averaging, and structural analysis.
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Affiliation(s)
- Longsheng Lai
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yee-Wai Cheung
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Matthew Martinez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stefan Steimle
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Han Q, Wang SF, Qian XX, Guo L, Shi YF, He R, Yuan JH, Hou YJ, Li DF. Flagellar brake protein YcgR interacts with motor proteins MotA and FliG to regulate the flagellar rotation speed and direction. Front Microbiol 2023; 14:1159974. [PMID: 37125196 PMCID: PMC10140304 DOI: 10.3389/fmicb.2023.1159974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
In E. coli and related species, flagellar brake protein YcgR responds to the elevated intracellular c-di-GMP, decreases the flagellar rotation speed, causes a CCW rotation bias, and regulates bacterial swimming. Boehm et al. suggested that c-di-GMP-activated YcgR directly interacted with the motor protein MotA to curb flagellar motor output. Paul et al. proposed that YcgR disrupted the organization of the FliG C-terminal domain to bias the flagellar rotation. The target proteins are controversial, and the role of motor proteins remains unclear in flagellar rotation speed and direction regulation by YcgR. Here we assayed the motor proteins' affinity via a modified FRET biosensor and accessed the role of those key residue via bead assays. We found that YcgR could interact with both MotA and FliG, and the affinities could be enhanced upon c-di-GMP binding. Furthermore, residue D54 of YcgR-N was needed for FliG binding. The mutation of the FliG binding residue D54 or the MotA binding ones, F117 and E232, restored flagellar rotation speed in wild-type cells and cells lacking chemotaxis response regulator CheY that switched the flagellar rotation direction and decreased the CCW ratio in wild-type cells. We propose that c-di-GMP-activated YcgR regulated the flagellar rotation speed and direction via its interaction with motor proteins MotA and FliG. Our work suggest the role of YcgR-motor proteins interaction in bacterial swimming regulation.
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Affiliation(s)
- Qun Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shao-Feng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Xin Qian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lu Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yi-Feng Shi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rui He
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Jun-Hua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Yan-Jie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Yan-Jie Hou,
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- De-Feng Li,
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44
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Singh PK, Cecchini G, Nakagawa T, Iverson TM. CryoEM structure of a post-assembly MS-ring reveals plasticity in stoichiometry and conformation. PLoS One 2023; 18:e0285343. [PMID: 37205674 DOI: 10.1371/journal.pone.0285343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023] Open
Abstract
The flagellar motor supports bacterial chemotaxis, a process that allows bacteria to move in response to their environment. A central feature of this motor is the MS-ring, which is composed entirely of repeats of the FliF subunit. This MS-ring is critical for the assembly and stability of the flagellar switch and the entire flagellum. Despite multiple independent cryoEM structures of the MS-ring, there remains a debate about the stoichiometry and organization of the ring-building motifs (RBMs). Here, we report the cryoEM structure of a Salmonella MS-ring that was purified from the assembled flagellar switch complex (MSC-ring). We term this the 'post-assembly' state. Using 2D class averages, we show that under these conditions, the post-assembly MS-ring can contain 32, 33, or 34 FliF subunits, with 33 being the most common. RBM3 has a single location with C32, C33, or C34 symmetry. RBM2 is found in two locations with RBM2inner having C21 or C22 symmetry and an RBM2outer-RBM1 having C11 symmetry. Comparison to previously reported structures identifies several differences. Most strikingly, we find that the membrane domain forms 11 regions of discrete density at the base of the structure rather than a contiguous ring, although density could not be unambiguously interpreted. We further find density in some previously unresolved areas, and we assigned amino acids to those regions. Finally, we find differences in interdomain angles in RBM3 that affect the diameter of the ring. Together, these investigations support a model of the flagellum with structural plasticity, which may be important for flagellar assembly and function.
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Affiliation(s)
- Prashant K Singh
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, United States of America
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, United States of America
| | - Terunaga Nakagawa
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States of America
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States of America
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States of America
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, United States of America
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45
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Schwan M, Khaledi A, Willger S, Papenfort K, Glatter T, Häußler S, Thormann KM. FlrA-independent production of flagellar proteins is required for proper flagellation in Shewanella putrefaciens. Mol Microbiol 2022; 118:670-682. [PMID: 36285560 DOI: 10.1111/mmi.14993] [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: 09/26/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 01/18/2023]
Abstract
Flagella are multiprotein complexes whose assembly and positioning require complex spatiotemporal control. Flagellar assembly is thought to be controlled by several transcriptional tiers, which are mediated through various master regulators. Here, we revisited the regulation of flagellar genes in polarly flagellated gammaproteobacteria by the regulators FlrA, RpoN (σ54 ) and FliA (σ28 ) in Shewanella putrefaciens CN-32 at the transcript and protein level. We found that a number of regulatory and structural proteins were present in the absence of the main regulators, suggesting that initiation of flagella assembly and motor activation relies on the abundance control of only a few structural key components that are required for the formation of the MS- and C-ring and the flagellar type III secretion system. We identified FlrA-independent promoters driving expression of the regulators of flagellar number and positioning, FlhF and FlhG. Reduction of the gene expression levels from these promoters resulted in the emergence of hyperflagellation. This finding indicates that basal expression is required to adjust the flagellar counter in Shewanella. This is adding a deeper layer to the regulation of flagellar synthesis and assembly.
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Affiliation(s)
- Meike Schwan
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Ariane Khaledi
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sven Willger
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kai Papenfort
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Mass Spectrometry and Proteomics, Marburg, Germany
| | - Susanne Häußler
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kai M Thormann
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
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46
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Minamino T, Kinoshita M, Morimoto YV, Namba K. Activation mechanism of the bacterial flagellar dual-fuel protein export engine. Biophys Physicobiol 2022; 19:e190046. [PMID: 36567733 PMCID: PMC9751260 DOI: 10.2142/biophysico.bppb-v19.0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/17/2022] [Indexed: 11/19/2022] Open
Abstract
Bacteria employ the flagellar type III secretion system (fT3SS) to construct flagellum, which acts as a supramolecular motility machine. The fT3SS of Salmonella enterica serovar Typhimurium is composed of a transmembrane export gate complex and a cytoplasmic ATPase ring complex. The transmembrane export gate complex is fueled by proton motive force across the cytoplasmic membrane and is divided into four distinct functional parts: a dual-fuel export engine; a polypeptide channel; a membrane voltage sensor; and a docking platform. ATP hydrolysis by the cytoplasmic ATPase complex converts the export gate complex into a highly efficient proton (H+)/protein antiporter that couples inward-directed H+ flow with outward-directed protein export. When the ATPase ring complex does not work well in a given environment, the export gate complex will remain inactive. However, when the electric potential difference, which is defined as membrane voltage, rises above a certain threshold value, the export gate complex becomes an active H+/protein antiporter to a considerable degree, suggesting that the export gate complex has a voltage-gated activation mechanism. Furthermore, the export gate complex also has a sodium ion (Na+) channel to couple Na+ influx with flagellar protein export. In this article, we review our current understanding of the activation mechanism of the dual-fuel protein export engine of the fT3SS. This review article is an extended version of a Japanese article, Membrane voltage-dependent activation of the transmembrane export gate complex in the bacterial flagellar type III secretion system, published in SEIBUTSU BUTSURI Vol. 62, p165-169 (2022).
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Affiliation(s)
- Tohru Minamino
- Graduate school of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Miki Kinoshita
- Graduate school of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yusuke V. Morimoto
- Department of Physics and Information Technology, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan,Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Keiichi Namba
- Graduate school of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan,RIKEN SPring-8 Center, Suita, Osaka 565-0871, Japan,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka 565-0871, Japan
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47
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Li Q. Geometric basis of action potential of skeletal muscle cells and neurons. Open Life Sci 2022; 17:1191-1199. [PMID: 36185399 PMCID: PMC9482420 DOI: 10.1515/biol-2022-0488] [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: 02/23/2022] [Revised: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/15/2022] Open
Abstract
Although we know something about single-cell neuromuscular junctions, it is still unclear how multiple skeletal muscle cells coordinate to complete intricate spatial curve movement. Here, we hypothesize that skeletal muscle cell populations with action potentials are aligned according to curved manifolds in space (a curved shape in space). When a specific motor nerve impulse is transmitted, the skeletal muscle also moves according to the corresponding shape (manifolds). The action potential of motor nerve fibers has the characteristics of a time curve manifold, and this time-manifold curve of motor nerve fibers comes from the visual cortex in which spatial geometric manifolds are formed within the synaptic connection of neurons. This spatial geometric manifold of the synaptic connection of neurons originates from spatial geometric manifolds outside nature that are transmitted to the brain through the cone cells and ganglion cells of the retina. The essence of life is that life is an object that can move autonomously, and the essence of life's autonomous movement is the movement of proteins. Theoretically, because of the infinite diversity of geometric manifold shapes in nature, the arrangement and combination of 20 amino acids should have infinite diversity, and the geometric manifold formed by the protein three-dimensional spatial structure should also have infinite diversity.
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Affiliation(s)
- Qing Li
- Department of Function, ShiJiaZhuang Traditional Chinese Medical Hospital, No. 233, ZhongShan West Road, ShiJiaZhuang, HeBei Province 050051, China
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48
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Homma M, Takekawa N, Fujiwara K, Hao Y, Onoue Y, Kojima S. Formation of multiple flagella caused by a mutation of the flagellar rotor protein FliM in Vibrio alginolyticus. Genes Cells 2022; 27:568-578. [PMID: 35842835 DOI: 10.1111/gtc.12975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Marine bacterium Vibrio alginolyticus forms a single flagellum at a cell pole. In Vibrio, two proteins (GTPase FlhF and ATPase FlhG) regulate the number of flagella. We previously isolated the NMB155 mutant that forms multiple flagella despite the absence of mutations in flhF and flhG. Whole-genome sequencing of NMB155 identified an E9K mutation in FliM that is a component of C-ring in the flagellar rotor. Mutations in FliM result in defects in flagellar formation (fla) and flagellar rotation (che or mot); however, there are a few reports indicating that FliM mutations increase the number of flagella. Here, we determined that the E9K mutation confers the multi-flagellar phenotype and also the che phenotype. The co-expression of wild-type FliM and FliM-E9K indicated that they were competitive in regard to determining the flagellar number. The ATPase activity of FlhG has been correlated with the number of flagella. We observed that the ATPase activity of FlhG was increased by the addition of FliM but not by the addition of FliM-E9K in vitro. This indicates that FliM interacts with FlhG to increase its ATPase activity, and the E9K mutation may inhibit this interaction. FliM may control the ATPase activity of FlhG to properly regulate the number of the polar flagellum at the cell pole. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Norihiro Takekawa
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Osaka, Japan
| | - Kazushi Fujiwara
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yuxi Hao
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yasuhiro Onoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
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49
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Exploring protein symmetry at the RCSB Protein Data Bank. Emerg Top Life Sci 2022; 6:231-243. [PMID: 35801924 PMCID: PMC9472815 DOI: 10.1042/etls20210267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022]
Abstract
The symmetry of biological molecules has fascinated structural biologists ever since the structure of hemoglobin was determined. The Protein Data Bank (PDB) archive is the central global archive of three-dimensional (3D), atomic-level structures of biomolecules, providing open access to the results of structural biology research with no limitations on usage. Roughly 40% of the structures in the archive exhibit some type of symmetry, including formal global symmetry, local symmetry, or pseudosymmetry. The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (founding member of the Worldwide Protein Data Bank partnership that jointly manages, curates, and disseminates the archive) provides a variety of tools to assist users interested in exploring the symmetry of biological macromolecules. These tools include multiple modalities for searching and browsing the archive, turnkey methods for biomolecular visualization, documentation, and outreach materials for exploring functional biomolecular symmetry.
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50
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Cao H, Gu Y, Diao J, Xu L, Xu T, Jin T, Gai C. Phenotypic and genomic characterization of pathogenic Providencia rettgeri from kuruma shrimp Marsupenaeus japonicus. Transbound Emerg Dis 2022; 69:e2967-e2977. [PMID: 35768955 DOI: 10.1111/tbed.14647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 06/05/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022]
Abstract
Providencia rettgeri has been recognized as a zoonotic pathogen of humans and aquaculture animals, which has become a global public-health concern. Yet scarce information is available on characterization of pathogenic P. rettgeri from kuruma shrimp Marsupenaeus japonicus. In the present study, a P. rettgeri isolate (KM4) was confirmed as a causative agent of red leg disease in cultured M. japonicus, which showed the median lethal dose (LD50 ) value of 5.01×105 CFU·mL-1 , and had multiple resistances to aminoglycosides, sulfonamides and tetracyclines antimicrobials used in aquaculture. In addition, the whole genome of isolate KM4 was sequenced and found to consist of a single circular chromosome of 4,378,712 bp and a circular plasmid of 171,394 bp. The genome sequence analysis further revealed the presence of potential virulence and antibiotic resistance genes in isolate KM4, which probably rendered this isolate particularly virulent. To our knowledge, this is the first study to characterize P. rettgeri pathogen from kuruma shrimp infected with red leg disease. The findings of this study can provide novel insights into the presence and distribution of pathogenicity-associated genes in shrimp-pathogenic P. rettgeri. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Haipeng Cao
- National Pathogen Collection Center for Aquatic Animals, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, P.R. China
| | - Ying Gu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, P.R. China
| | - Jing Diao
- Marine Science Research Institute of Shandong Province, Qingdao, 266104, P.R. China
| | - La Xu
- Marine Science Research Institute of Shandong Province, Qingdao, 266104, P.R. China
| | - Tianyue Xu
- National Pathogen Collection Center for Aquatic Animals, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, P.R. China
| | - Tongtong Jin
- National Pathogen Collection Center for Aquatic Animals, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, P.R. China
| | - Chunlei Gai
- Marine Science Research Institute of Shandong Province, Qingdao, 266104, P.R. China
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