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Zhang S, Shu Y, Zhang W, Xu Z, Li Y, Li S, Li Q, Xiong R, Long Y, Liu J, Zhang Y, Chen C, Lu Y. Quorum sensing N-acyl homoserine lactones-SdiA enhances the biofilm formation of E. coli by regulating sRNA CsrB expression. Heliyon 2023; 9:e21658. [PMID: 38027585 PMCID: PMC10651509 DOI: 10.1016/j.heliyon.2023.e21658] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
As an important virulence phenotype of Escherichia coli, the regulation mechanism of biofilm by non-coding RNA and quorum sensing system has not been clarified. Here, by transcriptome sequencing and RT-PCR analysis, we found CsrB, a non-coding RNA of the carbon storage regulation system, was positively regulated by the LuxR protein SdiA. Furthermore, β-galactosidase reporter assays showed that SdiA enhanced promoter transcriptional activity of csrB. The consistent dynamic expression levels of SdiA and CsrB during Escherichia coli growth were also detected. Moreover, curli assays and biofilm assays showed sdiA deficiency in Escherichia coli SM10λπ or BW25113 led to a decreased formation of biofilm, and was significantly restored by over-expression of CsrB. Interestingly, the regulations of SdiA on CsrB in biofilm formation were enhanced by quorum sensing signal molecules AHLs. In conclusion, SdiA plays a crucial role in Escherichia coli biofilm formation by regulating the expression of non-coding RNA CsrB. Our study provides new insights into SdiA-non-coding RNA regulatory network involved in Escherichia coli biofilm formation.
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Affiliation(s)
- Shebin Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Yurong Shu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Weizheng Zhang
- Department of Laboratory Medicine, Guangzhou No.11 People's Hospital, Guangzhou Cadre Health Management Center, Guangzhou, PR China
| | - Zhenjie Xu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Youqiang Li
- Department of Laboratory Medicine, The Affiliated Hexian Memorial Hospital of Southern Medical University, Guangzhou, PR China
| | - Song Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Qiwei Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Rui Xiong
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Yifei Long
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Jianping Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Yunyan Zhang
- Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, PR China
| | - Cha Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
| | - Yang Lu
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital Guangzhou, Qingyuan, PR China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, PR China
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2
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Alotaibi BS. Targeting Filamenting temperature-sensitive mutant Z (FtsZ) with bioactive phytoconstituents: An emerging strategy for antibacterial therapy. PLoS One 2023; 18:e0290852. [PMID: 37647309 PMCID: PMC10468062 DOI: 10.1371/journal.pone.0290852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
The rise and widespread occurrence of bacterial resistance has created an evident need for novel antibacterial drugs. Filamenting temperature-sensitive mutant Z (FtsZ) is a crucial bacterial protein that forms a ring-like structure known as the Z-ring, playing a significant role in cell division. Targeting FtsZ is an effective approach for developing antibiotics that disrupt bacterial cell division and halt growth. This study aimed to use a virtual screening approach to search for bioactive phytoconstituents with the potential to inhibit FtsZ. The screening process proceeded with the filtering compounds from the IMPPAT library of phytochemicals based on their physicochemical properties using the Lipinski rule of five. This was followed by molecular docking, Pan-assay interference compounds (PAINS) filter, absorption, distribution, metabolism, excretion, and toxicity (ADMET), prediction of activity spectra for biologically active substances (PASS), and molecular dynamics (MD) simulations. These filters ensured that any adverse effects that could impede the identification of potential inhibitors of FtsZ were eliminated. Following this, two phytocompounds, Withaperuvin C and Trifolirhizin, were selected after the screening, demonstrating noteworthy binding potential with FtsZ's GTP binding pocket, acting as potent GTP-competitive inhibitors of FtsZ. The study suggested that these compounds could be further investigated for developing a novel class of antibiotics after required studies.
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Affiliation(s)
- Bader Saud Alotaibi
- Department of Laboratories Sciences, College of Applied Medical Sciences, Shaqra University, Alquwayiyah, Saudi Arabia
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3
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Kurisu M, Katayama R, Sakuma Y, Kawakatsu T, Walde P, Imai M. Synthesising a minimal cell with artificial metabolic pathways. Commun Chem 2023; 6:56. [PMID: 36977828 PMCID: PMC10050237 DOI: 10.1038/s42004-023-00856-y] [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: 12/07/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
A "synthetic minimal cell" is considered here as a cell-like artificial vesicle reproduction system in which a chemical and physico-chemical transformation network is regulated by information polymers. Here we synthesise such a minimal cell consisting of three units: energy production, information polymer synthesis, and vesicle reproduction. Supplied ingredients are converted to energy currencies which trigger the synthesis of an information polymer, where the vesicle membrane plays the role of a template. The information polymer promotes membrane growth. By tuning the membrane composition and permeability to osmolytes, the growing vesicles show recursive reproduction over several generations. Our "synthetic minimal cell" greatly simplifies the scheme of contemporary living cells while keeping their essence. The chemical pathways and the vesicle reproduction pathways are well described by kinetic equations and by applying the membrane elasticity model, respectively. This study provides new insights to better understand the differences and similarities between non-living forms of matter and life.
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Affiliation(s)
- Minoru Kurisu
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai, 980-8578, Japan
| | - Ryosuke Katayama
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai, 980-8578, Japan
| | - Yuka Sakuma
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai, 980-8578, Japan
| | - Toshihiro Kawakatsu
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai, 980-8578, Japan
| | - Peter Walde
- Department of Materials, ETH Zürich, Vladmir-Prelog-Weg 5, CH-8093, Zürich, Switzerland
| | - Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai, 980-8578, Japan.
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4
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Sharma AK, Poddar SM, Chakraborty J, Nayak BS, Kalathil S, Mitra N, Gayathri P, Srinivasan R. A mechanism of salt bridge-mediated resistance to FtsZ inhibitor PC190723 revealed by a cell-based screen. Mol Biol Cell 2023; 34:ar16. [PMID: 36652338 PMCID: PMC10011733 DOI: 10.1091/mbc.e22-12-0538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Bacterial cell division proteins, especially the tubulin homologue FtsZ, have emerged as strong targets for developing new antibiotics. Here, we have utilized the fission yeast heterologous expression system to develop a cell-based assay to screen for small molecules that directly and specifically target the bacterial cell division protein FtsZ. The strategy also allows for simultaneous assessment of the toxicity of the drugs to eukaryotic yeast cells. As a proof-of-concept of the utility of this assay, we demonstrate the effect of the inhibitors sanguinarine, berberine, and PC190723 on FtsZ. Though sanguinarine and berberine affect FtsZ polymerization, they exert a toxic effect on the cells. Further, using this assay system, we show that PC190723 affects Helicobacter pylori FtsZ function and gain new insights into the molecular determinants of resistance to PC190723. On the basis of sequence and structural analysis and site-specific mutations, we demonstrate that the presence of salt bridge interactions between the central H7 helix and β-strands S9 and S10 mediates resistance to PC190723 in FtsZ. The single-step in vivo cell-based assay using fission yeast enabled us to dissect the contribution of sequence-specific features of FtsZ and cell permeability effects associated with bacterial cell envelopes. Thus, our assay serves as a potent tool to rapidly identify novel compounds targeting polymeric bacterial cytoskeletal proteins like FtsZ to understand how they alter polymerization dynamics and address resistance determinants in targets.
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Affiliation(s)
- Ajay Kumar Sharma
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Sakshi Mahesh Poddar
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Joyeeta Chakraborty
- Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Bhagyashri Soumya Nayak
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Srilakshmi Kalathil
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Nivedita Mitra
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
| | - Pananghat Gayathri
- Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Centre for Interdisciplinary Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India.,Homi Bhabha National Institutes, Anushakti Nagar, Mumbai 400094, India
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5
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Imai M, Sakuma Y, Kurisu M, Walde P. From vesicles toward protocells and minimal cells. SOFT MATTER 2022; 18:4823-4849. [PMID: 35722879 DOI: 10.1039/d1sm01695d] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In contrast to ordinary condensed matter systems, "living systems" are unique. They are based on molecular compartments that reproduce themselves through (i) an uptake of ingredients and energy from the environment, and (ii) spatially and timely coordinated internal chemical transformations. These occur on the basis of instructions encoded in information molecules (DNAs). Life originated on Earth about 4 billion years ago as self-organised systems of inorganic compounds and organic molecules including macromolecules (e.g. nucleic acids and proteins) and low molar mass amphiphiles (lipids). Before the first living systems emerged from non-living forms of matter, functional molecules and dynamic molecular assemblies must have been formed as prebiotic soft matter systems. These hypothetical cell-like compartment systems often are called "protocells". Other systems that are considered as bridging units between non-living and living systems are called "minimal cells". They are synthetic, autonomous and sustainable reproducing compartment systems, but their constituents are not limited to prebiotic substances. In this review, we focus on both membrane-bounded (vesicular) protocells and minimal cells, and provide a membrane physics background which helps to understand how morphological transformations of vesicle systems might have happened and how vesicle reproduction might be coupled with metabolic reactions and information molecules. This research, which bridges matter and life, is a great challenge in which soft matter physics, systems chemistry, and synthetic biology must take joined efforts to better understand how the transformation of protocells into living systems might have occurred at the origin of life.
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Affiliation(s)
- Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Yuka Sakuma
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Minoru Kurisu
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Peter Walde
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland
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6
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Effect of Gold Nanostars Plus Amikacin against Carbapenem-Resistant Klebsiella pneumoniae Biofilms. BIOLOGY 2022; 11:biology11020162. [PMID: 35205029 PMCID: PMC8869706 DOI: 10.3390/biology11020162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 01/16/2023]
Abstract
Simple Summary Carbapenem-resistant Klebsiella pneumoniae (CR-KP) infection rates represent a challenging treatment since the pipeline for effective antibiotics against this pathogen, such as beta-lactams among others, is practically nil. This study aims to evaluate the antibacterial effect of gold nanostars (GNS) alone or associated with some of the most widely used antibiotics for the treatment of CR-KP strains, i.e., meropenem or amikacin, on both planktonic or free-living and sessile forms. GNS were able to inhibit the planktonic growth of CR-KP at 80 µM, to eradicate the bacterial viability at 160 µM, and were unable to inhibit or eradicate the biofilm growth of this bacterium. GNS gave rise to filamentous bacteria through mechanisms mediated by the inhibition of energy-dependent cytoplasmic proteases. The combination of GNS and amikacin was able to inhibit or even eradicate the CR-KP biofilm. This combination was administered to greater wax moth larvae (Galleria mellonella), and this treatment was found to be tolerated well and to prevent the CR-KP infection. Thus, GNS in combination with amikacin represent a promising anti-CR-KP nanomaterial. Abstract (1) Background: Carbapenem-resistant Klesiella pneumoniae (CR-KP) infection rates depict an almost pre-antibiotic scenario since the pipeline for effective antibiotics against this pathogen has been almost entirely depleted. This study aims to evaluate the antibacterial effect of gold nanostars (GNS) alone or associated with some of the most widely used antibiotics for the treatment of CR-KP strains, i.e., meropenem or amikacin, on both planktonic and sessile forms. Additionally, we measured the effect of GNS on cell proliferation and biocompatibility in invertebrate in vivo models. (2) Materials and methods: GNS were made from gold seeds grown using a seeded-growth surfactant-free method assisted by silver ions and functionalized with mercapto-poly(ethylene glycol)amino by ligand exchange. The antimicrobial capacity, effect on cell proliferation, and biocompatibility of the most effective combination was evaluated in a Galleria mellonella model. (3) Results: The minimum inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) were 80 and 160 µM of GNS for all strains, respectively. The minimum biofilm inhibitory concentration (MBIC) and minimum biofilm eradication concentration (MBEC) were >320 µM of GNS for both. A synergy was found between GNS and amikacin. Larvae administered GNS plus amikacin were found to tolerate the treatment well, which prevented infection. (4) Conclusions: GNS are a promising anti-CR-KP nanomaterial.
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7
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Bhando T, Bhattacharyya T, Gaurav A, Akhter J, Saini M, Gupta VK, Srivastava SK, Sen H, Navani NK, Gupta V, Biswas D, Chaudhry R, Pathania R. Antibacterial properties and in vivo efficacy of a novel nitrofuran, IITR06144, against MDR pathogens. J Antimicrob Chemother 2021; 75:418-428. [PMID: 31665357 DOI: 10.1093/jac/dkz428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES The emergence of MDR Gram-negative pathogens and increasing prevalence of chronic infections presents an unmet need for the discovery of novel antibacterial agents. The aim of this study was to evaluate the biological properties of a small molecule, IITR06144, identified in a phenotypic screen against the Gram-negative model organism Escherichia coli. METHODS A small-molecule library of 10956 compounds was screened for growth inhibition against E. coli ATCC 25922 at concentration 50 μM. MICs of lead compounds were determined by the broth microdilution method. Time-kill kinetics, anti-persister activity, spontaneous frequency of resistance, biofilm inhibition and disruption were assessed by standard protocols. Resistant mutants were generated by serial passaging followed by WGS. In vitro toxicity studies were carried out via the MTT assay. In vivo toxicity and efficacy in a mouse model were also evaluated. RESULTS IITR06144 was identified as the most promising candidate amongst 29 other potential antibacterial leads, exhibiting the lowest MIC, 0.5 mg/L. IITR06144 belongs to the nitrofuran class and exhibited broad-spectrum bactericidal activity against most MDR bacteria, including the 'priority pathogen', carbapenem-resistant Acinetobacter baumannii. IITR06144 retained its potency against nitrofurantoin-resistant clinical isolates. It displayed anti-persister, anti-biofilm activity and lack of spontaneous resistance development. IITR06144 demonstrated a large therapeutic index with no associated in vitro and in vivo toxicity. CONCLUSIONS In the light of excellent in vitro properties displayed by IITR06144 coupled with its considerable in vivo efficacy, further evaluation of IITR06144 as a therapeutic lead against antibiotic-resistant infections is warranted.
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Affiliation(s)
- Timsy Bhando
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Tapas Bhattacharyya
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Amit Gaurav
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Jawed Akhter
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Mahak Saini
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Vivek Kumar Gupta
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | | | - Himanshu Sen
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Naveen K Navani
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Varsha Gupta
- Department of Microbiology, Government Medical College & Hospital, Chandigarh, India
| | - Debasis Biswas
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Ranjana Pathania
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
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8
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Yang J, He C, Zhang H, Liu M, Zhao H, Ren L, Wu D, Du F, Liu B, Han X, He S, Chen Z. Evaluation and Differential Diagnosis of a Genetic Marked Brucella Vaccine A19ΔvirB12 for Cattle. Front Immunol 2021; 12:679560. [PMID: 34163479 PMCID: PMC8215367 DOI: 10.3389/fimmu.2021.679560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/10/2021] [Indexed: 01/23/2023] Open
Abstract
Brucella abortus is an important zoonotic pathogen that causes severe economic loss to husbandry and poses a threat to human health. The B. abortus A19 live vaccine has been extensively used to prevent bovine brucellosis in China. However, it is difficult to distinguish the serological response induced by A19 from that induced by natural infection. In this study, a novel genetically marked vaccine, A19ΔvirB12, was generated and evaluated. The results indicated that A19ΔvirB12 was able to provide effective protection against B. abortus 2308 (S2308) challenge in mice. Furthermore, the safety and protective efficacy of A19ΔvirB12 have been confirmed in natural host cattle. Additionally, the VirB12 protein allowed for serological differentiation between the S2308 challenge/natural infection and A19ΔvirB12 vaccination. However, previous studies have found that the accuracy of the serological detection based on VirB12 needs to be improved. Therefore, we attempted to identify potential supplementary antigens with differential diagnostic functions by combining label-free quantitative proteomics and protein chip technology. Twenty-six proteins identified only in S2308 were screened; among them, five proteins were considered as potential supplementary antigens. Thus, the accuracy of the differential diagnosis between A19ΔvirB12 immunization and field infection may be improved through multi-antigen detection. In addition, we explored the possible attenuation factors of Brucella vaccine strain. Nine virulence factors were downregulated in A19ΔvirB12. The downregulation pathways of A19ΔvirB12 were significantly enriched in quorum sensing, ATP-binding cassette transporter, and metabolism. Several proteins related to cell division were significantly downregulated, while some proteins involved in transcription were upregulated in S2308. In conclusion, our results contribute to the control and eradication of brucellosis and provide insights into the mechanisms underlying the attenuation of A19ΔvirB12.
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Affiliation(s)
- Jianghua Yang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chuanyu He
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.,Tecon Biological Co. Ltd., Urumqi, China
| | - Huan Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | | | | | - Lisong Ren
- Tecon Biological Co. Ltd., Urumqi, China
| | | | - Fangyuan Du
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Baoshan Liu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaohu Han
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Sun He
- Tecon Biological Co. Ltd., Urumqi, China
| | - Zeliang Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.,Brucellosis Prevention and Treatment Engineering Technology Research Center of Inner Mongolia Autonomous Region, Inner Mongolia University for Nationalities, Tongliao, China.,School of Public Health, Sun Yat-sen University, Guangzhou, China
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9
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Luo N, Wang S, Lu J, Ouyang X, You L. Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa. Mol Syst Biol 2021; 17:e10089. [PMID: 33900031 PMCID: PMC8073002 DOI: 10.15252/msb.202010089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 01/11/2023] Open
Abstract
Branching pattern formation is common in many microbes. Extensive studies have focused on addressing how such patterns emerge from local cell-cell and cell-environment interactions. However, little is known about whether and to what extent these patterns play a physiological role. Here, we consider the colonization of bacteria as an optimization problem to find the colony patterns that maximize colony growth efficiency under different environmental conditions. We demonstrate that Pseudomonas aeruginosa colonies develop branching patterns with characteristics comparable to the prediction of modeling; for example, colonies form thin branches in a nutrient-poor environment. Hence, the formation of branching patterns represents an optimal strategy for the growth of Pseudomonas aeruginosa colonies. The quantitative relationship between colony patterns and growth conditions enables us to develop a coarse-grained model to predict diverse colony patterns under more complex conditions, which we validated experimentally. Our results offer new insights into branching pattern formation as a problem-solving social behavior in microbes and enable fast and accurate predictions of complex spatial patterns in branching colonies.
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Affiliation(s)
- Nan Luo
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
| | - Shangying Wang
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
| | - Jia Lu
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
| | | | - Lingchong You
- Department of Biomedical EngineeringDuke UniversityDurhamNCUSA
- Center for Genomic and Computational BiologyDuke UniversityDurhamNCUSA
- Department of Molecular Genetics and MicrobiologyDuke University School of MedicineDurhamNCUSA
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10
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TusA Is a Versatile Protein That Links Translation Efficiency to Cell Division in Escherichia coli. J Bacteriol 2021; 203:JB.00659-20. [PMID: 33526615 DOI: 10.1128/jb.00659-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/11/2021] [Indexed: 11/20/2022] Open
Abstract
To enable accurate and efficient translation, sulfur modifications are introduced posttranscriptionally into nucleosides in tRNAs. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems for the incorporation of sulfur atoms in different nucleosides of tRNA. One of the proteins that is involved in inserting the sulfur for 5-methylaminomethyl-2-thiouridine (mnm5s2U34) modifications in tRNAs is the TusA protein. TusA, however, is a versatile protein that is also involved in numerous other cellular pathways. Despite its role as a sulfur transfer protein for the 2-thiouridine formation in tRNA, a fundamental role of TusA in the general physiology of Escherichia coli has also been discovered. Poor viability, a defect in cell division, and a filamentous cell morphology have been described previously for tusA-deficient cells. In this report, we aimed to dissect the role of TusA for cell viability. We were able to show that the lack of the thiolation status of wobble uridine (U34) nucleotides present on Lys, Gln, or Glu in tRNAs has a major consequence on the translation efficiency of proteins; among the affected targets are the proteins RpoS and Fis. Both proteins are major regulatory factors, and the deregulation of their abundance consequently has a major effect on the cellular regulatory network, with one consequence being a defect in cell division by regulating the FtsZ ring formation.IMPORTANCE More than 100 different modifications are found in RNAs. One of these modifications is the mnm5s2U modification at the wobble position 34 of tRNAs for Lys, Gln, and Glu. The functional significance of U34 modifications is substantial since it restricts the conformational flexibility of the anticodon, thus providing translational fidelity. We show that in an Escherichia coli TusA mutant strain, involved in sulfur transfer for the mnm5s2U34 thio modifications, the translation efficiency of RpoS and Fis, two major cellular regulatory proteins, is altered. Therefore, in addition to the transcriptional regulation and the factors that influence protein stability, tRNA modifications that ensure the translational efficiency provide an additional crucial regulatory factor for protein synthesis.
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11
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Chaudhary R, Mishra S, Kota S, Misra H. Molecular interactions and their predictive roles in cell pole determination in bacteria. Crit Rev Microbiol 2021; 47:141-161. [PMID: 33423591 DOI: 10.1080/1040841x.2020.1857686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bacterial cell cycle is divided into well-coordinated phases; chromosome duplication and segregation, cell elongation, septum formation, and cytokinesis. The temporal separation of these phases depends upon the growth rates and doubling time in different bacteria. The entire process of cell division starts with the assembly of divisome complex at mid-cell position followed by constriction of the cell wall and septum formation. In the mapping of mid-cell position for septum formation, the gradient of oscillating Min proteins across the poles plays a pivotal role in several bacteria genus. The cues in the cell that defines the poles and plane of cell division are not fully characterized in cocci. Recent studies have shed some lights on molecular interactions at the poles and the underlying mechanisms involved in pole determination in non-cocci. In this review, we have brought forth recent findings on these aspects together, which would suggest a model to explain the mechanisms of pole determination in rod shaped bacteria and could be extrapolated as a working model in cocci.
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Affiliation(s)
- Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Hari Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
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12
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Biochemical characterization of an E. coli cell division factor FtsE shows ATPase cycles similar to the NBDs of ABC-transporters. Biosci Rep 2021; 41:227313. [PMID: 33320186 PMCID: PMC7791547 DOI: 10.1042/bsr20203034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 11/17/2022] Open
Abstract
The peptidoglycan (PG) layer is an intricate and dynamic component of the bacterial cell wall, which requires a constant balance between its synthesis and hydrolysis. FtsEX complex present on the inner membrane is shown to transduce signals to induce PG hydrolysis. FtsE has sequence similarity with the nucleotide-binding domains (NBDs) of ABC transporters. The NBDs in most of the ABC transporters couple ATP hydrolysis to transport molecules inside or outside the cell. Also, this reaction cycle is driven by the dimerization of NBDs. Though extensive studies have been carried out on the Escherchia coli FtsEX complex, it remains elusive regarding how FtsEX complex helps in signal transduction or transportation of molecules. Also, very little is known about the biochemical properties and ATPase activities of FtsE. Because of its strong interaction with the membrane-bound protein FtsX, FtsE stays insoluble upon overexpression in E. coli, and thus, most studies on E. coli FtsE (FtsEEc) in the past have used refolded FtsE. Here in the present paper, for the first time, we report the soluble expression, purification, and biochemical characterization of FtsE from E. coli. The purified soluble FtsE exhibits high thermal stability, exhibits ATPase activity and has more than one ATP-binding site. We have also demonstrated a direct interaction between FtsE and the cytoplasmic loop of FtsX. Together, our findings suggest that during bacterial division, the ATPase cycle of FtsE and its interaction with the FtsX cytoplasmic loop may help to regulate the PG hydrolysis at the mid cell.
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13
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Hinzke T, Kleiner M, Meister M, Schlüter R, Hentschker C, Pané-Farré J, Hildebrandt P, Felbeck H, Sievert SM, Bonn F, Völker U, Becher D, Schweder T, Markert S. Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. eLife 2021; 10:58371. [PMID: 33404502 PMCID: PMC7787665 DOI: 10.7554/elife.58371] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/05/2020] [Indexed: 12/13/2022] Open
Abstract
The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.
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Affiliation(s)
- Tjorven Hinzke
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany.,Energy Bioengineering Group, University of Calgary, Calgary, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Mareike Meister
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.,Leibniz Institute for Plasma Science and Technology, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Christian Hentschker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Petra Hildebrandt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Horst Felbeck
- Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, United States
| | - Florian Bonn
- Institute of Biochemistry, University Hospital, Goethe University School of Medicine Frankfurt, Frankfurt, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
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14
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Yang J, Liu M, Liu J, Liu B, He C, Chen Z. Proteomic Analysis of Stationary Growth Stage Adaptation and Nutritional Deficiency Response of Brucella abortus. Front Microbiol 2020; 11:598797. [PMID: 33384672 PMCID: PMC7769873 DOI: 10.3389/fmicb.2020.598797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/11/2020] [Indexed: 11/15/2022] Open
Abstract
Brucellosis, an important bacterial zoonosis caused by Brucella species, has drawn increasing attention worldwide. As an intracellular pathogen, the ability of Brucella to deal with stress within the host cell is closely related to its virulence. Due to the similarity between the survival pressure on Brucella within host cells and that during the stationary phase, a label-free proteomics approach was used to study the adaptive response of Brucella abortus in the stationary stage to reveal the possible intracellular adaptation mechanism in this study. A total of 182 downregulated and 140 upregulated proteins were found in the stationary-phase B. abortus. B. abortus adapted to adverse environmental changes by regulating virulence, reproduction, transcription, translation, stress response, and energy production. In addition, both exponential- and stationary-phase B. abortus were treated with short-term starvation. The exponential B. abortus restricted cell reproduction and energy utilization and enhanced material transport in response to nutritional stress. Compared with the exponential phase, stationary Brucella adjusted their protein expression to a lesser extent under starvation. Therefore, B. abortus in the two growth stages significantly differed in the regulation of protein expression in response to the same stress. Overall, we outlined the adaptive mechanisms that B. abortus may employ during growth and compared the differences between exponential- and stationary-phase B. abortus in response to starvation.
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Affiliation(s)
- Jianghua Yang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | | | - Jinling Liu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Baoshan Liu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chuanyu He
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeliang Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.,Brucellosis Prevention and Treatment Engineering Technology Research Center of Inner Mongolia Autonomous Region, Inner Mongolia University for Nationalities, Tongliao, China.,School of Public Health, Sun Yat-sen University, Guangzhou, China
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15
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Nachtigall C, Vogel C, Rohm H, Jaros D. How Capsular Exopolysaccharides Affect Cell Surface Properties of Lactic Acid Bacteria. Microorganisms 2020; 8:E1904. [PMID: 33266168 PMCID: PMC7759885 DOI: 10.3390/microorganisms8121904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/11/2022] Open
Abstract
Some lactic acid bacteria are able to produce exopolysaccharides that, based on localization, can be distinguished in free and capsular or cell-bound exopolysaccharides (CPS). Up to now, the former were the focus of current research, mainly because of the technofunctional benefits they exhibit on fermented dairy products. On the other hand, CPS affect the surface properties of bacteria cells and thus also the textural properties of fermented foods, but data are very scarce. As the cell surface properties are strongly strain dependent, we present a new approach to investigate the impact of CPS on cell surface hydrophobicity and moisture load. CPS positive and negative Streptococcus thermophilus and Weissella cibaria were subjected to ultrasonication suitable to detach CPS without cell damage. The success of the method was verified by scanning electron and light microscopy as well as by cultivation experiments. Before applying ultrasonication cells with CPS exhibiting an increased hydrophilic character, enhanced moisture load, and faster water adsorption compared to the cells after CPS removal, emphasizing the importance of CPS on the textural properties of fermented products. The ultrasonic treatment did not alter the cell surface properties of the CPS negative strains.
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Affiliation(s)
- Carsten Nachtigall
- Institute of Natural Materials Technology, Technische Universität Dresden, 01062 Dresden, Germany; (H.R.); (D.J.)
| | - Cordula Vogel
- Institute of Soil Science and Site Ecology, Technische Universität Dresden, 01062 Dresden, Germany;
| | - Harald Rohm
- Institute of Natural Materials Technology, Technische Universität Dresden, 01062 Dresden, Germany; (H.R.); (D.J.)
| | - Doris Jaros
- Institute of Natural Materials Technology, Technische Universität Dresden, 01062 Dresden, Germany; (H.R.); (D.J.)
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16
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Abstract
Chlamydia is an obligate intracellular bacterial pathogen that has significantly reduced its genome size in adapting to its intracellular niche. Among the genes that Chlamydia has eliminated is ftsZ, encoding the central organizer of cell division that directs cell wall synthesis in the division septum. These Gram-negative pathogens have cell envelopes that lack peptidoglycan (PG), yet they use PG for cell division purposes. Recent research into chlamydial PG synthesis, components of the chlamydial divisome, and the mechanism of chlamydial division have significantly advanced our understanding of these processes in a unique and important pathogen. For example, it has been definitively confirmed that chlamydiae synthesize a canonical PG structure during cell division. Various studies have suggested and provided evidence that Chlamydia uses MreB to substitute for FtsZ in organizing and coordinating the divisome during division, components of which have been identified and characterized. Finally, as opposed to using an FtsZ-dependent binary fission process, Chlamydia employs an MreB-dependent polarized budding process to divide. A brief historical context for these key advances is presented along with a discussion of the current state of knowledge of chlamydial cell division.
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17
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Khare S, Hsin J, Sorto NA, Nepomuceno GM, Shaw JT, Shi H, Huang KC. FtsZ-Independent Mechanism of Division Inhibition by the Small Molecule PC190723 in Escherichia coli. ACTA ACUST UNITED AC 2020; 3:e1900021. [PMID: 32648693 DOI: 10.1002/adbi.201900021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/07/2019] [Indexed: 11/12/2022]
Abstract
While cell division is a critical process in cellular proliferation, very few antibiotics have been identified that target the bacterial cell-division machinery. Recent studies have shown that the small molecule PC190723 inhibits cell division in several Gram-positive bacteria, with a hypothesized mechanism of action involving direct targeting of the tubulin homolog FtsZ, which is essential for division in virtually all bacterial species. Here, it is shown that PC190723 also inhibits cell division in the Gram-negative bacterium Escherichia coli if the outer membrane permeability barrier is compromised genetically or chemically. The results show that the equivalent FtsZ mutations conferring PC190723 resistance in Staphylococcus aureus do not protect E. coli against PC190723, and that suppressors of PC190723 sensitivity in E. coli, which do not generically decrease outer membrane permeability, do not map to FtsZ or other division proteins. These suppressors display a wide range of morphological and growth phenotypes, and one exhibits a death phenotype in the stationary phase similar to that of a mutant with disrupted lipid homeostasis. Finally, a complementing FtsZ-msfGFP fusion is used to show that PC190723 does not affect the Z-ring structure. Taken together, the findings suggest that PC190723 inhibits growth and division in E. coli without targeting FtsZ. This study highlights the importance of utilizing a combination of genetic, chemical, and single-cell approaches to dissect the mechanisms of action of new antibiotics, which are not necessarily conserved across bacterial species.
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Affiliation(s)
- Somya Khare
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Jen Hsin
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Nohemy A Sorto
- Department of Chemistry, University of California at Davis, Davis, CA, 95616, USA
| | | | - Jared T Shaw
- Department of Chemistry, University of California at Davis, Davis, CA, 95616, USA
| | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
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18
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Exploring antibiofilm potential of bacitracin against streptococcus mutans. Microb Pathog 2020; 149:104279. [PMID: 32512154 DOI: 10.1016/j.micpath.2020.104279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/19/2020] [Accepted: 05/25/2020] [Indexed: 11/21/2022]
Abstract
Bacitracin has well familiar effects on growth and colonization of bacteria but its antibiofilm action on majority of bacteria is still not studied. Bacitracin is a bactericidal antibiotic that primarily acts on Gram positive bacteria by obstructing the process of cell wall synthesis. In this study, we have investigated antibiofilm potential and the mechanism of bacitracin against a cariogenic bacteria 'Streptococcus mutans' which has not been reported so far. Bacitracin has been found to affect propensity of S. mutans to form biofilm. On treatment with sub-MIC concentration of bacitracin resulted in significant reduction in bifilm formation as evaluated by crystal violet and congo red assays. The architecture of S. mutans biofilm was observed by scanning electron microscopy which revealed astonishing phenotype of biofilm. Deficient biofilm was found to be composed of abnormally elongated cells. Transmission electron microscopy showed multiple septa formation in each cell of biofilm thereby indicating, cell division defect as the most probable cause of cell elongation. To elucidate the effect of bacitracin on molecular level, expression profiling of genes critically important for cell division and biofilm formation was performed, which were found many folds downregulated. Bacitracin at very low concentration has been found to have potent antibiofilm activity, therefore is a potential antibiofilm agent to treat oral biofilms. It is being anticipated, this study will offer novel information to identify potential targets and effectively creates true innovation to understand the biofilm's basic biology. Besides, discovering new uses for currently marketed drugs makes commercial as well as research sense.
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19
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Abstract
The FtsZ protein is a highly conserved bacterial tubulin homolog. In vivo, the functional form of FtsZ is the polymeric, ring-like structure (Z-ring) assembled at the future division site during cell division. While it is clear that the Z-ring plays an essential role in orchestrating cytokinesis, precisely what its functions are and how these functions are achieved remain elusive. In this article, we review what we have learned during the past decade about the Z-ring's structure, function, and dynamics, with a particular focus on insights generated by recent high-resolution imaging and single-molecule analyses. We suggest that the major function of the Z-ring is to govern nascent cell pole morphogenesis by directing the spatiotemporal distribution of septal cell wall remodeling enzymes through the Z-ring's GTP hydrolysis-dependent treadmilling dynamics. In this role, FtsZ functions in cell division as the counterpart of the cell shape-determining actin homolog MreB in cell elongation.
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Affiliation(s)
- Ryan McQuillen
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; ,
| | - Jie Xiao
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; ,
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20
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Moreno A. The Origin of a Trans-Generational Organization in the Phenomenon of Biogenesis. Front Physiol 2019; 10:1222. [PMID: 31611810 PMCID: PMC6769072 DOI: 10.3389/fphys.2019.01222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/09/2019] [Indexed: 11/24/2022] Open
Abstract
One of the central issues of the whole process of biogenesis is how to understand the progressive constitution of a large (in spatial and temporal terms) system that transcends the individual sphere of proto-metabolic organizations and includes collective networks, both synchronous (i.e., proto-ecosystem webs) and asynchronous (i.e., trans-generational protocell populations). This paper analyzes the appearance of a minimal form of reproduction in the process of biogenesis from an organizational perspective. This perspective highlights the problem of how a process transcending the actual organization of the reproducing entities (i.e., protocells) could have a causal power. It is proposed that this problem may be explained if we consider that reproduction generates a kind of feedback between the actual concatenation of the processes of each reproducing cycle and the type continuity that a reliable iteration of these cycles creates. Thus, reproduction generates a new form of self-maintaining system linking "organismal" and "evolutionary" domains, since the consequence of the iteration of self-reproducing cycles is the long-term continuity of a specific type of SM compartmentalized organization, and the functional role of a particular self-reproducing organization (token) lies in its capacity to trigger a diachronic succession of similar self-reproducing organizations, i.e., a lineage.
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Affiliation(s)
- Alvaro Moreno
- Department of Logic and Philosophy of Science, IAS-Research Centre for Life, Mind and Society, University of the Basque Country (UPV/EHU), San Sebastian, Spain
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21
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Choudhary E, Sharma R, Kumar Y, Agarwal N. Conditional Silencing by CRISPRi Reveals the Role of DNA Gyrase in Formation of Drug-Tolerant Persister Population in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2019; 9:70. [PMID: 30972304 PMCID: PMC6443821 DOI: 10.3389/fcimb.2019.00070] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/04/2019] [Indexed: 12/21/2022] Open
Abstract
Drug tolerance in mycobacterial pathogens is a global concern. Fluoroquinolone (FQ) treatment is widely used for induction of persisters in bacteria. Although FQs that target DNA gyrase are currently used as second-line anti-tuberculosis (TB) drugs, little is known about their impact on Mycobacterium tuberculosis (Mtb) persister formation. Here we explored the CRISPRi-based genetic repression for better understanding the effect of DNA gyrase depletion on Mtb physiology and response to anti-TB drugs. We find that suppression of DNA gyrase drastically affects intra- and extracellular growth of Mtb. Interestingly, gyrase depletion in Mtb leads to activation of RecA/LexA-mediated SOS response and drug tolerance via induction of persister subpopulation. Chemical inhibition of RecA in gyrase-depleted bacteria results in reversion of persister phenotype and better killing by antibiotics. This study provides evidence that inhibition of SOS response can be advantageous in improving the efficacy of anti-TB drugs and shortening the duration of current TB treatment.
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Affiliation(s)
- Eira Choudhary
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India.,Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Rishabh Sharma
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
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22
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Sekar K, Rusconi R, Sauls JT, Fuhrer T, Noor E, Nguyen J, Fernandez VI, Buffing MF, Berney M, Jun S, Stocker R, Sauer U. Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria. Mol Syst Biol 2018; 14:e8623. [PMID: 30397005 PMCID: PMC6217170 DOI: 10.15252/msb.20188623] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 12/21/2022] Open
Abstract
In natural environments, microbes are typically non-dividing and gauge when nutrients permit division. Current models are phenomenological and specific to nutrient-rich, exponentially growing cells, thus cannot predict the first division under limiting nutrient availability. To assess this regime, we supplied starving Escherichia coli with glucose pulses at increasing frequencies. Real-time metabolomics and microfluidic single-cell microscopy revealed unexpected, rapid protein, and nucleic acid synthesis already from minuscule glucose pulses in non-dividing cells. Additionally, the lag time to first division shortened as pulsing frequency increased. We pinpointed division timing and dependence on nutrient frequency to the changing abundance of the division protein FtsZ. A dynamic, mechanistic model quantitatively relates lag time to FtsZ synthesis from nutrient pulses and FtsZ protease-dependent degradation. Lag time changed in model-congruent manners, when we experimentally modulated the synthesis or degradation of FtsZ. Thus, limiting abundance of FtsZ can quantitatively predict timing of the first cell division.
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Affiliation(s)
- Karthik Sekar
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Roberto Rusconi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - John T Sauls
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Tobias Fuhrer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jen Nguyen
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vicente I Fernandez
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Marieke F Buffing
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Michael Berney
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Suckjoon Jun
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
- Section of Molecular Biology, Division of Biological Science, University of California at San Diego, La Jolla, CA, USA
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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23
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Hayes S, Vincentelli R, Mahony J, Nauta A, Ramond L, Lugli GA, Ventura M, van Sinderen D, Cambillau C. Functional carbohydrate binding modules identified in evolved dits from siphophages infecting various Gram-positive bacteria. Mol Microbiol 2018; 110:777-795. [DOI: 10.1111/mmi.14124] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Stephen Hayes
- School of Microbiology; University College Cork; Cork Ireland
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques; Aix-Marseille Université; Campus de Luminy Marseille France
- Architecture et Fonction des Macromolécules Biologiques; Centre National de la Recherche Scientifique (CNRS); Campus de Luminy Marseille France
| | - Jennifer Mahony
- School of Microbiology; University College Cork; Cork Ireland
| | - Arjen Nauta
- FrieslandCampina; Amersfoort The Netherlands
| | - Laurie Ramond
- Architecture et Fonction des Macromolécules Biologiques; Aix-Marseille Université; Campus de Luminy Marseille France
- Architecture et Fonction des Macromolécules Biologiques; Centre National de la Recherche Scientifique (CNRS); Campus de Luminy Marseille France
| | - Gabriele A. Lugli
- Laboratory of Probiogenomics, Department of Life Sciences; University of Parma; Parma Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences; University of Parma; Parma Italy
| | - Douwe van Sinderen
- School of Microbiology; University College Cork; Cork Ireland
- APC Microbiome Ireland, University College Cork; Cork Ireland
| | - Christian Cambillau
- School of Microbiology; University College Cork; Cork Ireland
- Architecture et Fonction des Macromolécules Biologiques; Aix-Marseille Université; Campus de Luminy Marseille France
- Architecture et Fonction des Macromolécules Biologiques; Centre National de la Recherche Scientifique (CNRS); Campus de Luminy Marseille France
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24
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Singh S, Sevalkar RR, Sarkar D, Karthikeyan S. Characteristics of the essential pathogenicity factor Rv1828, a MerR family transcription regulator from Mycobacterium tuberculosis. FEBS J 2018; 285:4424-4444. [PMID: 30306715 DOI: 10.1111/febs.14676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/02/2018] [Accepted: 10/08/2018] [Indexed: 01/16/2023]
Abstract
The gene Rv1828 in Mycobacterium tuberculosis is shown to be essential for the pathogen and encodes for an uncharacterized protein. In this study, we have carried out biochemical and structural characterization of Rv1828 at the molecular level to understand its mechanism of action. The Rv1828 is annotated as helix-turn-helix (HTH)-type MerR family transcription regulator based on its N-terminal amino acid sequence similarity. The MerR family protein binds to a specific DNA sequence in the spacer region between -35 and -10 elements of a promoter through its N-terminal domain (NTD) and acts as transcriptional repressor or activator depending on the absence or presence of effector that binds to its C-terminal domain (CTD). A characteristic feature of MerR family protein is its ability to bind to 19 ± 1 bp DNA sequence in the spacer region between -35 and -10 elements which is otherwise a suboptimal length for transcription initiation by RNA polymerase. Here, we show the Rv1828 through its NTD binds to a specific DNA sequence that exists on its own as well as in other promoter regions. Moreover, the crystal structure of CTD of Rv1828, determined by single-wavelength anomalous diffraction method, reveals a distinctive dimerization. The biochemical and structural analysis reveals that Rv1828 specifically binds to an everted repeat through its winged-HTH motif. Taken together, we demonstrate that the Rv1828 encodes for a MerR family transcription regulator.
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Affiliation(s)
- Suruchi Singh
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Ritesh Rajesh Sevalkar
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Dibyendu Sarkar
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Subramanian Karthikeyan
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
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25
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Song Y, Michaels TCT, Ma Q, Liu Z, Yuan H, Takayama S, Knowles TPJ, Shum HC. Budding-like division of all-aqueous emulsion droplets modulated by networks of protein nanofibrils. Nat Commun 2018; 9:2110. [PMID: 29844310 PMCID: PMC5974351 DOI: 10.1038/s41467-018-04510-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/30/2018] [Indexed: 01/01/2023] Open
Abstract
Networks of natural protein nanofibrils, such as cytoskeletal filaments, control the shape and the division of cells, yet mimicking this functionality in a synthetic setting has proved challenging. Here, we demonstrate that artificial networks of protein nanofibrils can induce controlled deformation and division of all-aqueous emulsion droplets with budding-like morphologies. We show that this process is driven by the difference in the immersional wetting energy of the nanofibril network, and that both the size and the number of the daughter droplets formed during division can be controlled by modulating the fibril concentration and the chemical properties of the fibril network. Our results demonstrate a route for achieving biomimetic division with synthetic self-assembling fibrils and offer an engineered approach to regulate the morphology of protein gels.
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Affiliation(s)
- Yang Song
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, 999077, Hong Kong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Thomas C T Michaels
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Qingming Ma
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, 999077, Hong Kong
- HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI), 518000, Shenzhen, China
| | - Zhou Liu
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, 999077, Hong Kong
- HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI), 518000, Shenzhen, China
| | - Hao Yuan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, 999077, Hong Kong
- HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI), 518000, Shenzhen, China
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam, 999077, Hong Kong.
- HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI), 518000, Shenzhen, China.
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26
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Kamran M, Dubey P, Verma V, Dasgupta S, Dhar SK. Helicobacter pylori shows asymmetric and polar cell divisome assembly associated with DNA replisome. FEBS J 2018; 285:2531-2547. [PMID: 29745002 DOI: 10.1111/febs.14499] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/31/2018] [Accepted: 05/02/2018] [Indexed: 11/28/2022]
Abstract
DNA replication and cell division are two fundamental processes in the life cycle of a cell. The majority of prokaryotic cells undergo division by means of binary fission in coordination with replication of the genome. Both processes, but especially their coordination, are poorly understood in Helicobacter pylori. Here, we studied the cell divisome assembly and the subsequent processes of membrane and peptidoglycan synthesis in the bacterium. To our surprise, we found the cell divisome assembly to be polar, which was well-corroborated by the asymmetric membrane and peptidoglycan synthesis at the poles. The divisome components showed its assembly to be synchronous with that of the replisome and the two remained associated throughout the cell cycle, demonstrating a tight coordination among chromosome replication, segregation and cell division in H. pylori. To our knowledge, this is the first report where both DNA replication and cell division along with their possible association have been demonstrated for this pathogenic bacterium.
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Affiliation(s)
- Mohammad Kamran
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Priyanka Dubey
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Vijay Verma
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Suman K Dhar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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27
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Urakami N, Jimbo T, Sakuma Y, Imai M. Molecular mechanism of vesicle division induced by coupling between lipid geometry and membrane curvatures. SOFT MATTER 2018. [PMID: 29517793 DOI: 10.1039/c7sm02188g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We investigated the effects of lipid geometry on vesicle division using coarse grained molecular dynamics simulations. When the vesicle is composed of zero and negative spontaneous curvature lipids (ZSLs and NSLs), the difference in their molecular spontaneous curvatures destabilizes the neck of the limiting shape vesicle. In the vesicle division pathway, the neck developed into the stalk intermediates. The stalk was broken when the NSLs were expelled from the stalk. Free energy analysis shows that the coupling between the lipid geometry and the Gaussian rigidity is responsible for the observed vesicle division.
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Affiliation(s)
- Naohito Urakami
- Department of Physics and Informatics, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512, Japan.
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28
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Egan AJF. Bacterial outer membrane constriction. Mol Microbiol 2018; 107:676-687. [DOI: 10.1111/mmi.13908] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Alexander J. F. Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences; Newcastle University, Baddiley-Clarke Building; Newcastle upon Tyne UK
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29
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Wang Y, Lazor KM, DeMeester KE, Liang H, Heiss TK, Grimes CL. Postsynthetic Modification of Bacterial Peptidoglycan Using Bioorthogonal N-Acetylcysteamine Analogs and Peptidoglycan O-Acetyltransferase B. J Am Chem Soc 2017; 139:13596-13599. [PMID: 28898061 PMCID: PMC5837961 DOI: 10.1021/jacs.7b06820] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bacteria have the natural ability to install protective postsynthetic modifications onto its bacterial peptidoglycan (PG), the coat woven into bacterial cell wall. Peptidoglycan O-acetyltransferase B (PatB) catalyzes the O-acetylation of PG in Gram (-) bacteria, which aids in bacterial survival, as it prevents autolysins such as lysozyme from cleaving the PG. We explored the mechanistic details of PatB's acetylation function and determined that PatB has substrate specificity for bioorthgonal short N-acetyl cysteamine (SNAc) donors. A variety of functionality including azides and alkynes were installed on tri-N-acetylglucosamine (NAG)3, a PG mimic, as well as PG isolated from various Gram (+) and Gram (-) bacterial species. The bioorthogonal modifications protect the isolated PG against lysozyme degradation in vitro. We further demonstrate that this postsynthetic modification of PG can be extended to use click chemistry to fluorescently label the mature PG in whole bacterial cells of Bacillus subtilis. Modifying PG postsynthetically can aid in the development of antibiotics and immune modulators by expanding the understanding of how PG is processed by lytic enzymes.
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Affiliation(s)
- Yiben Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Klare M. Lazor
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Kristen E. DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Tyler K. Heiss
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Catherine L. Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
- Department of Biological Chemistry, University of Delaware, Newark, DE 19716, USA
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30
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Liu X, Basu U, Miller P, McMullen LM. Differential gene expression and filamentation of Listeria monocytogenes 08-5923 exposed to sodium lactate and sodium diacetate. Food Microbiol 2017; 63:153-158. [DOI: 10.1016/j.fm.2016.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 11/02/2016] [Accepted: 11/15/2016] [Indexed: 11/25/2022]
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31
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An amidase is required for proper intercellular communication in the filamentous cyanobacterium Anabaena sp. PCC 7120. Proc Natl Acad Sci U S A 2017; 114:E1405-E1412. [PMID: 28159891 DOI: 10.1073/pnas.1621424114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Channels that cross cell walls and connect the cytoplasm of neighboring cells in multicellular cyanobacteria are pivotal for intercellular communication. We find that the product of the gene all1140 of the filamentous cyanobacterium Anabaena sp. PCC 7120 is required for proper channel formation. All1140 encodes an amidase that hydrolyses purified peptidoglycans. An All1140-GFP fusion protein is located at the Z-ring in the periplasmic space during most of the cell cycle. An all1140-null mutant (M40) was unable to grow diazotrophically, and no mature heterocysts were observed in the absence of combined nitrogen. Expression of two key genes, hetR and patS, was studied in M40 using GFP as a reporter. Upon nitrogen step-down, the patterned distribution of green fluorescent cells in filaments seen in the wild type were not observed in mutant M40. Intercellular communication in M40 was studied by measuring fluorescence recovery after photobleaching (FRAP). Movement of calcein (622 Da) was aborted in M40, suggesting that the channels connecting the cytoplasm of neighboring cells are impaired in the mutant. The channels were examined with electron tomography; their diameters were nearly identical, 12.7 nm for the wild type and 12.4 nm for M40, suggesting that AmiC3 is not required for channel formation. However, when the cell wall sacculi isolated by boiling were examined by EM, the average sizes of the channels of the wild type and M40 were 20 nm and 12 nm, respectively, suggesting that the channel walls of the wild type are expandable and that this expandability requires AmiC3.
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32
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Jimbo T, Sakuma Y, Urakami N, Ziherl P, Imai M. Role of Inverse-Cone-Shape Lipids in Temperature-Controlled Self-Reproduction of Binary Vesicles. Biophys J 2016; 110:1551-1562. [PMID: 27074680 DOI: 10.1016/j.bpj.2016.02.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 02/17/2016] [Accepted: 02/19/2016] [Indexed: 11/29/2022] Open
Abstract
We investigate a temperature-driven recursive division of binary giant unilamellar vesicles (GUVs). During the heating step of the heating-cooling cycle, the spherical mother vesicle deforms to a budded limiting shape using up the excess area produced by the chain melting of the lipids and then splits off into two daughter vesicles. Upon cooling, the daughter vesicle opens a pore and recovers the spherical shape of the mother vesicle. Our GUVs are composed of DLPE (1,2-dilauroyl-sn-glycero-3-phosphoethanolamine) and DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine). During each cycle, vesicle deformation is monitored by a fast confocal microscope and the images are analyzed to obtain the time evolution of reduced volume and reduced monolayer area difference as the key geometric parameters that quantify vesicle shape. By interpreting the deformation pathway using the area-difference elasticity theory, we conclude that vesicle division relies on (1) a tiny asymmetric distribution of DLPE within the bilayer, which controls the observed deformation from the sphere to the budded shape; and (2) redistribution of DLPE during the deformation-division stage, which ensures that the process is recursive. The spontaneous coupling between membrane curvature and PE lipid distribution is responsible for the observed recursive division of GUVs. These results shed light on the mechanisms of vesicle self-reproduction.
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Affiliation(s)
- Takehiro Jimbo
- Department of Physics, Tohoku University, Aoba, Sendai, Japan
| | - Yuka Sakuma
- Department of Physics, Tohoku University, Aoba, Sendai, Japan
| | - Naohito Urakami
- Department of Physics and Information Sciences, Yamaguchi University, Yamaguchi, Japan
| | - Primož Ziherl
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia; Jožef Stefan Institute, Ljubljana, Slovenia
| | - Masayuki Imai
- Department of Physics, Tohoku University, Aoba, Sendai, Japan.
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33
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Bajaj R, Bruce KE, Davidson AL, Rued BE, Stauffacher CV, Winkler ME. Biochemical characterization of essential cell division proteins FtsX and FtsE that mediate peptidoglycan hydrolysis by PcsB in Streptococcus pneumoniae. Microbiologyopen 2016; 5:738-752. [PMID: 27167971 PMCID: PMC5061712 DOI: 10.1002/mbo3.366] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/14/2016] [Accepted: 03/23/2016] [Indexed: 01/02/2023] Open
Abstract
The FtsEX:PcsB complex forms a molecular machine that carries out peptidoglycan (PG) hydrolysis during normal cell division of the major respiratory pathogenic bacterium, Streptococcus pneumoniae (pneumococcus). FtsX is an integral membrane protein and FtsE is a cytoplasmic ATPase that together structurally resemble ABC transporters. Instead of transport, FtsEX transduces signals from the cell division apparatus to stimulate PG hydrolysis by PcsB, which interacts with extracellular domains of FtsX. Structural studies of PcsB and one extracellular domain of FtsX have recently appeared, but little is known about the biochemical properties of the FtsE ATPase or the intact FtsX transducer protein. We report here purifications and characterizations of tagged FtsX and FtsE proteins. Pneumococcal FtsX‐GFP‐His and FtsX‐His could be overexpressed in Escherichia coli without toxicity, and FtsE‐His remained soluble during purification. FtsX‐His dimerizes in detergent micelles and when reconstituted in phospholipid nanodiscs. FtsE‐His binds an ATP analog with an affinity comparable to that of ATPase subunits of ABC transporters, and FtsE‐His preparations have a low, detectable ATPase activity. However, attempts to detect complexes of purified FtsX‐His, FtsE‐His, and PcsB‐His or coexpressed tagged FtsX and FtsE were not successful with the constructs and conditions tested so far. In working with nanodiscs, we found that PcsB‐His has an affinity for charged phospholipids, mediated partly by interactions with its coiled‐coil domain. Together, these findings represent first steps toward reconstituting the FtsEX:PcsB complex biochemically and provide information that may be relevant to the assembly of the complex on the surface of pneumococcal cells.
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Affiliation(s)
- Ruchika Bajaj
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | - Kevin E Bruce
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, 47405
| | - Amy L Davidson
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | - Britta E Rued
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, 47405
| | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907
| | - Malcolm E Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, 47405.
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34
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Grazziotin AL, Vidal NM, Venancio TM. Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea. FEBS J 2015; 282:3395-3411. [PMID: 26084810 DOI: 10.1111/febs.13350] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/02/2015] [Accepted: 06/15/2015] [Indexed: 12/19/2022]
Abstract
Identification of essential genes is critical to understanding the physiology of a species, proposing novel drug targets and uncovering minimal gene sets required for life. Although essential gene sets of several organisms have been determined using large-scale mutagenesis techniques, systematic studies addressing their conservation, genomic context and functions remain scant. Here we integrate 17 essential gene sets from genome-wide in vitro screenings and three gene collections required for growth in vivo, encompassing 15 Bacteria and one Archaea. We refine and generalize important theories proposed using Escherichia coli. Essential genes are typically monogenic and more conserved than nonessential genes. Genes required in vivo are less conserved than those essential in vitro, suggesting that more divergent strategies are deployed when the organism is stressed by the host immune system and unstable nutrient availability. We identified essential analogous pathways that would probably be missed by orthology-based essentiality prediction strategies. For example, Streptococcus sanguinis carries horizontally transferred isoprenoid biosynthesis genes that are widespread in Archaea. Genes specifically essential in Mycobacterium tuberculosis and Burkholderia pseudomallei are reported as potential drug targets. Moreover, essential genes are not only preferentially located in operons, but also occupy the first position therein, supporting the influence of their regulatory regions in driving transcription of whole operons. Finally, these important genomic features are shared between Bacteria and at least one Archaea, suggesting that high order properties of gene essentiality and genome architecture were probably present in the last universal common ancestor or evolved independently in the prokaryotic domains.
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Affiliation(s)
- Ana Laura Grazziotin
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Newton Medeiros Vidal
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Thiago Motta Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
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35
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Li X, Ma S. Advances in the discovery of novel antimicrobials targeting the assembly of bacterial cell division protein FtsZ. Eur J Med Chem 2015; 95:1-15. [DOI: 10.1016/j.ejmech.2015.03.026] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/10/2015] [Accepted: 03/12/2015] [Indexed: 01/23/2023]
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36
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A multi-layered protein network stabilizes the Escherichia coli FtsZ-ring and modulates constriction dynamics. PLoS Genet 2015; 11:e1005128. [PMID: 25848771 PMCID: PMC4388696 DOI: 10.1371/journal.pgen.1005128] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/04/2015] [Indexed: 11/19/2022] Open
Abstract
The prokaryotic tubulin homolog, FtsZ, forms a ring-like structure (FtsZ-ring) at midcell. The FtsZ-ring establishes the division plane and enables the assembly of the macromolecular division machinery (divisome). Although many molecular components of the divisome have been identified and their interactions extensively characterized, the spatial organization of these proteins within the divisome is unclear. Consequently, the physical mechanisms that drive divisome assembly, maintenance, and constriction remain elusive. Here we applied single-molecule based superresolution imaging, combined with genetic and biophysical investigations, to reveal the spatial organization of cellular structures formed by four important divisome proteins in E. coli: FtsZ, ZapA, ZapB and MatP. We show that these interacting proteins are arranged into a multi-layered protein network extending from the cell membrane to the chromosome, each with unique structural and dynamic properties. Further, we find that this protein network stabilizes the FtsZ-ring, and unexpectedly, slows down cell constriction, suggesting a new, unrecognized role for this network in bacterial cell division. Our results provide new insight into the structure and function of the divisome, and highlight the importance of coordinated cell constriction and chromosome segregation. Bacterial cell division is a highly regulated process that must be coordinated with other cellular processes (i.e. DNA replication and chromosome segregation) to promote faithful reproduction. In Escherichia coli, this regulation is most often mediated through the polymerization of the prokaryotic tubulin homolog, FtsZ, which forms a ring-like structure (FtsZ-ring) at midcell. The establishment of the FtsZ-ring marks the site of division and enables the assembly of the macromolecular division machinery (divisome). Here we applied single-molecule based superresolution imaging to reveal the three-dimensional structure of FtsZ in the context of its regulatory proteins: ZapA, ZapB and MatP. We found that these four proteins exist in a multi-layered network that extends from the cell membrane to the chromosome. This layered organization not only helps to stabilize the FtsZ-ring, but also serves to coordinate division with DNA status by influencing constriction rate. Our results not only provide a comprehensive view of the divisome, but also allow new insight to be garnered regarding the structure and function of the divisome.
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37
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Miguel A, Hsin J, Liu T, Tang G, Altman RB, Huang KC. Variations in the binding pocket of an inhibitor of the bacterial division protein FtsZ across genotypes and species. PLoS Comput Biol 2015; 11:e1004117. [PMID: 25811761 PMCID: PMC4374959 DOI: 10.1371/journal.pcbi.1004117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/08/2015] [Indexed: 01/28/2023] Open
Abstract
The recent increase in antibiotic resistance in pathogenic bacteria calls for new approaches to drug-target selection and drug development. Targeting the mechanisms of action of proteins involved in bacterial cell division bypasses problems associated with increasingly ineffective variants of older antibiotics; to this end, the essential bacterial cytoskeletal protein FtsZ is a promising target. Recent work on its allosteric inhibitor, PC190723, revealed in vitro activity on Staphylococcus aureus FtsZ and in vivo antimicrobial activities. However, the mechanism of drug action and its effect on FtsZ in other bacterial species are unclear. Here, we examine the structural environment of the PC190723 binding pocket using PocketFEATURE, a statistical method that scores the similarity between pairs of small-molecule binding sites based on 3D structure information about the local microenvironment, and molecular dynamics (MD) simulations. We observed that species and nucleotide-binding state have significant impacts on the structural properties of the binding site, with substantially disparate microenvironments for bacterial species not from the Staphylococcus genus. Based on PocketFEATURE analysis of MD simulations of S. aureus FtsZ bound to GTP or with mutations that are known to confer PC190723 resistance, we predict that PC190723 strongly prefers to bind Staphylococcus FtsZ in the nucleotide-bound state. Furthermore, MD simulations of an FtsZ dimer indicated that polymerization may enhance PC190723 binding. Taken together, our results demonstrate that a drug-binding pocket can vary significantly across species, genetic perturbations, and in different polymerization states, yielding important information for the further development of FtsZ inhibitors.
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Affiliation(s)
- Amanda Miguel
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Jen Hsin
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Tianyun Liu
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Grace Tang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Russ B. Altman
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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38
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Liu X, Miller P, Basu U, McMullen LM. Sodium chloride-induced filamentation and alternative gene expression offts,murZ,andgndinListeria monocytogenes08-5923 on vacuum-packaged ham. FEMS Microbiol Lett 2014; 360:152-6. [DOI: 10.1111/1574-6968.12599] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/21/2014] [Accepted: 09/11/2014] [Indexed: 11/26/2022] Open
Affiliation(s)
- Xiaoji Liu
- Department of Agricultural, Food and Nutritional Science; University of Alberta; Edmonton AB Canada
| | - Petr Miller
- Department of Agricultural, Food and Nutritional Science; University of Alberta; Edmonton AB Canada
| | - Urmila Basu
- Department of Agricultural, Food and Nutritional Science; University of Alberta; Edmonton AB Canada
| | - Lynn M. McMullen
- Department of Agricultural, Food and Nutritional Science; University of Alberta; Edmonton AB Canada
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Moon JH, Lee JH, Lee JY. Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate. BMC Microbiol 2014; 14:218. [PMID: 25148905 PMCID: PMC4236598 DOI: 10.1186/s12866-014-0218-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/12/2014] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Polyphosphate (polyP) has bactericidal activity against a gram-negative periodontopathogen Porphyromonas gingivalis, a black-pigmented gram-negative anaerobic rod. However, current knowledge about the mode of action of polyP against P. gingivalis is incomplete. To elucidate the mechanisms of antibacterial action of polyP against P. gingivalis, we performed the full-genome gene expression microarrays, and gene ontology (GO) and protein-protein interaction network analysis of differentially expressed genes (DEGs). RESULTS We successfully identified 349 up-regulated genes and 357 down-regulated genes (>1.5-fold, P < 0.05) in P. gingivalis W83 treated with polyP75 (sodium polyphosphate, Na(n+2)P(n)O3(n+1); n = 75). Real-time PCR confirmed the up- and down-regulation of some selected genes. GO analysis of the DEGs identified distinct biological themes. Using 202 DEGs belonging to the biological themes, we generated the protein-protein interaction network based on a database of known and predicted protein interactions. The network analysis identified biological meaningful clusters related to hemin acquisition, energy metabolism, cell envelope and cell division, ribosomal proteins, and transposon function. CONCLUSIONS polyP probably exerts its antibacterial effect through inhibition of hemin acquisition by the bacterium, resulting in severe perturbation of energy metabolism, cell envelope biosynthesis and cell division, and elevated transposition. Further studies will be needed to elucidate the exact mechanism by which polyP induces up-regulation of the genes related to ribosomal proteins. Our results will shed new light on the study of the antibacterial mechanism of polyP against other related bacteria belonging to the black-pigmented Bacteroides species.
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Affiliation(s)
- Ji-Hoi Moon
- Department of Maxillofacial Biomedical Engineering, School of Dentistry, and Institute of Oral Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 130-701, Republic of Korea
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Jae-Hyung Lee
- Department of Maxillofacial Biomedical Engineering, School of Dentistry, and Institute of Oral Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 130-701, Republic of Korea
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 130-701, Republic of Korea
| | - Jin-Yong Lee
- Department of Maxillofacial Biomedical Engineering, School of Dentistry, and Institute of Oral Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 130-701, Republic of Korea
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40
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Jones-Carson J, Zweifel AE, Tapscott T, Austin C, Brown JM, Jones KL, Voskuil MI, Vázquez-Torres A. Nitric oxide from IFNγ-primed macrophages modulates the antimicrobial activity of β-lactams against the intracellular pathogens Burkholderia pseudomallei and Nontyphoidal Salmonella. PLoS Negl Trop Dis 2014; 8:e3079. [PMID: 25121731 PMCID: PMC4133387 DOI: 10.1371/journal.pntd.0003079] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 06/26/2014] [Indexed: 12/26/2022] Open
Abstract
Our investigations show that nonlethal concentrations of nitric oxide (NO) abrogate the antibiotic activity of β-lactam antibiotics against Burkholderia pseudomallei, Escherichia coli and nontyphoidal Salmonella enterica serovar Typhimurium. NO protects B. pseudomallei already exposed to β-lactams, suggesting that this diatomic radical tolerizes bacteria against the antimicrobial activity of this important class of antibiotics. The concentrations of NO that elicit antibiotic tolerance repress consumption of oxygen (O2), while stimulating hydrogen peroxide (H2O2) synthesis. Transposon insertions in genes encoding cytochrome c oxidase-related functions and molybdenum assimilation confer B. pseudomallei a selective advantage against the antimicrobial activity of the β-lactam antibiotic imipenem. Cumulatively, these data support a model by which NO induces antibiotic tolerance through the inhibition of the electron transport chain, rather than by potentiating antioxidant defenses as previously proposed. Accordingly, pharmacological inhibition of terminal oxidases and nitrate reductases tolerizes aerobic and anaerobic bacteria to β-lactams. The degree of NO-induced β-lactam antibiotic tolerance seems to be inversely proportional to the proton motive force (PMF), and thus the dissipation of ΔH+ and ΔΨ electrochemical gradients of the PMF prevents β-lactam-mediated killing. According to this model, NO generated by IFNγ-primed macrophages protects intracellular Salmonella against imipenem. On the other hand, sublethal concentrations of imipenem potentiate the killing of B. pseudomallei by NO generated enzymatically from IFNγ-primed macrophages. Our investigations indicate that NO modulates the antimicrobial activity of β-lactam antibiotics. β-lactam drugs that inhibit peptidoglycan biosynthesis are often used in the treatment of bacterial infections, including melioidosis. Independent of their antibiotic activity, we have noted that submicromolar concentrations of β-lactams potentiate the killing of intracellular B. pseudomallei supported by NO generated by IFNγ-primed macrophages. The production of NO can nonetheless be a double-edged sword, as indicated by our observations that sublethal concentrations of nitric oxide (NO), a diatomic radical produced by phylogenetically diverse organisms to regulate neurotransmission, vascular tone and host defense, tolerize B. pseudomallei, nontyphoidal Salmonella and E. coli against the antimicrobial activity of β-lactams. Accordingly, NO produced in the inflammatory response of macrophages protects nontyphoidal Salmonella against β-lactam antibiotics. NO mediates bacterial tolerance to β-lactam antibiotics by inhibiting the electrochemical gradient supported by terminal cytochrome oxidases of the respiratory chain, rather than by decreasing oxidative stress as previously thought.
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Affiliation(s)
- Jessica Jones-Carson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Adrienne E. Zweifel
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Timothy Tapscott
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Chad Austin
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Joseph M. Brown
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Kenneth L. Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Martin I. Voskuil
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado, United States of America
- * E-mail:
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41
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Abstract
All life on earth can be naturally classified into cellular life forms and virus-like selfish elements, the latter being fully dependent on the former for their reproduction. Cells are reproducers that not only replicate their genome but also reproduce the cellular organization that depends on semipermeable, energy-transforming membranes and cannot be recovered from the genome alone, under the famous dictum of Rudolf Virchow, Omnis cellula e cellula. In contrast, simple selfish elements are replicators that can complete their life cycles within the host cell starting from genomic RNA or DNA alone. The origin of the cellular organization is the central and perhaps the hardest problem of evolutionary biology. I argue that the origin of cells can be understood only in conjunction with the origin and evolution of selfish genetic elements. A scenario of precellular evolution is presented that involves cohesion of the genomes of the emerging cellular life forms from primordial pools of small genetic elements that eventually segregated into hosts and parasites. I further present a model of the coevolution of primordial membranes and membrane proteins, discuss protocellular and non-cellular models of early evolution, and examine the habitats on the primordial earth that could have been conducive to precellular evolution and the origin of cells.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD, 20894, USA,
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42
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Shimada T, Shimada K, Matsui M, Kitai Y, Igarashi J, Suga H, Ishihama A. Roles of cell division control factor SdiA: recognition of quorum sensing signals and modulation of transcription regulation targets. Genes Cells 2014; 19:405-18. [DOI: 10.1111/gtc.12139] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/14/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Tomohiro Shimada
- Department of Frontier Bioscience; Hosei University; Koganei Tokyo 184-8584 Japan
- Research Center for Micro-Nano Technology; Hosei University; Koganei Tokyo 184-8584 Japan
- Chemical Resources Laboratory; Tokyo Institute of Technology; Nagatsuda Yokohama 226-8503 Japan
| | - Kaori Shimada
- Department of Frontier Bioscience; Hosei University; Koganei Tokyo 184-8584 Japan
| | - Makoto Matsui
- Department of Frontier Bioscience; Hosei University; Koganei Tokyo 184-8584 Japan
| | - Yuichi Kitai
- Department of Frontier Bioscience; Hosei University; Koganei Tokyo 184-8584 Japan
| | - Jun Igarashi
- Department of Chemistry and Biotechnology; Graduate School of Science; University of Tokyo; Tokyo 113-0033 Japan
| | - Hiroaki Suga
- Department of Chemistry and Biotechnology; Graduate School of Science; University of Tokyo; Tokyo 113-0033 Japan
| | - Akira Ishihama
- Department of Frontier Bioscience; Hosei University; Koganei Tokyo 184-8584 Japan
- Research Center for Micro-Nano Technology; Hosei University; Koganei Tokyo 184-8584 Japan
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43
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Morigen M, Flåtten I, Skarstad K. The Escherichia coli datA site promotes proper regulation of cell division. MICROBIOLOGY-SGM 2014; 160:703-710. [PMID: 24574433 DOI: 10.1099/mic.0.074898-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In Escherichia coli inhibition of replication leads to a block of cell division. This checkpoint mechanism ensures that no cell divides without having two complete copies of the genome to pass on to the two daughter cells. The chromosomal datA site is a 1 kb region that contains binding sites for the DnaA replication initiator protein, and which contributes to the inactivation of DnaA. An excess of datA sites provided on plasmids has been found to lead to both a delay in initiation of replication and in cell division during exponential growth. Here we have investigated the effect of datA on the cell division block that occurs upon inhibition of replication initiation in a dnaC2 mutant. We found that this checkpoint mechanism was aided by the presence of datA. In cells where datA was deleted or an excess of DnaA was provided, cell division occurred in the absence of replication and anucleate cells were formed. This finding indicates that loss of datA and/or excess of DnaA protein promote cell division. This conclusion was supported by the finding that the lethality of the division-compromised mutants ftsZ84 and ftsI23 was suppressed by deletion of datA, at the lowest non-permissive temperature. We propose that the cell division block that occurs upon inhibition of DNA replication is, at least in part, due to a drop in the concentration of the ATP-DnaA protein.
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Affiliation(s)
- Morigen Morigen
- College of Life Sciences, Inner Mongolia University, Da Xue Xi Lu 235, Hohhot, 010021, PR China.,Department of Cell Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo 0310, Norway
| | - Ingvild Flåtten
- Department of Cell Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo 0310, Norway
| | - Kirsten Skarstad
- Department of Cell Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo 0310, Norway
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44
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Salinity-dependent impacts of ProQ, Prc, and Spr deficiencies on Escherichia coli cell structure. J Bacteriol 2014; 196:1286-96. [PMID: 24443528 DOI: 10.1128/jb.00827-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
ProQ is a cytoplasmic protein with RNA chaperone activities that reside in FinO- and Hfq-like domains. Lesions at proQ decrease the level of the osmoregulatory glycine betaine transporter ProP. Lesions at proQ eliminated ProQ and Prc, the periplasmic protease encoded by the downstream gene prc. They dramatically slowed the growth of Escherichia coli populations and altered the morphologies of E. coli cells in high-salinity medium. ProQ and Prc deficiencies were associated with different phenotypes. ProQ-deficient bacteria were elongated unless glycine betaine was provided. High-salinity cultures of Prc-deficient bacteria included spherical cells with an enlarged periplasm and an eccentric nucleoid. The nucleoid-containing compartment was bounded by the cytoplasmic membrane and peptidoglycan. This phenotype was not evident in bacteria cultivated at low or moderate salinity, nor was it associated with murein lipoprotein (Lpp) deficiency, and it differed from those elicited by the MreB inhibitor A-22 or the FtsI inhibitor aztreonam at low or high salinity. It was suppressed by deletion of spr, which encodes one of three murein hydrolases that are redundantly essential for enlargement of the murein sacculus. Prc deficiency may alter bacterial morphology by impairing control of Spr activity at high salinity. ProQ and Prc deficiencies lowered the ProP activity of bacteria cultivated at moderate salinity by approximately 70% and 30%, respectively, but did not affect other osmoregulatory functions. The effects of ProQ and Prc deficiencies on ProP activity are indirect, reflecting their roles in the maintenance of cell structure.
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45
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MinC, MinD, and MinE drive counter-oscillation of early-cell-division proteins prior to Escherichia coli septum formation. mBio 2013; 4:e00856-13. [PMID: 24327341 PMCID: PMC3870257 DOI: 10.1128/mbio.00856-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Bacterial cell division initiates with the formation of a ring-like structure at the cell center composed of the tubulin homolog FtsZ (the Z-ring), which acts as a scaffold for the assembly of the cell division complex, the divisome. Previous studies have suggested that the divisome is initially composed of FtsZ polymers stabilized by membrane anchors FtsA and ZipA, which then recruit the remaining division proteins. The MinCDE proteins prevent the formation of the Z-ring at poles by oscillating from pole to pole, thereby ensuring that the concentration of the Z-ring inhibitor, MinC, is lowest at the cell center. We show that prior to septum formation, the early-division proteins ZipA, ZapA, and ZapB, along with FtsZ, assemble into complexes that counter-oscillate with respect to MinC, and with the same period. We propose that FtsZ molecules distal from high concentrations of MinC form relatively slowly diffusing filaments that are bound by ZapAB and targeted to the inner membrane by ZipA or FtsA. These complexes may facilitate the early stages of divisome assembly at midcell. As MinC oscillates toward these complexes, FtsZ oligomerization and bundling are inhibited, leading to shorter or monomeric FtsZ complexes, which become less visible by epifluorescence microscopy because of their rapid diffusion. Reconstitution of FtsZ-Min waves on lipid bilayers shows that FtsZ bundles partition away from high concentrations of MinC and that ZapA appears to protect FtsZ from MinC by inhibiting FtsZ turnover. A big issue in biology for the past 100 years has been that of how a cell finds its middle. In Escherichia coli, over 20 proteins assemble at the cell center at the time of division. We show that the MinCDE proteins, which prevent the formation of septa at the cell pole by inhibiting FtsZ, drive the counter-oscillation of early-cell-division proteins ZapA, ZapB, and ZipA, along with FtsZ. We propose that FtsZ forms filaments at the pole where the MinC concentration is the lowest and acts as a scaffold for binding of ZapA, ZapB, and ZipA: such complexes are disassembled by MinC and reform within the MinC oscillation period before accumulating at the cell center at the time of division. The ability of FtsZ to be targeted to the cell center in the form of oligomers bound by ZipA and ZapAB may facilitate the early stages of divisome assembly.
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46
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Shimada K, Ogasawara H, Yamada K, Shimura M, Kori A, Shimada T, Yamanaka Y, Yamamoto K, Ishihama A. Screening of promoter-specific transcription factors: multiple regulators for the sdiA gene involved in cell division control and quorum sensing. Microbiology (Reading) 2013; 159:2501-2512. [DOI: 10.1099/mic.0.067538-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Kaori Shimada
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Hiroshi Ogasawara
- Research Center for Human and Environmental Sciences, Shinshu University, Ueda, Nagano 386-8567, Japan
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Kayoko Yamada
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Miki Shimura
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Ayako Kori
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Tomohiro Shimada
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama 226-8503, Japan
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Yuki Yamanaka
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Kaneyoshi Yamamoto
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184-8584, Japan
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47
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Bhattacharya A, Jindal B, Singh P, Datta A, Panda D. Plumbagin inhibits cytokinesis inBacillus subtilisby inhibiting FtsZ assembly - a mechanistic study of its antibacterial activity. FEBS J 2013; 280:4585-99. [DOI: 10.1111/febs.12429] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/24/2013] [Accepted: 07/04/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Anusri Bhattacharya
- Department of Chemistry; Indian Institute of Technology Bombay; Mumbai India
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
| | - Bhavya Jindal
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
| | - Parminder Singh
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
| | - Anindya Datta
- Department of Chemistry; Indian Institute of Technology Bombay; Mumbai India
| | - Dulal Panda
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
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48
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Doan T, Coleman J, Marquis KA, Meeske AJ, Burton BM, Karatekin E, Rudner DZ. FisB mediates membrane fission during sporulation in Bacillus subtilis. Genes Dev 2013; 27:322-34. [PMID: 23388828 DOI: 10.1101/gad.209049.112] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
How bacteria catalyze membrane fission during growth and differentiation is an outstanding question in prokaryotic cell biology. Here, we describe a protein (FisB, for fission protein B) that mediates membrane fission during the morphological process of spore formation in Bacillus subtilis. Sporulating cells divide asymmetrically, generating a large mother cell and smaller forespore. After division, the mother cell membranes migrate around the forespore in a phagocytic-like process called engulfment. Membrane fission releases the forespore into the mother cell cytoplasm. Cells lacking FisB are severely and specifically impaired in the fission reaction. Moreover, GFP-FisB forms dynamic foci that become immobilized at the site of fission. Purified FisB catalyzes lipid mixing in vitro and is only required in one of the fusing membranes, suggesting that FisB-lipid interactions drive membrane remodeling. Consistent with this idea, the extracytoplasmic domain of FisB binds with remarkable specificity to cardiolipin, a lipid enriched in the engulfing membranes and regions of negative curvature. We propose that membrane topology at the final stage of engulfment and FisB-cardiolipin interactions ensure that the mother cell membranes are severed at the right time and place. The unique properties of FisB set it apart from the known fission machineries in eukaryotes, suggesting that it represents a new class of fission proteins.
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Affiliation(s)
- Thierry Doan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
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49
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Lehner J, Berendt S, Dörsam B, Pérez R, Forchhammer K, Maldener I. Prokaryotic multicellularity: a nanopore array for bacterial cell communication. FASEB J 2013; 27:2293-300. [PMID: 23444428 DOI: 10.1096/fj.12-225854] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The transition from unicellular to multicellular life, which occurred several times during evolution, requires tight interaction and communication of neighboring cells. The multicellular cyanobacterium Nostoc punctiforme ATCC 29133 forms filaments of hundreds of interacting cells exchanging metabolites and signal molecules and is able to differentiate specialized cells in response to environmental stimuli. Mutation of cell wall amidase AmiC2 leads to a severe phenotype with formation of aberrant septa in the distorted filaments, which completely lack cell communication and potential for cell differentiation. Here we demonstrate the function of the amidase AmiC2 in formation of cell-joining structures. The AmiC2 protein localizes to the young septum between cells and shows bona fide amidase activity in vivo and in vitro. Vancomycin staining identified the overall septum morphology in living cells. By electron microscopy of isolated peptidoglycan sacculi, the submicroscopic structure of the cell junctions could be visualized, revealing a novel function for a cell wall amidase: AmiC2 drills holes into the cross-walls, forming an array of ~155 nanopores with a diameter of ~20 nm each. These nanopores seem to constitute a framework for cell-joining proteins, penetrating the cell wall. The entire array of junctional nanopores appears as a novel bacterial organelle, establishing multicellularity in a filamentous prokaryote.
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Affiliation(s)
- Josef Lehner
- Department of Microbiology/Organismic Interactions, University of Tübingen, Tübingen, Germany
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50
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Microscopic studies on Thermosipho globiformans implicate a role of the large periplasm of Thermotogales. Extremophiles 2012; 16:863-70. [DOI: 10.1007/s00792-012-0481-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 08/27/2012] [Indexed: 10/27/2022]
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