1
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Herdman M, Isbilir B, von Kügelgen A, Schulze U, Wainman A, Bharat TAM. Cell cycle dependent coordination of surface layer biogenesis in Caulobacter crescentus. Nat Commun 2024; 15:3355. [PMID: 38637514 PMCID: PMC11026435 DOI: 10.1038/s41467-024-47529-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Surface layers (S-layers) are proteinaceous, two-dimensional paracrystalline arrays that constitute a major component of the cell envelope in many prokaryotic species. In this study, we investigated S-layer biogenesis in the bacterial model organism Caulobacter crescentus. Fluorescence microscopy revealed localised incorporation of new S-layer at the poles and mid-cell, consistent with regions of cell growth in the cell cycle. Light microscopy and electron cryotomography investigations of drug-treated bacteria revealed that localised S-layer insertion is retained when cell division is inhibited, but is disrupted upon dysregulation of MreB or lipopolysaccharide. We further uncovered that S-layer biogenesis follows new peptidoglycan synthesis and localises to regions of high cell wall turnover. Finally, correlated cryo-light microscopy and electron cryotomographic analysis of regions of S-layer insertion showed the presence of discontinuities in the hexagonal S-layer lattice, contrasting with other S-layers completed by defined symmetric defects. Our findings present insights into how C. crescentus cells form an ordered S-layer on their surface in coordination with the biogenesis of other cell envelope components.
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Affiliation(s)
- Matthew Herdman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Buse Isbilir
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Ulrike Schulze
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Alan Wainman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
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2
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Lakey BD, Alberge F, Parrell D, Wright ER, Noguera DR, Donohue TJ. The role of CenKR in the coordination of Rhodobacter sphaeroides cell elongation and division. mBio 2023; 14:e0063123. [PMID: 37283520 PMCID: PMC10470753 DOI: 10.1128/mbio.00631-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 06/08/2023] Open
Abstract
Cell elongation and division are essential aspects of the bacterial life cycle that must be coordinated for viability and replication. The impact of misregulation of these processes is not well understood as these systems are often not amenable to traditional genetic manipulation. Recently, we reported on the CenKR two-component system (TCS) in the Gram-negative bacterium Rhodobacter sphaeroides that is genetically tractable, widely conserved in α-proteobacteria, and directly regulates the expression of components crucial for cell elongation and division, including genes encoding subunit of the Tol-Pal complex. In this work, we show that overexpression of cenK results in cell filamentation and chaining. Using cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), we generated high-resolution two-dimensional (2D) images and three-dimensional (3D) volumes of the cell envelope and division septum of wild-type cells and a cenK overexpression strain finding that these morphological changes stem from defects in outer membrane (OM) and peptidoglycan (PG) constriction. By monitoring the localization of Pal, PG biosynthesis, and the bacterial cytoskeletal proteins MreB and FtsZ, we developed a model for how increased CenKR activity leads to changes in cell elongation and division. This model predicts that increased CenKR activity decreases the mobility of Pal, delaying OM constriction, and ultimately disrupting the midcell positioning of MreB and FtsZ and interfering with the spatial regulation of PG synthesis and remodeling. IMPORTANCE By coordinating cell elongation and division, bacteria maintain their shape, support critical envelope functions, and orchestrate division. Regulatory and assembly systems have been implicated in these processes in some well-studied Gram-negative bacteria. However, we lack information on these processes and their conservation across the bacterial phylogeny. In R. sphaeroides and other α-proteobacteria, CenKR is an essential two-component system (TCS) that regulates the expression of genes known or predicted to function in cell envelope biosynthesis, elongation, and/or division. Here, we leverage unique features of CenKR to understand how increasing its activity impacts cell elongation/division and use antibiotics to identify how modulating the activity of this TCS leads to changes in cell morphology. Our results provide new insight into how CenKR activity controls the structure and function of the bacterial envelope, the localization of cell elongation and division machinery, and cellular processes in organisms with importance in health, host-microbe interactions, and biotechnology.
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Affiliation(s)
- Bryan D. Lakey
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - François Alberge
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel Parrell
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Elizabeth R. Wright
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Cryo-Electron Microscopy Research Center,Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel R. Noguera
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy J. Donohue
- Wisconsin Energy Institute, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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3
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Figueroa-Cuilan WM, Irazoki O, Feeley M, Smith E, Nguyen T, Cava F, Goley ED. Quantitative analysis of morphogenesis and growth dynamics in an obligate intracellular bacterium. Mol Biol Cell 2023; 34:ar69. [PMID: 37017481 PMCID: PMC10295487 DOI: 10.1091/mbc.e23-01-0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 04/06/2023] Open
Abstract
Obligate intracellular bacteria of the order Rickettsiales include important human pathogens. However, our understanding of the biology of Rickettsia species is limited by challenges imposed by their obligate intracellular lifestyle. To overcome this roadblock, we developed methods to assess cell wall composition, growth, and morphology of Rickettsia parkeri, a human pathogen in the spotted fever group of the Rickettsia genus. Analysis of the cell wall of R. parkeri revealed unique features that distinguish it from free-living alphaproteobacteria. Using a novel fluorescence microscopy approach, we quantified R. parkeri morphology in live host cells and found that the fraction of the population undergoing cell division decreased over the course of infection. We further demonstrated the feasibility of localizing fluorescence fusions, for example, to the cell division protein ZapA, in live R. parkeri for the first time. To evaluate population growth kinetics, we developed an imaging-based assay that improves on the throughput and resolution of other methods. Finally, we applied these tools to quantitatively demonstrate that the actin homologue MreB is required for R. parkeri growth and rod shape. Collectively, a toolkit was developed of high-throughput, quantitative tools to understand growth and morphogenesis of R. parkeri that is translatable to other obligate intracellular bacteria.
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Affiliation(s)
- Wanda M. Figueroa-Cuilan
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Oihane Irazoki
- Laboratory for Molecular Infection Medicine, Umeå Center for Microbial Research, Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Marissa Feeley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Erika Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Trung Nguyen
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine, Umeå Center for Microbial Research, Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Erin D. Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2185
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4
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Tian D, Wang C, Liu Y, Zhang Y, Caliari A, Lu H, Xia Y, Xu B, Xu J, Yomo T. Cell Sorting-Directed Selection of Bacterial Cells in Bigger Sizes Analyzed by Imaging Flow Cytometry during Experimental Evolution. Int J Mol Sci 2023; 24:ijms24043243. [PMID: 36834655 PMCID: PMC9966196 DOI: 10.3390/ijms24043243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Cell morphology is an essential and phenotypic trait that can be easily tracked during adaptation and evolution to environmental changes. Thanks to the rapid development of quantitative analytical techniques for large populations of cells based on their optical properties, morphology can be easily determined and tracked during experimental evolution. Furthermore, the directed evolution of new culturable morphological phenotypes can find use in synthetic biology to refine fermentation processes. It remains unknown whether and how fast we can obtain a stable mutant with distinct morphologies using fluorescence-activated cell sorting (FACS)-directed experimental evolution. Taking advantage of FACS and imaging flow cytometry (IFC), we direct the experimental evolution of the E. coli population undergoing continuous passage of sorted cells with specific optical properties. After ten rounds of sorting and culturing, a lineage with large cells resulting from incomplete closure of the division ring was obtained. Genome sequencing highlighted a stop-gain mutation in amiC, leading to a dysfunctional AmiC division protein. The combination of FACS-based selection with IFC analysis to track the evolution of the bacteria population in real-time holds promise to rapidly select and culture new morphologies and association tendencies with many potential applications.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jian Xu
- Correspondence: (J.X.); (T.Y.); Tel.: +86-(21)-62233727 (J.X. & T.Y.)
| | - Tetsuya Yomo
- Correspondence: (J.X.); (T.Y.); Tel.: +86-(21)-62233727 (J.X. & T.Y.)
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5
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Novel MreB inhibitors with antibacterial activity against Gram (-) bacteria. Med Chem Res 2022; 31:1679-1704. [PMID: 37077288 PMCID: PMC10112653 DOI: 10.1007/s00044-022-02967-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
MreB is a cytoskeleton protein present in rod-shaped bacteria that is both essential for bacterial cell division and highly conserved. Because most Gram (-) bacteria require MreB for cell division, chromosome segregation, cell wall morphogenesis, and cell polarity, it is an attractive target for antibacterial drug discovery. As MreB modulation is not associated with the activity of antibiotics in clinical use, acquired resistance to MreB inhibitors is also unlikely. Compounds, such as A22 and CBR-4830, are known to disrupt MreB function by inhibition of ATPase activity. However, the toxicity of these compounds has hindered efforts to assess the in vivo efficacy of these MreB inhibitors. The present study further examines the structure-activity of analogs related to CBR-4830 as it relates to relative antibiotic activity and improved drug properties. These data reveal that certain analogs have enhanced antibiotic activity. In addition, we evaluated several representative analogs (9, 10, 14, 26, and 31) for their abilities to target purified E. coli MreB (EcMreB) and inhibit its ATPase activity. Except for 14, all these analogs were more potent than CBR-4830 as inhibitors of the ATPase activity of EcMreB with corresponding IC50 values ranging from 6 ± 2 to 29 ± 9 μM.
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6
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Pseudomonas aeruginosa Alters Peptidoglycan Composition under Nutrient Conditions Resembling Cystic Fibrosis Lung Infections. mSystems 2022; 7:e0015622. [PMID: 35545925 PMCID: PMC9239049 DOI: 10.1128/msystems.00156-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Epidemic strains of Pseudomonas aeruginosa are highly virulent opportunistic pathogens with increased transmissibility and enhanced antimicrobial resistance. Understanding the cellular mechanisms behind this heightened virulence and resistance is critical. Peptidoglycan (PG) is an integral component of P. aeruginosa cells that is essential to its survival and a target for antimicrobials. Here, we examined the global PG composition of two P. aeruginosa epidemic strains, LESB58 and LESlike1, and compared them to the common laboratory strains PAO1 and PA14. We also examined changes in PG composition when the strains were cultured under nutrient conditions that resembled cystic fibrosis lung infections. We identified 448 unique muropeptides and provide the first evidence for stem peptides modified with O-methylation, meso-diaminopimelic acid (mDAP) deamination, and novel substitutions of mDAP residues within P. aeruginosa PG. Our results also present the first evidence for both d,l- and l,d-endopeptidase activity on the PG sacculus of a Gram-negative organism. The PG composition of the epidemic strains varied significantly when grown under conditions resembling cystic fibrosis (CF) lung infections, showing increases in O-methylated stem peptides and decreases in l,d-endopeptidase activity as well as an increased abundance of de-N-acetylated sugars and l,d-transpeptidase activity, which are related to bacterial virulence and antibiotic resistance, respectively. We also identified strain-specific changes where LESlike1 increased the addition of unique amino acids to the terminus of the stem peptide and LESB58 increased amidase activity. Overall, this study demonstrates that P. aeruginosa PG composition is primarily influenced by nutrient conditions that mimic the CF lung; however, inherent strain-to-strain differences also exist. IMPORTANCE Using peptidoglycomics to examine the global composition of the peptidoglycan (PG) allows insights into the enzymatic activity that functions on this important biopolymer. Changes within the PG structure have implications for numerous physiological processes, including virulence and antimicrobial resistance. The identification of highly unique PG modifications illustrates the complexity of this biopolymer in Pseudomonas aeruginosa. Analyzing the PG composition of clinical P. aeruginosa epidemic strains provides insights into the increased virulence and antimicrobial resistance of these difficult-to-eradicate infections.
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7
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Choi Y, Park JS, Kim J, Min K, Mahasenan K, Kim C, Yoon HJ, Lim S, Cheon DH, Lee Y, Ryu S, Mobashery S, Kim BM, Lee HH. Structure-based inhibitor design for reshaping bacterial morphology. Commun Biol 2022; 5:395. [PMID: 35484224 PMCID: PMC9050674 DOI: 10.1038/s42003-022-03355-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/12/2022] [Indexed: 11/09/2022] Open
Abstract
The spiral shape of intestinal pathogen Campylobacter jejuni is critical for invasion of intestinal mucosa epithelial cells. Insofar as this cell morphology plays a role in the pathology of C. jejuni infection, its restructuring by pharmacological intervention could be an unexplored means to prevention of infection. We recently described that peptidoglycan hydrolase 3 (Pgp3) is involved in the spiral-shape formation of C. jejuni. We report herein the design and synthesis of the hydroxamate-based inhibitors targeting Pgp3. C. jejuni cells exposed to these inhibitors changed from the helical- to rod-shaped morphology, comparable to the case of the pgp3-deletion mutant. Evidence for the mechanism of action was provided by crystal structures of Pgp3 in complex with inhibitors, shedding light into the binding modes of inhibitors within the active site, supported by kinetics and molecular-dynamics simulations. C. jejuni exposed to these inhibitors underwent the morphological change from helical- to rod-shaped bacteria, an event that reduce the ability for invasion of the host cells. This proof of concept suggests that alteration of morphology affects the interference with the bacterial infection.
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Affiliation(s)
- Yuri Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Ji Su Park
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jinshil Kim
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Korea
| | - Kyungjin Min
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Kiran Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, 46556, United States
| | - Choon Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, 46556, United States
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Sewon Lim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Dae Hee Cheon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Yan Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Korea
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, 46556, United States.
| | - B Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea.
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea.
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8
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Nutritional and Volatile Characterisation of Milk Inoculated with Thermo-Tolerant Lactobacillus bulgaricus through Adaptive Laboratory Evolution. Foods 2021; 10:foods10122944. [PMID: 34945497 PMCID: PMC8701330 DOI: 10.3390/foods10122944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
In this study, thermo-tolerant strain of Lactobacillus bulgaricus (L. bulgaricus) was developed using gradual increase in temperature to induce Adaptive Laboratory Evolution (ALE). Viable colony count of 1.87 ± 0.98 log cfu/mL was achieved at 52 °C, using MRS agar supplemented with 2% lactose. Changes in bacteria morphology were discovered, from rod (control) to filament (52 °C) to cocci after frozen storage (−80 °C). When milk was inoculated with thermo-tolerant L. bulgaricus, lactic acid production was absent, leaving pH at 6.84 ± 0.13. This has caused weakening of the protein network, resulting in high whey separation and lower water-holding capacity (37.1 ± 0.35%) compared to the control (98.10 ± 0.60%). Significantly higher proteolytic activity was observed through free amino acids analysis by LC-MS. Arginine and methionine (237.24 ± 5.94 and 98.83 ± 1.78 µg/100 g, respectively) were found to be 115- and 275-fold higher than the control, contributing to changing the aroma similar to cheese. Further volatile analysis through SPME-GC-MS has confirmed significant increase in cheese-aroma volatiles compared to the control, with increase in diacetyl formation. Further work on DNA profiling, metabolomics and peptidomics will help to answer mechanisms behind the observed changes made in the study.
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9
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Zhao W, Zhu H, Wei F, Zhou D, Li Y, Zhang XX. Investigating the Involvement of Cytoskeletal Proteins MreB and FtsZ in the Origin of Legume-Rhizobial Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:547-559. [PMID: 33596109 DOI: 10.1094/mpmi-10-20-0299-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rhizobia are rod-shaped bacteria that form nitrogen-fixing root nodules on leguminous plants; however, they don't carry MreB, a key determinant of rod-like cell shape. Here, we introduced an actin-like mreB homolog from a pseudomonad into Mesorhizobium huakuii 7653R (a microsymbiont of Astragalus sinicus L.) and examined the molecular, cellular, and symbiotic phenotypes of the resultant mutant. Exogenous mreB caused an enlarged cell size and slower growth in laboratory medium. However, the mutant formed small, ineffective nodules on A. sinicus (Nod+ Fix-), and rhizobial cells in the infection zone were unable to differentiate into bacteroids. RNA sequencing analysis also revealed minor effects of mreB on global gene expression in free-living cells but larger effects for cells grown in planta. Differentially expressed nodule-specific genes include cell cycle regulators such as the tubulin-like ftsZ1 and ftsZ2. Unlike the ubiquitous FtsZ1, an FtsZ2 homolog was commonly found in Rhizobium, Sinorhizobium, and Mesorhizobium spp. but not in closely related nonsymbiotic species. Bacterial two-hybrid analysis revealed that MreB interacts with FtsZ1 and FtsZ2, which are targeted by the host-derived nodule-specific cysteine-rich peptides. Significantly, MreB mutation D283A disrupted the protein-protein interactions and restored the aforementioned phenotypic defects caused by MreB in M. huakuii. Together, our data indicate that MreB is detrimental for modern rhizobia and its interaction with FtsZ1 and FtsZ2 causes the symbiotic process to cease at the late stage of bacteroid differentiation. These findings led to a hypothesis that loss of mreB in the common ancestor of members of Rhizobiales and subsequent acquisition of ftsZ2 are critical evolutionary steps leading to legume-rhizobial symbiosis.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Wenlong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Huixia Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Feng Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Donglai Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xue-Xian Zhang
- School of Natural and Computational Sciences, Massey University, Auckland 0745, New Zealand
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10
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Bersch K, DeMeester KE, Zagani R, Chen S, Wodzanowski KA, Liu S, Mashayekh S, Reinecker HC, Grimes CL. Bacterial Peptidoglycan Fragments Differentially Regulate Innate Immune Signaling. ACS CENTRAL SCIENCE 2021; 7:688-696. [PMID: 34056099 PMCID: PMC8155477 DOI: 10.1021/acscentsci.1c00200] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Indexed: 05/07/2023]
Abstract
The human innate immune system responds to both pathogen and commensal bacteria at the molecular level using bacterial peptidoglycan (PG) recognition elements. Traditionally, synthetic and commercially accessible PG monosaccharide units known as muramyl dipeptide (MDP) and N-glycolyl MDP (ng-MDP) have been used to probe the mechanism of innate immune activation of pattern recognition receptors, such as NOD-like receptors. However, bacterial PG is a dynamic and complex structure, with various chemical modifications and trimming mechanisms that result in the production of disaccharide-containing elements. These molecules pose as attractive targets for immunostimulatory screening; however, studies are limited because of their synthetic accessibility. Inspired by disaccharide-containing compounds produced from the gut microbe Lactobacillus acidophilus, a robust and scalable chemical synthesis of PG-based disaccharide ligands was implemented. Together with a monosaccharide PG library, compounds were screened for their ability to stimulate proinflammatory genes in bone-marrow-derived macrophages. The data reveal distinct gene induction patterns for monosaccharide and disaccharide PG units, suggesting that PG innate immune signaling is more complex than a one activator-one pathway program, as biologically relevant fragments induce transcriptional programs to different degrees. These disaccharide molecules will serve as critical immunostimulatory tools to more precisely define specialized innate immune regulatory mechanisms that distinguish between commensal and pathogenic bacteria residing in the microbiome.
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Affiliation(s)
- Klare
L. Bersch
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Kristen E. DeMeester
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Rachid Zagani
- Department
of Medicine, Gastrointestinal Unit and Center for the Study of Inflammatory
Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Shuyuan Chen
- Department
of Medicine, Division of Digestive and Liver Diseases, and Department
of Immunology, University of Texas Southwestern
Medical Center, 5959 Harry Hines Boulevard, Dallas, Texas 75390, United
States
| | - Kimberly A. Wodzanowski
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Shuzhen Liu
- Department
of Medicine, Division of Digestive and Liver Diseases, and Department
of Immunology, University of Texas Southwestern
Medical Center, 5959 Harry Hines Boulevard, Dallas, Texas 75390, United
States
| | - Siavash Mashayekh
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
| | - Hans-Christian Reinecker
- Department
of Medicine, Gastrointestinal Unit and Center for the Study of Inflammatory
Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department
of Medicine, Division of Digestive and Liver Diseases, and Department
of Immunology, University of Texas Southwestern
Medical Center, 5959 Harry Hines Boulevard, Dallas, Texas 75390, United
States
| | - Catherine L. Grimes
- Department
of Chemistry and Biochemistry, University
of Delaware, Newark, Delaware 19716, United States
- Department
of Biological Sciences, University of Delaware, Newark, Delaware 19716, United States
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11
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Class A Penicillin-Binding Protein-Mediated Cell Wall Synthesis Promotes Structural Integrity during Peptidoglycan Endopeptidase Insufficiency in Vibrio cholerae. mBio 2021; 12:mBio.03596-20. [PMID: 33824203 PMCID: PMC8092314 DOI: 10.1128/mbio.03596-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial cell wall is composed primarily of peptidoglycan (PG), a poly-aminosugar that is essential to sustain cell shape, growth, and structural integrity. PG is synthesized by class A/B penicillin-binding proteins (a/bPBPs) and shape, elongation, division, and sporulation (SEDS) proteins like RodA (as part of the Rod system cell elongation machinery) and degraded by "autolytic" enzymes to accommodate growth processes. It is thought that autolysins (particularly endopeptidases [EPs]) are required for PG synthesis and incorporation by creating gaps that are patched and paved by PG synthases, but the exact relationship between autolysins and PG synthesis remains incompletely understood. Here, we have probed the consequences of EP depletion for PG synthesis in the diarrheal pathogen Vibrio cholerae We found that EP depletion resulted in severe morphological and division defects, but these cells continued to increase in mass and aberrantly incorporated new cell wall material. Mass increase proceeded in the presence of Rod system inhibitors, but cells lysed upon inhibition of aPBPs, suggesting that aPBPs are required for structural integrity under these conditions. The Rod system, although not essential for the observed mass increase, remained functional even after prolonged EP depletion. Last, heterologous expression of an EP from Neisseria gonorrhoeae fully complemented growth and morphology of an EP-insufficient V. cholerae, highlighting the possibility that the PG synthases may not necessarily function via direct interaction with EPs. Overall, our findings suggest that during EP insufficiency in V. cholerae, aPBPs become essential for structural integrity while the Rod system is unable to promote proper cell expansion.IMPORTANCE Synthesis and turnover of the bacterial cell wall must be tightly coordinated to avoid structural integrity failure and cell death. Details of this coordination are poorly understood, particularly if and how cell wall turnover enzymes are required for the activity of the different cell wall synthesis machines, the aPBPs and the Rod system. Our results suggest that in Vibrio cholerae, one class of turnover enzymes, the endopeptidases, are necessary for proper cell elongation and division. aPBPs become essential for maintaining structural integrity during EP insufficiency, while the Rod system remains active but contributes little to cell expansion under these conditions. Our results suggest that aPBPs are more versatile than the Rod system in their ability to recognize cell wall gaps formed by autolysins other than the major endopeptidases, adding to our understanding of the coordination between autolysins and cell wall synthases. A detailed understanding of autolysin biology may promote the development of antibiotics that target these essential turnover processes.
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12
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A CRISPR interference platform for selective downregulation of gene expression in Borrelia burgdorferi. Appl Environ Microbiol 2021; 87:AEM.02519-20. [PMID: 33257311 PMCID: PMC7851697 DOI: 10.1128/aem.02519-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The spirochete Borrelia burgdorferi causes Lyme disease, an increasingly prevalent infection. While previous studies have provided important insight into B. burgdorferi biology, many aspects, including basic cellular processes, remain underexplored. To help speed up the discovery process, we adapted a CRISPR interference (CRISPRi) platform for use in B. burgdorferi For efficiency and flexibility of use, we generated various CRISPRi template constructs that produce different basal and induced levels of dcas9 and carry different antibiotic resistance markers. We characterized the effectiveness of our CRISPRi platform by targeting the motility and cell morphogenesis genes flaB, mreB, rodA, and ftsI, whose native expression levels span two orders of magnitude. For all four genes, we obtained gene repression efficiencies of at least 95%. We showed by darkfield microscopy and cryo-electron tomography that flagellin (FlaB) depletion reduced the length and number of periplasmic flagella, which impaired cellular motility and resulted in cell straightening. Depletion of FtsI caused cell filamentation, implicating this protein in cell division in B. burgdorferi Finally, localized cell bulging in MreB- and RodA-depleted cells matched the locations of new peptidoglycan insertion specific to spirochetes of the Borrelia genus. These results therefore implicate MreB and RodA in the particular mode of cell wall elongation of these bacteria. Collectively, our results demonstrate the efficiency and ease of use of our B. burgdorferi CRISPRi platform, which should facilitate future genetic studies of this important pathogen.IMPORTANCE Gene function studies are facilitated by the availability of rapid and easy-to-use genetic tools. Homologous recombination-based methods traditionally used to genetically investigate gene function remain cumbersome to perform in B. burgdorferi, as they often are relatively inefficient. In comparison, our CRISPRi platform offers an easy and fast method to implement as it only requires a single plasmid transformation step and IPTG addition to obtain potent (>95%) downregulation of gene expression. To facilitate studies of various genes in wild-type and genetically modified strains, we provide over 30 CRISPRi plasmids that produce distinct levels of dcas9 expression and carry different antibiotic resistance markers. Our CRISPRi platform represents a useful and efficient complement to traditional genetic and chemical methods to study gene function in B. burgdorferi.
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13
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Garde S, Chodisetti PK, Reddy M. Peptidoglycan: Structure, Synthesis, and Regulation. EcoSal Plus 2021; 9:eESP-0010-2020. [PMID: 33470191 PMCID: PMC11168573 DOI: 10.1128/ecosalplus.esp-0010-2020] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Indexed: 02/06/2023]
Abstract
Peptidoglycan is a defining feature of the bacterial cell wall. Initially identified as a target of the revolutionary beta-lactam antibiotics, peptidoglycan has become a subject of much interest for its biology, its potential for the discovery of novel antibiotic targets, and its role in infection. Peptidoglycan is a large polymer that forms a mesh-like scaffold around the bacterial cytoplasmic membrane. Peptidoglycan synthesis is vital at several stages of the bacterial cell cycle: for expansion of the scaffold during cell elongation and for formation of a septum during cell division. It is a complex multifactorial process that includes formation of monomeric precursors in the cytoplasm, their transport to the periplasm, and polymerization to form a functional peptidoglycan sacculus. These processes require spatio-temporal regulation for successful assembly of a robust sacculus to protect the cell from turgor and determine cell shape. A century of research has uncovered the fundamentals of peptidoglycan biology, and recent studies employing advanced technologies have shed new light on the molecular interactions that govern peptidoglycan synthesis. Here, we describe the peptidoglycan structure, synthesis, and regulation in rod-shaped bacteria, particularly Escherichia coli, with a few examples from Salmonella and other diverse organisms. We focus on the pathway of peptidoglycan sacculus elongation, with special emphasis on discoveries of the past decade that have shaped our understanding of peptidoglycan biology.
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Affiliation(s)
- Shambhavi Garde
- These authors contributed equally
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
| | - Pavan Kumar Chodisetti
- These authors contributed equally
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India 500007
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14
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Zheng Y, Meng F, Zhu Z, Wei W, Sun Z, Chen J, Yu B, Lou C, Chen GQ. A tight cold-inducible switch built by coupling thermosensitive transcriptional and proteolytic regulatory parts. Nucleic Acids Res 2020; 47:e137. [PMID: 31750522 PMCID: PMC6868347 DOI: 10.1093/nar/gkz785] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/30/2019] [Accepted: 09/04/2019] [Indexed: 12/20/2022] Open
Abstract
Natural organisms have evolved intricate regulatory mechanisms that sense and respond to fluctuating environmental temperatures in a heat- or cold-inducible fashion. Unlike dominant heat-inducible switches, very few cold-inducible genetic switches are available in either natural or engineered systems. Moreover, the available cold-inducible switches still have many shortcomings, including high leaky gene expression, small dynamic range (<10-fold) or broad transition temperature (>10°C). To address these problems, a high-performance cold-inducible switch that can tightly control target gene expression is highly desired. Here, we introduce a tight and fast cold-inducible switch that couples two evolved thermosensitive variants, TFts and TEVts, as well as an additional Mycoplasma florum Lon protease (mf-Lon) to effectively turn-off target gene expression via transcriptional and proteolytic mechanisms. We validated the function of the switch in different culture media and various Escherichia coli strains and demonstrated its tightness by regulating two morphogenetic bacterial genes and expressing three heat-unstable recombinant proteins, respectively. Moreover, the additional protease module enabled the cold-inducible switch to actively remove the pre-existing proteins in slow-growing cells. This work establishes a high-performance cold-inducible system for tight and fast control of gene expression which has great potential for basic research, as well as industrial and biomedical applications.
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Affiliation(s)
- Yang Zheng
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fankang Meng
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Zihui Zhu
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weijia Wei
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Zhi Sun
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Jinchun Chen
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunbo Lou
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China.,College of Life Science, University of Science and Technology of China, Hefei 230027, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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15
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The evolution of spherical cell shape; progress and perspective. Biochem Soc Trans 2020; 47:1621-1634. [PMID: 31829405 PMCID: PMC6925525 DOI: 10.1042/bst20180634] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 01/29/2023]
Abstract
Bacterial cell shape is a key trait governing the extracellular and intracellular factors of bacterial life. Rod-like cell shape appears to be original which implies that the cell wall, division, and rod-like shape came together in ancient bacteria and that the myriad of shapes observed in extant bacteria have evolved from this ancestral shape. In order to understand its evolution, we must first understand how this trait is actively maintained through the construction and maintenance of the peptidoglycan cell wall. The proteins that are primarily responsible for cell shape are therefore the elements of the bacterial cytoskeleton, principally FtsZ, MreB, and the penicillin-binding proteins. MreB is particularly relevant in the transition between rod-like and spherical cell shape as it is often (but not always) lost early in the process. Here we will highlight what is known of this particular transition in cell shape and how it affects fitness before giving a brief perspective on what will be required in order to progress the field of cell shape evolution from a purely mechanistic discipline to one that has the perspective to both propose and to test reasonable hypotheses regarding the ecological drivers of cell shape change.
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16
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Rivas-Marin E, Peeters SH, Claret Fernández L, Jogler C, van Niftrik L, Wiegand S, Devos DP. Non-essentiality of canonical cell division genes in the planctomycete Planctopirus limnophila. Sci Rep 2020; 10:66. [PMID: 31919386 PMCID: PMC6952346 DOI: 10.1038/s41598-019-56978-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Most bacteria divide by binary fission using an FtsZ-based mechanism that relies on a multi-protein complex, the divisome. In the majority of non-spherical bacteria another multi-protein complex, the elongasome, is also required for the maintenance of cell shape. Components of these multi-protein assemblies are conserved and essential in most bacteria. Here, we provide evidence that at least three proteins of these two complexes are not essential in the FtsZ-less ovoid planctomycete bacterium Planctopirus limnophila which divides by budding. We attempted to construct P. limnophila knock-out mutants of the genes coding for the divisome proteins FtsI, FtsK, FtsW and the elongasome protein MreB. Surprisingly, ftsI, ftsW and mreB could be deleted without affecting the growth rate. On the other hand, the conserved ftsK appeared to be essential in this bacterium. In conclusion, the canonical bacterial cell division machinery is not essential in P. limnophila and this bacterium divides via budding using an unknown mechanism.
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Affiliation(s)
- Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain
| | - Stijn H Peeters
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Laura Claret Fernández
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain.,Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Christian Jogler
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, The Netherlands.,Institute of Microbiology, Department of Microbial Interactions, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Laura van Niftrik
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Sandra Wiegand
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain.
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17
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Stankeviciute G, Klein EA. Purification and HPLC Analysis of Cell Wall Muropeptides from Caulobacter crescentus. Bio Protoc 2019; 9:e3421. [PMID: 33654919 DOI: 10.21769/bioprotoc.3421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/13/2019] [Accepted: 10/17/2019] [Indexed: 11/02/2022] Open
Abstract
The peptidoglycan sacculus, or cell wall, is what defines bacterial cell shape. Cell wall composition can be best characterized at the molecular level by digesting the peptidoglycan murein polymer into its muropeptide subunits and quantifying the abundance of muropeptides using high-pressure liquid chromatography. Certain features of the cell wall including muropeptide composition, glycan strand length, degree of crosslinking, type of crosslinking and other peptidoglycan modifications can be quantified using this approach. Well-established protocols provide us with highly-resolved and quantitatively reproducible chromatographic data, which can be used to investigate bacterial cell wall composition under a variety of environmental or genetic perturbations. The method described here enables the purification of muropeptide samples, their quantification by HPLC, and fraction collection for peak identification by mass spectrometry. Although the methods for peptidoglycan purification and HPLC analysis have been previously published, our method includes important details on how to re-equilibrate the column between runs to allow for automated analysis of multiple samples.
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Affiliation(s)
- Gabriele Stankeviciute
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, 08102, USA
| | - Eric A Klein
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, 08102, USA.,Biology Department, Rutgers University-Camden, Camden, NJ, 08102, USA
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18
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Stankeviciute G, Miguel AV, Radkov A, Chou S, Huang KC, Klein EA. Differential modes of crosslinking establish spatially distinct regions of peptidoglycan in
Caulobacter crescentus. Mol Microbiol 2019; 111:995-1008. [DOI: 10.1111/mmi.14199] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriele Stankeviciute
- Center for Computational and Integrative Biology Rutgers University‐Camden Camden NJ 08102USA
| | - Amanda V. Miguel
- Department of Bioengineering Stanford University Stanford CA 94305USA
| | - Atanas Radkov
- Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA 94158USA
| | - Seemay Chou
- Department of Biochemistry and Biophysics University of California San Francisco San Francisco CA 94158USA
- Chan Zuckerberg Biohub San Francisco CA 94158USA
| | - Kerwyn Casey Huang
- Department of Bioengineering Stanford University Stanford CA 94305USA
- Chan Zuckerberg Biohub San Francisco CA 94158USA
- Department of Microbiology and Immunology Stanford University School of Medicine Stanford CA 94305USA
| | - Eric A. Klein
- Center for Computational and Integrative Biology Rutgers University‐Camden Camden NJ 08102USA
- Biology Department Rutgers University‐Camden Camden NJ 08102USA
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19
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A specialized MreB-dependent cell wall biosynthetic complex mediates the formation of stalk-specific peptidoglycan in Caulobacter crescentus. PLoS Genet 2019; 15:e1007897. [PMID: 30707707 PMCID: PMC6373972 DOI: 10.1371/journal.pgen.1007897] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/13/2019] [Accepted: 12/14/2018] [Indexed: 11/19/2022] Open
Abstract
Many bacteria have complex cell shapes, but the mechanisms producing their distinctive morphologies are still poorly understood. Caulobacter crescentus, for instance, exhibits a stalk-like extension that carries an adhesive holdfast mediating surface attachment. This structure forms through zonal peptidoglycan biosynthesis at the old cell pole and elongates extensively under phosphate-limiting conditions. We analyzed the composition of cell body and stalk peptidoglycan and identified significant differences in the nature and proportion of peptide crosslinks, indicating that the stalk represents a distinct subcellular domain with specific mechanical properties. To identify factors that participate in stalk formation, we systematically inactivated and localized predicted components of the cell wall biosynthetic machinery of C. crescentus. Our results show that the biosynthesis of stalk peptidoglycan involves a dedicated peptidoglycan biosynthetic complex that combines specific components of the divisome and elongasome, suggesting that the repurposing of preexisting machinery provides a straightforward means to evolve new morphological traits.
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20
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Pathway-Directed Screen for Inhibitors of the Bacterial Cell Elongation Machinery. Antimicrob Agents Chemother 2018; 63:AAC.01530-18. [PMID: 30323039 DOI: 10.1128/aac.01530-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
New antibiotics are needed to combat the growing problem of resistant bacterial infections. An attractive avenue toward the discovery of such next-generation therapies is to identify novel inhibitors of clinically validated targets, like cell wall biogenesis. We have therefore developed a pathway-directed whole-cell screen for small molecules that block the activity of the Rod system of Escherichia coli This conserved multiprotein complex is required for cell elongation and the morphogenesis of rod-shaped bacteria. It is composed of cell wall synthases and membrane proteins of unknown function that are organized by filaments of the actin-like MreB protein. Our screen takes advantage of the conditional essentiality of the Rod system and the ability of the beta-lactam mecillinam (also known as amdinocillin) to cause a toxic malfunctioning of the machinery. Rod system inhibitors can therefore be identified as molecules that promote growth in the presence of mecillinam under conditions permissive for the growth of Rod- cells. A screen of ∼690,000 compounds identified 1,300 compounds that were active against E. coli Pathway-directed screening of a majority of this subset of compounds for Rod inhibitors successfully identified eight analogs of the MreB antagonist A22. Further characterization of the A22 analogs identified showed that their antibiotic activity under conditions where the Rod system is essential was strongly correlated with their ability to suppress mecillinam toxicity. This result combined with those from additional biological studies reinforce the notion that A22-like molecules are relatively specific for MreB and suggest that the lipoprotein transport factor LolA is unlikely to be a physiologically relevant target as previously proposed.
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21
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Melzer ES, Sein CE, Chambers JJ, Siegrist MS. DivIVA concentrates mycobacterial cell envelope assembly for initiation and stabilization of polar growth. Cytoskeleton (Hoboken) 2018; 75:498-507. [PMID: 30160378 PMCID: PMC6644302 DOI: 10.1002/cm.21490] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/07/2018] [Accepted: 06/27/2018] [Indexed: 12/31/2022]
Abstract
In many model organisms, diffuse patterning of cell wall peptidoglycan synthesis by the actin homolog MreB enables the bacteria to maintain their characteristic rod shape. In Caulobacter crescentus and Escherichia coli, MreB is also required to sculpt this morphology de novo. Mycobacteria are rod-shaped but expand their cell wall from discrete polar or subpolar zones. In this genus, the tropomyosin-like protein DivIVA is required for the maintenance of cell morphology. DivIVA has also been proposed to direct peptidoglycan synthesis to the tips of the mycobacterial cell. The precise nature of this regulation is unclear, as is its role in creating rod shape from scratch. We find that DivIVA localizes nascent cell wall and covalently associated mycomembrane but is dispensable for the assembly process itself. Mycobacterium smegmatis rendered spherical by peptidoglycan digestion or by DivIVA depletion are able to regain rod shape at the population level in the presence of DivIVA. At the single cell level, there is a close spatiotemporal correlation between DivIVA foci, rod extrusion and concentrated cell wall synthesis. Thus, although the precise mechanistic details differ from other organisms, M. smegmatis also establish and propagate rod shape by cytoskeleton-controlled patterning of peptidoglycan. Our data further support the emerging notion that morphology is a hardwired trait of bacterial cells.
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Affiliation(s)
- Emily S Melzer
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - Caralyn E Sein
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts
| | - James J Chambers
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts.,Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts
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22
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Genetic Determinants of Penicillin Tolerance in Vibrio cholerae. Antimicrob Agents Chemother 2018; 62:AAC.01326-18. [PMID: 30061291 DOI: 10.1128/aac.01326-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 07/26/2018] [Indexed: 12/25/2022] Open
Abstract
Many bacteria are resistant to killing (tolerant) by typically bactericidal antibiotics due to their ability to counteract drug-induced cell damage. Vibrio cholerae, the cholera agent, displays an unusually high tolerance to diverse inhibitors of cell wall synthesis. Exposure to these agents, which in other bacteria leads to lysis and death, results in a breakdown of the cell wall and subsequent sphere formation in V. cholerae Spheres readily recover to rod-shaped cells upon antibiotic removal, but the mechanisms mediating the recovery process are not well characterized. Here, we found that the mechanisms of recovery are dependent on environmental conditions. Interestingly, on agarose pads, spheres undergo characteristic stages during the restoration of rod shape. Drug inhibition and microscopy experiments suggest that class A penicillin binding proteins (aPBPs) play a more active role than the Rod system, especially early in sphere recovery. Transposon insertion sequencing (TnSeq) analyses revealed that lipopolysaccharide (LPS) and cell wall biogenesis genes, as well as the sigma E cell envelope stress response, were particularly critical for recovery. LPS core and O-antigen appear to be more critical for sphere formation/integrity and viability than lipid A modifications. Overall, our findings demonstrate that the outer membrane is a key contributor to beta lactam tolerance and suggest a role for aPBPs in cell wall biogenesis in the absence of rod-shape cues. Factors required for postantibiotic recovery could serve as targets for antibiotic adjuvants that enhance the efficacy of antibiotics that inhibit cell wall biogenesis.
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23
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Horspool AM, Schertzer JW. Reciprocal cross-species induction of outer membrane vesicle biogenesis via secreted factors. Sci Rep 2018; 8:9873. [PMID: 29959355 PMCID: PMC6026191 DOI: 10.1038/s41598-018-28042-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 06/14/2018] [Indexed: 11/09/2022] Open
Abstract
Delivery of cargo to target cells is fundamental to bacterial competitiveness. One important but poorly understood system, ubiquitous among Gram-negative organisms, involves packaging cargo into outer membrane vesicles (OMVs). These biological nanoparticles are involved in processes ranging from toxin delivery to cell-cell communication. Despite this, we know comparatively little about how OMVs are formed. Building upon the discovery that the Pseudomonas Quinolone Signal (PQS) stimulates OMV biogenesis in Pseudomonas aeruginosa, we proposed a model where PQS interacts with the outer membrane to induce curvature and ultimately OMV formation. Though this model is well supported in P. aeruginosa, it remained unclear whether other organisms produce similar compounds. Here we describe the development of a tightly controlled experimental system to test the interaction of bacterially-produced factors with target cells. Using this system, we show that multiple species respond to PQS by increasing OMV formation, that PQS accumulates in the induced vesicles, and that other bacteria secrete OMV-promoting factors. Analysis of induced vesicles indicates that recipient-mediated mechanisms exist to control vesicle size and that relatedness to the producer organism can dictate susceptibility to OMV-inducing compounds. This work provides evidence that small molecule induced OMV biogenesis is a widely conserved process and that cross-talk between systems may influence OMV production in neighboring bacteria.
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Affiliation(s)
- Alexander M Horspool
- Department of Biological Sciences, Binghamton University, Binghamton, New York, USA
- Binghamton Biofilm Research Center, Binghamton University, Binghamton, New York, USA
| | - Jeffrey W Schertzer
- Department of Biological Sciences, Binghamton University, Binghamton, New York, USA.
- Binghamton Biofilm Research Center, Binghamton University, Binghamton, New York, USA.
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24
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Targeting the Bacterial Cytoskeleton of the Burkholderia cepacia Complex for Antimicrobial Development: A Cautionary Tale. Int J Mol Sci 2018; 19:ijms19061604. [PMID: 29848957 PMCID: PMC6032157 DOI: 10.3390/ijms19061604] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/04/2018] [Accepted: 05/17/2018] [Indexed: 11/18/2022] Open
Abstract
Burkholderia cepacia complex (BCC) bacteria are a group of opportunistic pathogens that cause severe lung infections in cystic fibrosis (CF). Treatment of BCC infections is difficult, due to the inherent and acquired multidrug resistance of BCC. There is a pressing need to find new bacterial targets for antimicrobials. Here, we demonstrate that the novel compound Q22, which is related to the bacterial cytoskeleton destabilising compound A22, can reduce the growth rate and inhibit growth of BCC bacteria. We further analysed the phenotypic effects of Q22 treatment on BCC virulence traits, to assess its feasibility as an antimicrobial. BCC bacteria were grown in the presence of Q22 with a broad phenotypic analysis, including resistance to H2O2-induced oxidative stress, changes in the inflammatory potential of cell surface components, and in-vivo drug toxicity studies. The influence of the Q22 treatment on inflammatory potential was measured by monitoring the cytokine responses of BCC whole cell lysates, purified lipopolysaccharide, and purified peptidoglycan extracted from bacterial cultures grown in the presence or absence of Q22 in differentiated THP-1 cells. BCC bacteria grown in the presence of Q22 displayed varying levels of resistance to H2O2-induced oxidative stress, with some strains showing increased resistance after treatment. There was strain-to-strain variation in the pro-inflammatory ability of bacterial lysates to elicit TNFα and IL-1β from human myeloid cells. Despite minimal toxicity previously shown in vitro with primary CF cell lines, in-vivo studies demonstrated Q22 toxicity in both zebrafish and mouse infection models. In summary, destabilisation of the bacterial cytoskeleton in BCC, using compounds such as Q22, led to increased virulence-related traits in vitro. These changes appear to vary depending on strain and BCC species. Future development of antimicrobials targeting the BCC bacterial cytoskeleton may be hampered if such effects translate into the in-vivo environment of the CF infection.
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25
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Molecular imaging of glycan chains couples cell-wall polysaccharide architecture to bacterial cell morphology. Nat Commun 2018; 9:1263. [PMID: 29593214 PMCID: PMC5871751 DOI: 10.1038/s41467-018-03551-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/22/2018] [Indexed: 01/08/2023] Open
Abstract
Biopolymer composite cell walls maintain cell shape and resist forces in plants, fungi and bacteria. Peptidoglycan, a crucial antibiotic target and immunomodulator, performs this role in bacteria. The textbook structural model of peptidoglycan is a highly ordered, crystalline material. Here we use atomic force microscopy (AFM) to image individual glycan chains in peptidoglycan from Escherichia coli in unprecedented detail. We quantify and map the extent to which chains are oriented in a similar direction (orientational order), showing it is much less ordered than previously depicted. Combining AFM with size exclusion chromatography, we reveal glycan chains up to 200 nm long. We show that altered cell shape is associated with substantial changes in peptidoglycan biophysical properties. Glycans from E. coli in its normal rod shape are long and circumferentially oriented, but when a spheroid shape is induced (chemically or genetically) glycans become short and disordered.
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26
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Pende N, Wang J, Weber PM, Verheul J, Kuru E, Rittmann SKMR, Leisch N, VanNieuwenhze MS, Brun YV, den Blaauwen T, Bulgheresi S. Host-Polarized Cell Growth in Animal Symbionts. Curr Biol 2018; 28:1039-1051.e5. [PMID: 29576473 PMCID: PMC6611161 DOI: 10.1016/j.cub.2018.02.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 12/13/2017] [Accepted: 02/15/2018] [Indexed: 01/16/2023]
Abstract
To determine the fundamentals of cell growth, we must extend cell
biological studies to non-model organisms. Here, we investigated the growth
modes of the only two rods known to widen instead of elongating,
Candidatus Thiosymbion oneisti and Thiosymbion
hypermnestrae. These bacteria are attached by one pole to the surface of their
respective nematode hosts. By incubating live Ca. T. oneisti
and T. hypermnestrae with a peptidoglycan metabolic probe, we observed that the
insertion of new cell wall starts at the poles and proceeds inward,
concomitantly with FtsZ-based membrane constriction. Remarkably, in
Ca. T. hypermnestrae, the proximal, animal-attached pole
grows before the distal, free pole, indicating that the peptidoglycan synthesis
machinery is host oriented. Immunostaining of the symbionts with an antibody
against the actin homolog MreB revealed that it was arranged
medially—that is, parallel to the cell long axis—throughout the
symbiont life cycle. Given that depolymerization of MreB abolished newly
synthesized peptidoglycan insertion and impaired divisome assembly, we conclude
that MreB function is required for symbiont widening and division. In
conclusion, our data invoke a reassessment of the localization and function of
the bacterial actin homolog. Pende et al. show that cell growth is host oriented in two marine
nematode-attached bacteria. In contrast to what is observed in model rods, the
actin homolog MreB of the symbionts is arranged parallel to the cell long axis
throughout the cell cycle. This medial MreB ring is essential for symbiont
growth and division.
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Affiliation(s)
- Nika Pende
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, Althanstrasse 14, 1090 Vienna, Austria
| | - Jinglan Wang
- Bacterial Cell Biology and Physiology Swammerdam Institute for Life Sciences, University of Amsterdam, De Boelelaan 1108, 1081 Amsterdam, the Netherlands
| | - Philipp M Weber
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, Althanstrasse 14, 1090 Vienna, Austria
| | - Jolanda Verheul
- Bacterial Cell Biology and Physiology Swammerdam Institute for Life Sciences, University of Amsterdam, De Boelelaan 1108, 1081 Amsterdam, the Netherlands
| | - Erkin Kuru
- Department of Genetics, Harvard Medical School NRB, 77 Avenue Louis Pasteur, Boston, MA, USA
| | - Simon K-M R Rittmann
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, Althanstrasse 14, 1090 Vienna, Austria
| | - Nikolaus Leisch
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, Althanstrasse 14, 1090 Vienna, Austria
| | | | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology Swammerdam Institute for Life Sciences, University of Amsterdam, De Boelelaan 1108, 1081 Amsterdam, the Netherlands
| | - Silvia Bulgheresi
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, Althanstrasse 14, 1090 Vienna, Austria.
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27
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Logsdon MM, Aldridge BB. Stable Regulation of Cell Cycle Events in Mycobacteria: Insights From Inherently Heterogeneous Bacterial Populations. Front Microbiol 2018; 9:514. [PMID: 29619019 PMCID: PMC5871693 DOI: 10.3389/fmicb.2018.00514] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/06/2018] [Indexed: 11/24/2022] Open
Abstract
Model bacteria, such as E. coli and B. subtilis, tightly regulate cell cycle progression to achieve consistent cell size distributions and replication dynamics. Many of the hallmark features of these model bacteria, including lateral cell wall elongation and symmetric growth and division, do not occur in mycobacteria. Instead, mycobacterial growth is characterized by asymmetric polar growth and division. This innate asymmetry creates unequal birth sizes and growth rates for daughter cells with each division, generating a phenotypically heterogeneous population. Although the asymmetric growth patterns of mycobacteria lead to a larger variation in birth size than typically seen in model bacterial populations, the cell size distribution is stable over time. Here, we review the cellular mechanisms of growth, division, and cell cycle progression in mycobacteria in the face of asymmetry and inherent heterogeneity. These processes coalesce to control cell size. Although Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) utilize a novel model of cell size control, they are similar to previously studied bacteria in that initiation of DNA replication is a key checkpoint for cell division. We compare the regulation of DNA replication initiation and strategies used for cell size homeostasis in mycobacteria and model bacteria. Finally, we review the importance of cellular organization and chromosome segregation relating to the physiology of mycobacteria and consider how new frameworks could be applied across the wide spectrum of bacterial diversity.
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Affiliation(s)
- Michelle M Logsdon
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States.,Department of Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA, United States
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States.,Department of Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA, United States.,Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, United States
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28
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Farrell FD, Gralka M, Hallatschek O, Waclaw B. Mechanical interactions in bacterial colonies and the surfing probability of beneficial mutations. J R Soc Interface 2018; 14:rsif.2017.0073. [PMID: 28592660 PMCID: PMC5493792 DOI: 10.1098/rsif.2017.0073] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/12/2017] [Indexed: 11/12/2022] Open
Abstract
Bacterial conglomerates such as biofilms and microcolonies are ubiquitous in nature and play an important role in industry and medicine. In contrast to well-mixed cultures routinely used in microbial research, bacteria in a microcolony interact mechanically with one another and with the substrate to which they are attached. Here, we use a computer model of a microbial colony of rod-shaped cells to investigate how physical interactions between cells determine their motion in the colony and how this affects biological evolution. We show that the probability that a faster-growing mutant ‘surfs’ at the colony's frontier and creates a macroscopic sector depends on physical properties of cells (shape, elasticity and friction). Although all these factors contribute to the surfing probability in seemingly different ways, their effects can be summarized by two summary statistics that characterize the front roughness and cell alignment. Our predictions are confirmed by experiments in which we measure the surfing probability for colonies of different front roughness. Our results show that physical interactions between bacterial cells play an important role in biological evolution of new traits, and suggest that these interactions may be relevant to processes such as de novo evolution of antibiotic resistance.
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Affiliation(s)
- Fred D Farrell
- Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Matti Gralka
- Department of Physics, University of California, Berkeley, CA 94720, USA
| | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley, CA 94720, USA.,Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Bartlomiej Waclaw
- School of Physics and Astronomy, University of Edinburgh, JCMB, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK .,Centre for Synthetic and Systems Biology, University of Edinburgh, CH Waddington Building, Max Born Crescent, Edinburgh EH9 3BF, UK
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29
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Zielińska A, Billini M, Möll A, Kremer K, Briegel A, Izquierdo Martinez A, Jensen GJ, Thanbichler M. LytM factors affect the recruitment of autolysins to the cell division site in Caulobacter crescentus. Mol Microbiol 2017; 106:419-438. [PMID: 28833791 DOI: 10.1111/mmi.13775] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2017] [Indexed: 12/24/2022]
Abstract
Most bacteria possess a peptidoglycan cell wall that determines their morphology and provides mechanical robustness during osmotic challenges. The biosynthesis of this structure is achieved by a large set of synthetic and lytic enzymes with varying substrate specificities. Although the biochemical functions of these proteins are conserved and well-investigated, the precise roles of individual factors and the regulatory mechanisms coordinating their activities in time and space remain incompletely understood. Here, we comprehensively analyze the autolytic machinery of the alphaproteobacterial model organism Caulobacter crescentus, with a specific focus on LytM-like endopeptidases, soluble lytic transglycosylases and amidases. Our data reveal a high degree of redundancy within each protein family but also specialized functions for individual family members under stress conditions. In addition, we identify two lytic transglycosylases and an amidase as new divisome components that are recruited to midcell at distinct stages of the cell cycle. The midcell localization of these proteins is affected by two LytM factors with degenerate catalytic domains, DipM and LdpF, which may serve as regulatory hubs coordinating the activities of multiple autolytic enzymes during cell constriction and fission respectively. These findings set the stage for in-depth studies of the molecular mechanisms that control peptidoglycan remodeling in C. crescentus.
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Affiliation(s)
- Aleksandra Zielińska
- Faculty of Biology, Philipps-Universität, Marburg 35043, Germany.,Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Maria Billini
- Faculty of Biology, Philipps-Universität, Marburg 35043, Germany.,Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Andrea Möll
- Faculty of Biology, Philipps-Universität, Marburg 35043, Germany.,Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Katharina Kremer
- Faculty of Biology, Philipps-Universität, Marburg 35043, Germany
| | - Ariane Briegel
- Divison of Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Adrian Izquierdo Martinez
- Faculty of Biology, Philipps-Universität, Marburg 35043, Germany.,Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Grant J Jensen
- Divison of Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Martin Thanbichler
- Faculty of Biology, Philipps-Universität, Marburg 35043, Germany.,Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany.,LOEWE Center for Synthetic Microbiology, Marburg 35043, Germany
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30
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FtsEX-mediated regulation of the final stages of cell division reveals morphogenetic plasticity in Caulobacter crescentus. PLoS Genet 2017; 13:e1006999. [PMID: 28886022 PMCID: PMC5607218 DOI: 10.1371/journal.pgen.1006999] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 09/20/2017] [Accepted: 08/25/2017] [Indexed: 11/19/2022] Open
Abstract
During its life cycle, Caulobacter crescentus undergoes a series of coordinated shape changes, including generation of a polar stalk and reshaping of the cell envelope to produce new daughter cells through the process of cytokinesis. The mechanisms by which these morphogenetic processes are coordinated in time and space remain largely unknown. Here we demonstrate that the conserved division complex FtsEX controls both the early and late stages of cytokinesis in C. crescentus, namely initiation of constriction and final cell separation. ΔftsE cells display a striking phenotype: cells are chained, with skinny connections between cell bodies resulting from defects in inner membrane fusion and cell separation. Surprisingly, the thin connections in ΔftsE cells share morphological and molecular features with C. crescentus stalks. Our data uncover unanticipated morphogenetic plasticity in C. crescentus, with loss of FtsE causing a stalk-like program to take over at failed division sites. Bacterial cell shape is genetically hardwired and is critical for fitness and, in certain cases, pathogenesis. In most bacteria, a semi-rigid structure called the cell wall surrounds the inner membrane, offering protection against cell lysis while simultaneously maintaining cell shape. A highly dynamic macromolecular structure, the cell wall undergoes extensive remodeling as bacterial cells grow and divide. We demonstrate that a broadly conserved cell division complex, FtsEX, relays signals from the cytoplasm to the cell wall to regulate key developmental shape changes in the α-proteobacterium Caulobacter crescentus. Consistent with studies in diverse bacteria, we observe strong synthetic interactions between ftsE and cell wall hydrolytic factors, suggesting that regulation of cell wall remodeling is a conserved function of FtsEX. Loss of FtsE causes morphological defects associated with both the early and late stages of division. Intriguingly, without FtsE, cells frequently fail to separate and instead elaborate a thin, tubular structure between cell bodies, a growth mode observed in other α-proteobacteria. Overall, our results highlight the plasticity of bacterial cell shape and demonstrate how altering the activity of one morphogenetic program can produce diverse morphologies resembling those of other bacteria in nature.
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31
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van Teeseling MCF, de Pedro MA, Cava F. Determinants of Bacterial Morphology: From Fundamentals to Possibilities for Antimicrobial Targeting. Front Microbiol 2017; 8:1264. [PMID: 28740487 PMCID: PMC5502672 DOI: 10.3389/fmicb.2017.01264] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/23/2017] [Indexed: 12/11/2022] Open
Abstract
Bacterial morphology is extremely diverse. Specific shapes are the consequence of adaptive pressures optimizing bacterial fitness. Shape affects critical biological functions, including nutrient acquisition, motility, dispersion, stress resistance and interactions with other organisms. Although the characteristic shape of a bacterial species remains unchanged for vast numbers of generations, periodical variations occur throughout the cell (division) and life cycles, and these variations can be influenced by environmental conditions. Bacterial morphology is ultimately dictated by the net-like peptidoglycan (PG) sacculus. The species-specific shape of the PG sacculus at any time in the cell cycle is the product of multiple determinants. Some morphological determinants act as a cytoskeleton to guide biosynthetic complexes spatiotemporally, whereas others modify the PG sacculus after biosynthesis. Accumulating evidence supports critical roles of morphogenetic processes in bacteria-host interactions, including pathogenesis. Here, we review the molecular determinants underlying morphology, discuss the evidence linking bacterial morphology to niche adaptation and pathogenesis, and examine the potential of morphological determinants as antimicrobial targets.
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Affiliation(s)
- Muriel C F van Teeseling
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
| | - Miguel A de Pedro
- Centro de Biología Molecular "Severo Ochoa" - Consejo Superior de Investigaciones Científicas, Universidad Autónoma de MadridMadrid, Spain
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
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32
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Zepeda Gurrola RC, Fu Y, Rodríguez Luna IC, Benítez Cardoza CG, López López MDJ, López Vidal Y, Gutíerrez GRA, Rodríguez Pérez MA, Guo X. Novel protein interactions with an actin homolog (MreB) of Helicobacter pylori determined by bacterial two-hybrid system. Microbiol Res 2017; 201:39-45. [PMID: 28602400 DOI: 10.1016/j.micres.2017.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/24/2017] [Accepted: 04/22/2017] [Indexed: 02/06/2023]
Abstract
The bacterium Helicobacter pylori infects more than 50% of the world population and causes several gastroduodenal diseases, including gastric cancer. Nevertheless, we still need to explore some protein interactions that may be involved in pathogenesis. MreB, an actin homolog, showed some special characteristics in previous studies, indicating that it could have different functions. Protein functions could be realized via protein-protein interactions. In the present study, the MreB protein from H. pylori 26695 fused with two tags 10×His and GST in tandem was overexpressed and purified from Escherchia coli. The purified recombinant protein was used to perform a pull-down assay with H. pylori 26695 cell lysate. The pulled-down proteins were identified by mass spectrometry (MALDI-TOF), in which the known important proteins related to morphogenesis were absent but several proteins related to pathogenesis process were observed. The bacterial two-hybrid system was further used to evaluate the protein interactions and showed that new interactions of MreB respectively with VacA, UreB, HydB, HylB and AddA were confirmed but the interaction MreB-MreC was not validated. These results indicated that the protein MreB in H. pylori has a distinct interactome, does not participate in cell morphogenesis via MreB-MreC but could be related to pathogenesis.
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Affiliation(s)
| | - Yajuan Fu
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Cd. Reynosa Tamaulipas, Mexico
| | | | | | | | - Yolanda López Vidal
- Facultad de Medicina, División de Investigación, Universidad Nacional Autónoma de Mexico
| | - Germán Rubén Aguilar Gutíerrez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Mario A Rodríguez Pérez
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Cd. Reynosa Tamaulipas, Mexico
| | - Xianwu Guo
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Cd. Reynosa Tamaulipas, Mexico.
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33
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Shiomi D. Polar localization of MreB actin is inhibited by anionic phospholipids in the rod-shaped bacterium Escherichia coli. Curr Genet 2017; 63:845-848. [PMID: 28439631 DOI: 10.1007/s00294-017-0696-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 12/13/2022]
Abstract
Bacterial actin MreB is required for the maintenance of cell polarity. MreB is located underneath the cell membrane and mainly localizes at a central cylindrical part of the cell. In addition, it has recently been found that anionic phospholipids (aPLs: phosphatidylglycerol and cardiolipin) play a crucial role in excluding MreB from the cell poles. Subcellular localization of MreB is positively and negatively regulated by membrane curvature and aPLs, respectively.
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Affiliation(s)
- Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan.
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34
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Woldemeskel SA, Goley ED. Shapeshifting to Survive: Shape Determination and Regulation in Caulobacter crescentus. Trends Microbiol 2017; 25:673-687. [PMID: 28359631 DOI: 10.1016/j.tim.2017.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/28/2017] [Accepted: 03/06/2017] [Indexed: 01/05/2023]
Abstract
Bacterial cell shape is a genetically encoded and inherited feature that is optimized for efficient growth, survival, and propagation of bacteria. In addition, bacterial cell morphology is adaptable to changes in environmental conditions. Work in recent years has demonstrated that individual features of cell shape, such as length or curvature, arise through the spatial regulation of cell wall synthesis by cytoskeletal proteins. However, the mechanisms by which these different morphogenetic factors are coordinated and how they may be globally regulated in response to cell cycle and environmental cues are only beginning to emerge. Here, we have summarized recent advances that have been made to understand morphology in the dimorphic Gram-negative bacterium Caulobacter crescentus.
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Affiliation(s)
- Selamawit Abi Woldemeskel
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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35
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Kawazura T, Matsumoto K, Kojima K, Kato F, Kanai T, Niki H, Shiomi D. Exclusion of assembled MreB by anionic phospholipids at cell poles confers cell polarity for bidirectional growth. Mol Microbiol 2017; 104:472-486. [PMID: 28164388 DOI: 10.1111/mmi.13639] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2017] [Indexed: 12/21/2022]
Abstract
Cell polarity determines the direction of cell growth in bacteria. MreB actin spatially regulates peptidoglycan synthesis to enable cells to elongate bidirectionally. MreB densely localizes in the cylindrical part of the rod cell and not in polar regions in Escherichia coli. When treated with A22, which inhibits MreB polymerization, rod-shaped cells became round and MreB was diffusely distributed throughout the cytoplasmic membrane. A22 removal resulted in restoration of the rod shape. Initially, diffuse MreB started to re-assemble, and MreB-free zones were subsequently observed in the cytoplasmic membrane. These MreB-free zones finally became cell poles, allowing the cells to elongate bidirectionally. When MreB was artificially located at the cell poles, an additional pole was created, indicating that artificial localization of MreB at the cell pole induced local peptidoglycan synthesis. It was found that the anionic phospholipids (aPLs), phosphatidylglycerol and cardiolipin, which were enriched in cell poles preferentially interact with monomeric MreB compared with assembled MreB in vitro. MreB tended to localize to cell poles in cells lacking both aPLs, resulting in production of Y-shaped cells. Their findings indicated that aPLs exclude assembled MreB from cell poles to establish cell polarity, thereby allowing cells to elongate in a particular direction.
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Affiliation(s)
- Takuma Kawazura
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Kanon Matsumoto
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Koki Kojima
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Fumiya Kato
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Tomomi Kanai
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Hironori Niki
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, Sokendai, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Daisuke Shiomi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
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36
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Cserti E, Rosskopf S, Chang YW, Eisheuer S, Selter L, Shi J, Regh C, Koert U, Jensen GJ, Thanbichler M. Dynamics of the peptidoglycan biosynthetic machinery in the stalked budding bacteriumHyphomonas neptunium. Mol Microbiol 2017; 103:875-895. [DOI: 10.1111/mmi.13593] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Emöke Cserti
- Faculty of Biology; Philipps-Universität; Marburg 35043 Germany
- Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
| | - Sabine Rosskopf
- Faculty of Biology; Philipps-Universität; Marburg 35043 Germany
| | - Yi-Wei Chang
- Division of Biology and Bioengineering; California Institute of Technology; Pasadena CA 91125 USA
| | - Sabrina Eisheuer
- Faculty of Biology; Philipps-Universität; Marburg 35043 Germany
- Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
| | - Lars Selter
- Faculty of Chemistry; Philipps-Universität; Marburg Germany
| | - Jian Shi
- Division of Biology and Bioengineering; California Institute of Technology; Pasadena CA 91125 USA
| | - Christina Regh
- Faculty of Biology; Philipps-Universität; Marburg 35043 Germany
| | - Ulrich Koert
- Faculty of Chemistry; Philipps-Universität; Marburg Germany
| | - Grant J. Jensen
- Division of Biology and Bioengineering; California Institute of Technology; Pasadena CA 91125 USA
- Howard Hughes Medical Institute, California Institute of Technology; Pasadena CA 91125 USA
| | - Martin Thanbichler
- Faculty of Biology; Philipps-Universität; Marburg 35043 Germany
- Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
- LOEWE Center for Synthetic Microbiology; Marburg 35043 Germany
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Subramanian K, Tyson JJ. Spatiotemporal Models of the Asymmetric Division Cycle of Caulobacter crescentus. Results Probl Cell Differ 2017; 61:23-48. [PMID: 28409299 DOI: 10.1007/978-3-319-53150-2_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The spatial localization of proteins within the cytoplasm of bacteria is an underappreciated but critical aspect of cell cycle regulation for many prokaryotes. In Caulobacter crescentus-a model organism for the study of asymmetric cell reproduction in prokaryotes-heterogeneous localization of proteins has been identified as the underlying cause of asymmetry in cell morphology, DNA replication, and cell division. However, significant questions remain. Firstly, the mechanisms by which proteins localize in the organelle-free prokaryotic cytoplasm remain obscure. Furthermore, how variations in the spatial and temporal dynamics of cell fate determinants regulate signaling pathways and orchestrate the complex programs of asymmetric cell division and differentiation are subjects of ongoing research. In this chapter, we review current efforts in investigating these two questions. We describe how mathematical models of spatiotemporal protein dynamics are being used to generate and test competing hypotheses and provide complementary insight about the control mechanisms that regulate asymmetry in protein localization and cell division.
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Affiliation(s)
- Kartik Subramanian
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
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Cytoskeletal Proteins in Caulobacter crescentus: Spatial Orchestrators of Cell Cycle Progression, Development, and Cell Shape. Subcell Biochem 2017; 84:103-137. [PMID: 28500524 DOI: 10.1007/978-3-319-53047-5_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Caulobacter crescentus, an aquatic Gram-negative α-proteobacterium, is dimorphic, as a result of asymmetric cell divisions that give rise to a free-swimming swarmer daughter cell and a stationary stalked daughter. Cell polarity of vibrioid C. crescentus cells is marked by the presence of a stalk at one end in the stationary form and a polar flagellum in the motile form. Progression through the cell cycle and execution of the associated morphogenetic events are tightly controlled through regulation of the abundance and activity of key proteins. In synergy with the regulation of protein abundance or activity, cytoskeletal elements are key contributors to cell cycle progression through spatial regulation of developmental processes. These include: polarity establishment and maintenance, DNA segregation, cytokinesis, and cell elongation. Cytoskeletal proteins in C. crescentus are additionally required to maintain its rod shape, curvature, and pole morphology. In this chapter, we explore the mechanisms through which cytoskeletal proteins in C. crescentus orchestrate developmental processes by acting as scaffolds for protein recruitment, generating force, and/or restricting or directing the motion of molecular machines. We discuss each cytoskeletal element in turn, beginning with those important for organization of molecules at the cell poles and chromosome segregation, then cytokinesis, and finally cell shape.
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Abstract
A diverse set of protein polymers, structurally related to actin filaments contributes to the organization of bacterial cells as cytomotive or cytoskeletal filaments. This chapter describes actin homologs encoded by bacterial chromosomes. MamK filaments, unique to magnetotactic bacteria, help establishing magnetic biological compasses by interacting with magnetosomes. Magnetosomes are intracellular membrane invaginations containing biomineralized crystals of iron oxide that are positioned by MamK along the long-axis of the cell. FtsA is widespread across bacteria and it is one of the earliest components of the divisome to arrive at midcell, where it anchors the cell division machinery to the membrane. FtsA binds directly to FtsZ filaments and to the membrane through its C-terminus. FtsA shows altered domain architecture when compared to the canonical actin fold. FtsA's subdomain 1C replaces subdomain 1B of other members of the actin family and is located on the opposite side of the molecule. Nevertheless, when FtsA assembles into protofilaments, the protofilament structure is preserved, as subdomain 1C replaces subdomain IB of the following subunit in a canonical actin filament. MreB has an essential role in shape-maintenance of most rod-shaped bacteria. Unusually, MreB filaments assemble from two protofilaments in a flat and antiparallel arrangement. This non-polar architecture implies that both MreB filament ends are structurally identical. MreB filaments bind directly to membranes where they interact with both cytosolic and membrane proteins, thereby forming a key component of the elongasome. MreB filaments in cells are short and dynamic, moving around the long axis of rod-shaped cells, sensing curvature of the membrane and being implicated in peptidoglycan synthesis.
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Affiliation(s)
- Thierry Izoré
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Fusinita van den Ent
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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40
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Ouzounov N, Nguyen JP, Bratton BP, Jacobowitz D, Gitai Z, Shaevitz JW. MreB Orientation Correlates with Cell Diameter in Escherichia coli. Biophys J 2016; 111:1035-43. [PMID: 27602731 PMCID: PMC5018124 DOI: 10.1016/j.bpj.2016.07.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/14/2016] [Accepted: 07/01/2016] [Indexed: 10/21/2022] Open
Abstract
Bacteria have remarkably robust cell shape control mechanisms. For example, cell diameter only varies by a few percent across a given population. The bacterial actin homolog, MreB, is necessary for establishment and maintenance of rod shape although the detailed properties of MreB that are important for shape control remained unknown. In this study, we perturb MreB in two ways: by treating cells with the polymerization-inhibiting drug A22 and by creating point mutants in mreB. These perturbations modify the steady-state diameter of cells over a wide range, from 790 ± 30 nm to 1700 ± 20 nm. To determine which properties of MreB are important for diameter control, we correlated structural characteristics of fluorescently tagged MreB polymers with cell diameter by simultaneously analyzing three-dimensional images of MreB and cell shape. Our results indicate that the helical pitch angle of MreB inversely correlates with the cell diameter of Escherichia coli. Other correlations between MreB and cell diameter are not found to be significant. These results demonstrate that the physical properties of MreB filaments are important for shape control and support a model in which MreB organizes the cell wall growth machinery to produce a chiral cell wall structure and dictate cell diameter.
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Affiliation(s)
- Nikolay Ouzounov
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Jeffrey P Nguyen
- Department of Physics, Princeton University, Princeton, New Jersey
| | - Benjamin P Bratton
- Department of Molecular Biology, Princeton University, Princeton, New Jersey; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - David Jacobowitz
- Department of Physics, Princeton University, Princeton, New Jersey
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey
| | - Joshua W Shaevitz
- Department of Physics, Princeton University, Princeton, New Jersey; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey.
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41
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YodL and YisK Possess Shape-Modifying Activities That Are Suppressed by Mutations in Bacillus subtilis mreB and mbl. J Bacteriol 2016; 198:2074-88. [PMID: 27215790 DOI: 10.1128/jb.00183-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/18/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Many bacteria utilize actin-like proteins to direct peptidoglycan (PG) synthesis. MreB and MreB-like proteins are thought to act as scaffolds, guiding the localization and activity of key PG-synthesizing proteins during cell elongation. Despite their critical role in viability and cell shape maintenance, very little is known about how the activity of MreB family proteins is regulated. Using a Bacillus subtilis misexpression screen, we identified two genes, yodL and yisK, that when misexpressed lead to loss of cell width control and cell lysis. Expression analysis suggested that yodL and yisK are previously uncharacterized Spo0A-regulated genes, and consistent with these observations, a ΔyodL ΔyisK mutant exhibited reduced sporulation efficiency. Suppressors resistant to YodL's killing activity occurred primarily in mreB mutants and resulted in amino acid substitutions at the interface between MreB and the highly conserved morphogenic protein RodZ, whereas suppressors resistant to YisK occurred primarily in mbl mutants and mapped to Mbl's predicted ATP-binding pocket. YodL's shape-altering activity appears to require MreB, as a ΔmreB mutant was resistant to the effects of YodL but not YisK. Similarly, YisK appears to require Mbl, as a Δmbl mutant was resistant to the cell-widening effects of YisK but not of YodL. Collectively, our results suggest that YodL and YisK likely modulate MreB and Mbl activity, possibly during the early stages of sporulation. IMPORTANCE The peptidoglycan (PG) component of the cell envelope confers structural rigidity to bacteria and protects them from osmotic pressure. MreB and MreB-like proteins are thought to act as scaffolds for PG synthesis and are essential in bacteria exhibiting nonpolar growth. Despite the critical role of MreB-like proteins, we lack mechanistic insight into how their activities are regulated. Here, we describe the discovery of two B. subtilis proteins, YodL and YisK, which modulate MreB and Mbl activities. Our data suggest that YodL specifically targets MreB, whereas YisK targets Mbl. The apparent specificities with which YodL and YisK are able to differentially target MreB and Mbl make them potentially powerful tools for probing the mechanics of cytoskeletal function in bacteria.
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Liechti G, Kuru E, Packiam M, Hsu YP, Tekkam S, Hall E, Rittichier JT, VanNieuwenhze M, Brun YV, Maurelli AT. Pathogenic Chlamydia Lack a Classical Sacculus but Synthesize a Narrow, Mid-cell Peptidoglycan Ring, Regulated by MreB, for Cell Division. PLoS Pathog 2016; 12:e1005590. [PMID: 27144308 PMCID: PMC4856321 DOI: 10.1371/journal.ppat.1005590] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 04/01/2016] [Indexed: 01/28/2023] Open
Abstract
The peptidoglycan (PG) cell wall is a peptide cross-linked glycan polymer essential for bacterial division and maintenance of cell shape and hydrostatic pressure. Bacteria in the Chlamydiales were long thought to lack PG until recent advances in PG labeling technologies revealed the presence of this critical cell wall component in Chlamydia trachomatis. In this study, we utilize bio-orthogonal D-amino acid dipeptide probes combined with super-resolution microscopy to demonstrate that four pathogenic Chlamydiae species each possess a ≤ 140 nm wide PG ring limited to the division plane during the replicative phase of their developmental cycles. Assembly of this PG ring is rapid, processive, and linked to the bacterial actin-like protein, MreB. Both MreB polymerization and PG biosynthesis occur only in the intracellular form of pathogenic Chlamydia and are required for cell enlargement, division, and transition between the microbe’s developmental forms. Our kinetic, molecular, and biochemical analyses suggest that the development of this limited, transient, PG ring structure is the result of pathoadaptation by Chlamydia to an intracellular niche within its vertebrate host. Pathogenic Chlamydia do not assemble their peptidoglycan (PG) cell wall in a classical, mesh-like sacculus, but instead apparently confine it to the mid-cell in the actively dividing, non-infectious form. We characterize the assembly and aging of this PG-ring and link its synthesis to MreB, an actin-like protein associated with lateral cell wall synthesis in bacteria. As PG is recognized by the host innate immune system, we hypothesize that the limited amount of PG synthesized by Chlamydia is an adaptation to the microbe’s intracellular lifestyle.
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Affiliation(s)
- George Liechti
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Erkin Kuru
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Mathanraj Packiam
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Yen-Pang Hsu
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Srinivas Tekkam
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Edward Hall
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Jonathan T Rittichier
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Michael VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Anthony T Maurelli
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
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Fine-Tuning of the Cpx Envelope Stress Response Is Required for Cell Wall Homeostasis in Escherichia coli. mBio 2016; 7:e00047-16. [PMID: 26908573 PMCID: PMC4791840 DOI: 10.1128/mbio.00047-16] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The envelope of Gram-negative bacteria is an essential compartment that constitutes a protective and permeability barrier between the cell and its environment. The envelope also hosts the cell wall, a mesh-like structure made of peptidoglycan (PG) that determines cell shape and provides osmotic protection. Since the PG must grow and divide in a cell-cycle-synchronized manner, its synthesis and remodeling are tightly regulated. Here, we discovered that PG homeostasis is intimately linked to the levels of activation of the Cpx system, an envelope stress response system traditionally viewed as being involved in protein quality control in the envelope. We first show that Cpx is activated when PG integrity is challenged and that this activation provides protection to cells exposed to antibiotics inhibiting PG synthesis. By rerouting the outer membrane lipoprotein NlpE, a known Cpx activator, to a different envelope subcompartment, we managed to manipulate Cpx activation levels. We found that Cpx overactivation leads to aberrant cellular morphologies, to an increased sensitivity to β-lactams, and to dramatic division and growth defects, consistent with a loss of PG homeostasis. Remarkably, these phenotypes were largely abrogated by the deletion of ldtD, a Cpx-induced gene involved in noncanonical PG cross-linkage, suggesting that this transpeptidase is an important link between PG homeostasis and the Cpx system. Altogether our data show that fine-tuning of an envelope quality control system constitutes an important layer of regulation of the highly organized cell wall structure. The envelope of Gram-negative bacteria is essential for viability. First, it includes the cell wall, a continuous polymer of peptidoglycan (PG) that determines cell morphology and protects against osmotic stress. Moreover, the envelope constitutes a protective barrier between the cell interior and the environment. Therefore, mechanisms called envelope stress response systems (ESRS) exist to monitor and defend envelope integrity against harmful conditions. Cpx is a major ESRS that detects and manages the accumulation of misfolded proteins in the envelope of Escherichia coli. We found that this protein quality control system also plays a fundamental role in the regulation of PG assembly. Strikingly, the level of Cpx response is critical, as an excessive activation leads to phenotypes associated with a loss of cell wall integrity. Thus, by contributing to PG homeostasis, the Cpx system lies at the crossroads between key processes of bacterial life, including cell shape, growth, division, and antibiotic resistance.
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44
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Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape. Proc Natl Acad Sci U S A 2015; 112:E3689-98. [PMID: 26130803 DOI: 10.1073/pnas.1504281112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria are surrounded by a peptidoglycan (PG) cell wall that must be remodeled to allow cell growth. While many structural details and properties of PG and the individual enzymes involved are known, how the process is coordinated to maintain cell integrity and rod shape is not understood. We have developed a coarse-grained method to simulate how individual transglycosylases, transpeptidases, and endopeptidases could introduce new material into an existing unilayer PG network. We find that a simple model with no enzyme coordination fails to maintain cell wall integrity and rod shape. We then iteratively analyze failure modes and explore different mechanistic hypotheses about how each problem might be overcome by the macromolecules involved. In contrast to a current theory, which posits that long MreB filaments are needed to coordinate PG insertion sites, we find that local coordination of enzyme activities in individual complexes can be sufficient to maintain cell integrity and rod shape. We also present possible molecular explanations for the existence of monofunctional transpeptidases and glycosidases (glycoside hydrolases), trimeric peptide crosslinks, cell twisting during growth, and synthesis of new strands in pairs.
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45
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Sundararajan K, Miguel A, Desmarais SM, Meier EL, Casey Huang K, Goley ED. The bacterial tubulin FtsZ requires its intrinsically disordered linker to direct robust cell wall construction. Nat Commun 2015; 6:7281. [PMID: 26099469 PMCID: PMC4532373 DOI: 10.1038/ncomms8281] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/26/2015] [Indexed: 12/17/2022] Open
Abstract
The bacterial GTPase FtsZ forms a cytokinetic ring at midcell, recruits the division machinery, and orchestrates membrane and peptidoglycan cell wall invagination. However, the mechanism for FtsZ regulation of peptidoglycan metabolism is unknown. The FtsZ GTPase domain is separated from its membrane-anchoring C-terminal conserved (CTC) peptide by a disordered C-terminal linker (CTL). Here, we investigate CTL function in Caulobacter crescentus. Strikingly, production of FtsZ lacking the CTL (ΔCTL) is lethal: cells become filamentous, form envelope bulges, and lyse, resembling treatment with β-lactam antibiotics. This phenotype is produced by FtsZ polymers bearing the CTC and a CTL shorter than 14 residues. Peptidoglycan synthesis still occurs downstream of ΔCTL, however cells expressing ΔCTL exhibit reduced peptidoglycan crosslinking and longer glycan strands than wildtype. Importantly, midcell proteins are still recruited to sites of ΔCTL assembly. We propose that FtsZ regulates peptidoglycan metabolism through a CTL-dependent mechanism that extends beyond simple protein recruitment.
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Affiliation(s)
- Kousik Sundararajan
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Amanda Miguel
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Samantha M Desmarais
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Elizabeth L Meier
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Kerwyn Casey Huang
- 1] Department of Bioengineering, Stanford University, Stanford, California 94305, USA [2] Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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46
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de Pedro MA, Cava F. Structural constraints and dynamics of bacterial cell wall architecture. Front Microbiol 2015; 6:449. [PMID: 26005443 PMCID: PMC4424881 DOI: 10.3389/fmicb.2015.00449] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/25/2015] [Indexed: 12/23/2022] Open
Abstract
The peptidoglycan wall (PG) is a unique structure which confers physical strength and defined shape to bacteria. It consists of a net-like macromolecule of peptide interlinked glycan chains overlying the cell membrane. The structure and layout of the PG dictates that the wall has to be continuously modified as bacteria go through division, morphological differentiation, and adaptive responses. The PG is poorly known in structural terms. However, to understand morphogenesis a precise knowledge of glycan strand arrangement and of local effects of the different kinds of subunits is essential. The scarcity of data led to a conception of the PG as a regular, highly ordered structure which strongly influenced growth models. Here, we review the structure of the PG to define a more realistic conceptual framework. We discuss the consequences of the plasticity of murein architecture in morphogenesis and try to define a set of minimal structural constraints that must be fulfilled by any model to be compatible with present day information.
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Affiliation(s)
- Miguel A de Pedro
- Centro de Biología Molecular "Severo Ochoa" - Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid Madrid, Spain ; Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Center for Microbial Research, Umeå University, Umeå Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Center for Microbial Research, Umeå University, Umeå Sweden
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47
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Pathria S, Rolando M, Lieman K, Hayes S, Hardies S, Serwer P. Islands of non-essential genes, including a DNA translocation operon, in the genome of bacteriophage 0305ϕ8-36. BACTERIOPHAGE 2014; 2:25-35. [PMID: 22666654 PMCID: PMC3357382 DOI: 10.4161/bact.19546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We investigate genes of lytic, Bacillus thuringiensis bacteriophage 0305ϕ8-36 that are non-essential for laboratory propagation, but might have a function in the wild. We isolate deletion mutants to identify these genes. The non-permutation of the genome (218.948 Kb, with a 6.479 Kb terminal repeat and 247 identified orfs) simplifies isolation of deletion mutants. We find two islands of non-essential genes. The first island (3.01% of the genomic DNA) has an informatically identified DNA translocation operon. Deletion causes no detectable growth defect during propagation in a dilute agarose overlay. Identification of the DNA translocation operon begins with a DNA relaxase and continues with a translocase and membrane-binding anchor proteins. The relaxase is in a family, first identified here, with homologs in other bacteriophages. The second deleted island (3.71% of the genome) has genes for two metallo-protein chaperonins and two tRNAs. Deletion causes a significant growth defect. In addition, (1) we find by "in situ" (in-plaque) single-particle fluorescence microscopy that adsorption to the host occurs at the tip of the 486 nm long tail, (2) we develop a procedure of 0305ϕ8-36 purification that does not cause tail contraction, and (3) we then find by electron microscopy that 0305ϕ8-36 undergoes tail tip-tail tip dimerization that potentially blocks adsorption to host cells, presumably with effectiveness that increases as the bacteriophage particle concentration increases. These observations provide an explanation of the previous observation that 0305ϕ8-36 does not lyse liquid cultures, even though 0305ϕ8-36 is genomically lytic.
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Affiliation(s)
- Saurav Pathria
- Department of Biochemistry; The University of Texas Health Science Center; San Antonio, TX USA
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48
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Harris LK, Dye NA, Theriot JA. A Caulobacter MreB mutant with irregular cell shape exhibits compensatory widening to maintain a preferred surface area to volume ratio. Mol Microbiol 2014; 94:10.1111/mmi.12811. [PMID: 25266768 PMCID: PMC4379118 DOI: 10.1111/mmi.12811] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2014] [Indexed: 11/30/2022]
Abstract
Rod-shaped bacteria typically elongate at a uniform width. To investigate the genetic and physiological determinants involved in this process, we studied a mutation in the morphogenetic protein MreB in Caulobacter crescentus that gives rise to cells with a variable-width phenotype, where cells have regions that are both thinner and wider than wild-type. During growth, individual cells develop a balance of wide and thin regions, and mutant MreB dynamically localizes to poles and thin regions. Surprisingly, the surface area to volume ratio of these irregularly shaped cells is, on average, very similar to wild-type. We propose that, while mutant MreB localizes to thin regions and promotes rod-like growth there, wide regions develop as a compensatory mechanism, allowing cells to maintain a wild-type-like surface area to volume ratio. To support this model, we have shown that cell widening is abrogated in growth conditions that promote higher surface area to volume ratios, and we have observed individual cells with high ratios return to wild-type levels over several hours by developing wide regions, suggesting that compensation can take place at the level of individual cells.
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Affiliation(s)
- Leigh K. Harris
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Natalie A. Dye
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Julie A. Theriot
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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49
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Billings G, Ouzounov N, Ursell T, Desmarais SM, Shaevitz J, Gitai Z, Huang KC. De novo morphogenesis in L-forms via geometric control of cell growth. Mol Microbiol 2014; 93:883-96. [PMID: 24995493 DOI: 10.1111/mmi.12703] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2014] [Indexed: 01/06/2023]
Abstract
In virtually all bacteria, the cell wall is crucial for mechanical integrity and for determining cell shape. Escherichia coli's rod-like shape is maintained via the spatiotemporal patterning of cell-wall synthesis by the actin homologue MreB. Here, we transiently inhibited cell-wall synthesis in E. coli to generate cell-wall-deficient, spherical L-forms, and found that they robustly reverted to a rod-like shape within several generations after inhibition cessation. The chemical composition of the cell wall remained essentially unchanged during this process, as indicated by liquid chromatography. Throughout reversion, MreB localized to inwardly curved regions of the cell, and fluorescent cell wall labelling revealed that MreB targets synthesis to those regions. When exposed to the MreB inhibitor A22, reverting cells regrew a cell wall but failed to recover a rod-like shape. Our results suggest that MreB provides the geometric measure that allows E. coli to actively establish and regulate its morphology.
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Affiliation(s)
- Gabriel Billings
- Department of Physics, Stanford University, Stanford, CA, 94305, USA
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50
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Hernández SB, Cava F, Pucciarelli MG, García-Del Portillo F, de Pedro MA, Casadesús J. Bile-induced peptidoglycan remodelling in Salmonella enterica. Environ Microbiol 2014; 17:1081-9. [PMID: 24762004 DOI: 10.1111/1462-2920.12491] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/11/2014] [Accepted: 04/20/2014] [Indexed: 02/02/2023]
Abstract
Changes in the peptidoglycan (PG) structure of Salmonella enterica are detected in the presence of a sublethal concentration of sodium deoxycholate (DOC): (i) lower proportions of Braun lipoprotein (Lpp)-bound muropeptides; (ii) reduced levels of muropeptides cross-linked by L(meso)-diaminopimelyl-D(meso)-diaminopimelic acid (L-D) peptide bridges (3-3 cross-links). Similar structural changes are found in S. enterica cultures adapted to grow in the presence of a lethal concentration of DOC, suggesting that reduced anchoring of Braun protein to PG and low occurrence of 3-3 cross-links may increase S. enterica resistance to bile. This view is further supported by additional observations: (i) A triple mutant lacking L,D-transpeptidases YbiS, ErfK, and YcfS, which does not contain Lpp anchored to PG, is hyper-resistant to bile; (ii) enhanced 3-3 cross-linking upon overexpression of YnhG transpeptidase causes a decrease in bile resistance. These observations suggest that remodelling of the cell wall may be added to the list of adaptive responses that permit survival of S. enterica in the presence of bile.
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Affiliation(s)
- Sara B Hernández
- Facultad de Biología, Departamento de Genética, Universidad de Sevilla, Apartado 1095, 41080, Sevilla, Spain
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