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Abstract
Bacteria have traditionally been studied as single-cell organisms. In laboratory settings, aerobic bacteria are usually cultured in aerated flasks, where the cells are considered essentially homogenous. However, in many natural environments, bacteria and other microorganisms grow in mixed communities, often associated with surfaces. Biofilms are comprised of surface-associated microorganisms, their extracellular matrix material, and environmental chemicals that have adsorbed to the bacteria or their matrix material. While this definition of a biofilm is fairly simple, biofilms are complex and dynamic. Our understanding of the activities of individual biofilm cells and whole biofilm systems has developed rapidly, due in part to advances in molecular, analytical, and imaging tools and the miniaturization of tools designed to characterize biofilms at the enzyme level, cellular level, and systems level.
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202
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Fura JM, Pidgeon SE, Birabaharan M, Pires MM. Dipeptide-Based Metabolic Labeling of Bacterial Cells for Endogenous Antibody Recruitment. ACS Infect Dis 2016; 2:302-309. [PMID: 27294199 PMCID: PMC4898660 DOI: 10.1021/acsinfecdis.6b00007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 02/06/2023]
Abstract
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The number of antibiotic-resistant
bacterial infections has increased
dramatically over the past decade. To combat these pathogens, novel
antimicrobial strategies must be explored and developed. We previously
reported a strategy based on hapten-modified cell wall analogues to
induce recruitment of endogenous antibodies to bacterial cell surfaces.
Cell surface remodeling using unnatural single d-amino acid
cell wall analogues led to modification at the C-terminus of the peptidoglycan
stem peptide. During peptidoglycan processing, installed hapten-displaying
amino acids can be subsequently removed by cell wall enzymes. Herein,
we disclose a two-step dipeptide peptidoglycan remodeling strategy
aimed at introducing haptens at an alternative site within the stem
peptide to improve retention and diminish removal by cell wall enzymes.
Through this redesigned strategy, we determined size constraints of
peptidoglycan remodeling and applied these constraints to attain hapten–linker
conjugates that produced high levels of antibody recruitment to bacterial
cell surfaces.
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Affiliation(s)
- Jonathan M. Fura
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Sean E. Pidgeon
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Morgan Birabaharan
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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203
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Emancipating Chlamydia: Advances in the Genetic Manipulation of a Recalcitrant Intracellular Pathogen. Microbiol Mol Biol Rev 2016; 80:411-27. [PMID: 27030552 DOI: 10.1128/mmbr.00071-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Chlamydia species infect millions of individuals worldwide and are important etiological agents of sexually transmitted disease, infertility, and blinding trachoma. Historically, the genetic intractability of this intracellular pathogen has hindered the molecular dissection of virulence factors contributing to its pathogenesis. The obligate intracellular life cycle of Chlamydia and restrictions on the use of antibiotics as selectable markers have impeded the development of molecular tools to genetically manipulate these pathogens. However, recent developments in the field have resulted in significant gains in our ability to alter the genome of Chlamydia, which will expedite the elucidation of virulence mechanisms. In this review, we discuss the challenges affecting the development of molecular genetic tools for Chlamydia and the work that laid the foundation for recent advancements in the genetic analysis of this recalcitrant pathogen.
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204
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Discovery of the Elusive UDP-Diacylglucosamine Hydrolase in the Lipid A Biosynthetic Pathway in Chlamydia trachomatis. mBio 2016; 7:e00090. [PMID: 27006461 PMCID: PMC4807358 DOI: 10.1128/mbio.00090-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Constitutive biosynthesis of lipid A via the Raetz pathway is essential for the viability and fitness of Gram-negative bacteria, including Chlamydia trachomatis. Although nearly all of the enzymes in the lipid A biosynthetic pathway are highly conserved across Gram-negative bacteria, the cleavage of the pyrophosphate group of UDP-2,3-diacyl-GlcN (UDP-DAGn) to form lipid X is carried out by two unrelated enzymes: LpxH in beta- and gammaproteobacteria and LpxI in alphaproteobacteria. The intracellular pathogen C. trachomatis lacks an ortholog for either of these two enzymes, and yet, it synthesizes lipid A and exhibits conservation of genes encoding other lipid A enzymes. Employing a complementation screen against a C. trachomatis genomic library using a conditional-lethal lpxH mutant Escherichia coli strain, we have identified an open reading frame (Ct461, renamed lpxG) encoding a previously uncharacterized enzyme that complements the UDP-DAGn hydrolase function in E. coli and catalyzes the conversion of UDP-DAGn to lipid X in vitro. LpxG shows little sequence similarity to either LpxH or LpxI, highlighting LpxG as the founding member of a third class of UDP-DAGn hydrolases. Overexpression of LpxG results in toxic accumulation of lipid X and profoundly reduces the infectivity of C. trachomatis, validating LpxG as the long-sought-after UDP-DAGn pyrophosphatase in this prominent human pathogen. The complementation approach presented here overcomes the lack of suitable genetic tools for C. trachomatis and should be broadly applicable for the functional characterization of other essential C. trachomatis genes. Chlamydia trachomatis is a leading cause of infectious blindness and sexually transmitted disease. Due to the lack of robust genetic tools, the functions of many Chlamydia genes remain uncharacterized, including the essential gene encoding the UDP-DAGn pyrophosphatase activity for the biosynthesis of lipid A, the membrane anchor of lipooligosaccharide and the predominant lipid species of the outer leaflet of the bacterial outer membrane. We designed a complementation screen against the C. trachomatis genomic library using a conditional-lethal mutant of E. coli and identified the missing essential gene in the lipid A biosynthetic pathway, which we designated lpxG. We show that LpxG is a member of the calcineurin-like phosphatases and displays robust UDP-DAGn pyrophosphatase activity in vitro. Overexpression of LpxG in C. trachomatis leads to the accumulation of the predicted lipid intermediate and reduces bacterial infectivity, validating the in vivo function of LpxG and highlighting the importance of regulated lipid A biosynthesis in C. trachomatis.
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205
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Synthesis and conformational behavior of metallacyclicdipeptides derived from coordination of side chain alkynylamino acids to tungsten. J Organomet Chem 2016. [DOI: 10.1016/j.jorganchem.2016.01.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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206
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Penicillin G-Induced Chlamydial Stress Response in a Porcine Strain of Chlamydia pecorum. Int J Microbiol 2016; 2016:3832917. [PMID: 26997956 PMCID: PMC4779511 DOI: 10.1155/2016/3832917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/26/2016] [Indexed: 01/14/2023] Open
Abstract
Chlamydia pecorum causes asymptomatic infection and pathology in ruminants, pigs, and koalas. We characterized the antichlamydial effect of the beta lactam penicillin G on Chlamydia pecorum strain 1710S (porcine abortion isolate). Penicillin-exposed and mock-exposed infected host cells showed equivalent inclusions numbers. Penicillin-exposed inclusions contained aberrant bacterial forms and exhibited reduced infectivity, while mock-exposed inclusions contained normal bacterial forms and exhibited robust infectivity. Infectious bacteria production increased upon discontinuation of penicillin exposure, compared to continued exposure. Chlamydia-induced cell death occurred in mock-exposed controls; cell survival was improved in penicillin-exposed infected groups. Similar results were obtained both in the presence and in the absence of the eukaryotic protein translation inhibitor cycloheximide and at different times of initiation of penicillin exposure. These data demonstrate that penicillin G induces the chlamydial stress response (persistence) and is not bactericidal, for this chlamydial species/strain in vitro, regardless of host cell de novo protein synthesis.
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207
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Glycosyltransferases and Transpeptidases/Penicillin-Binding Proteins: Valuable Targets for New Antibacterials. Antibiotics (Basel) 2016; 5:antibiotics5010012. [PMID: 27025527 PMCID: PMC4810414 DOI: 10.3390/antibiotics5010012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/27/2016] [Accepted: 02/03/2016] [Indexed: 12/29/2022] Open
Abstract
Peptidoglycan (PG) is an essential macromolecular sacculus surrounding most bacteria. It is assembled by the glycosyltransferase (GT) and transpeptidase (TP) activities of multimodular penicillin-binding proteins (PBPs) within multiprotein complex machineries. Both activities are essential for the synthesis of a functional stress-bearing PG shell. Although good progress has been made in terms of the functional and structural understanding of GT, finding a clinically useful antibiotic against them has been challenging until now. In contrast, the TP/PBP module has been successfully targeted by β-lactam derivatives, but the extensive use of these antibiotics has selected resistant bacterial strains that employ a wide variety of mechanisms to escape the lethal action of these antibiotics. In addition to traditional β-lactams, other classes of molecules (non-β-lactams) that inhibit PBPs are now emerging, opening new perspectives for tackling the resistance problem while taking advantage of these valuable targets, for which a wealth of structural and functional knowledge has been accumulated. The overall evidence shows that PBPs are part of multiprotein machineries whose activities are modulated by cofactors. Perturbation of these systems could lead to lethal effects. Developing screening strategies to take advantage of these mechanisms could lead to new inhibitors of PG assembly. In this paper, we present a general background on the GTs and TPs/PBPs, a survey of recent issues of bacterial resistance and a review of recent works describing new inhibitors of these enzymes.
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208
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Pidgeon SE, Pires MM. Metabolic remodeling of bacterial surfaces via tetrazine ligations. Chem Commun (Camb) 2016; 51:10330-3. [PMID: 26027845 DOI: 10.1039/c5cc01693b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Bioorthogonal click ligations are extensively used for the introduction of functional groups in biological systems. Tetrazine ligations are attractive in that they are catalyst-free and display favorable kinetics. We describe the efficient remodeling of bacterial cell surfaces using unnatural d-amino acids derivatized with tetrazine ligation handles. The metabolic incorporation of these unnatural d-amino acids onto bacterial cell surfaces resulted in a site-selective installation of fluorophores.
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Affiliation(s)
- S E Pidgeon
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, USA.
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209
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Quantitative Proteomics of the Infectious and Replicative Forms of Chlamydia trachomatis. PLoS One 2016; 11:e0149011. [PMID: 26871455 PMCID: PMC4752267 DOI: 10.1371/journal.pone.0149011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/26/2016] [Indexed: 12/24/2022] Open
Abstract
The obligate intracellular developmental cycle of Chlamydia trachomatis presents significant challenges in defining its proteome. In this study we have applied quantitative proteomics to both the intracellular reticulate body (RB) and the extracellular elementary body (EB) from C. trachomatis. We used C. trachomatis L2 as a model chlamydial isolate for our study since it has a high infectivity:particle ratio and there is an excellent quality genome sequence. EBs and RBs (>99% pure) were quantified by chromosomal and plasmid copy number using PCR, from which the concentrations of chlamydial proteins per bacterial cell/genome were determined. RBs harvested at 15h post infection (PI) were purified by three successive rounds of gradient centrifugation. This is the earliest possible time to obtain purified RBs, free from host cell components in quantity, within the constraints of the technology. EBs were purified at 48h PI. We then used two-dimensional reverse phase UPLC to fractionate RB or EB peptides before mass spectroscopic analysis, providing absolute amount estimates of chlamydial proteins. The ability to express the data as molecules per cell gave ranking in both abundance and energy requirements for synthesis, allowing meaningful identification of rate-limiting components. The study assigned 562 proteins with high confidence and provided absolute estimates of protein concentration for 489 proteins. Interestingly, the data showed an increase in TTS capacity at 15h PI. Most of the enzymes involved in peptidoglycan biosynthesis were detected along with high levels of muramidase (in EBs) suggesting breakdown of peptidoglycan occurs in the non-dividing form of the microorganism. All the genome-encoded enzymes for glycolysis, pentose phosphate pathway and tricarboxylic acid cycle were identified and quantified; these data supported the observation that the EB is metabolically active. The availability of detailed, accurate quantitative proteomic data will be invaluable for investigations into gene regulation and function.
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210
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Slade J, Hall JV, Kintner J, Schoborg RV. Chlamydial Pre-Infection Protects from Subsequent Herpes Simplex Virus-2 Challenge in a Murine Vaginal Super-Infection Model. PLoS One 2016; 11:e0146186. [PMID: 26726882 PMCID: PMC4699815 DOI: 10.1371/journal.pone.0146186] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/14/2015] [Indexed: 11/18/2022] Open
Abstract
Chlamydia trachomatis and Herpes Simplex Virus-2 (HSV-2) genital tract co-infections have been reported in humans and studied in vitro but the clinical consequences are unknown. Limited epidemiologic evidence suggests that these co-infections could be more severe than single infections of either pathogen, but the host-pathogen interactions during co-infection remain uncharacterized. To determine whether disease progression and/or pathogen shedding differs between singly-infected and super-infected animals, we developed an in vivo super-infection model in which female BALB/c mice were vaginally infected with Chlamydia muridarum (Cm) followed later by HSV-2. Pre-infection with Chlamydia 3 or 9 days prior to HSV-2 super-infection conferred significant protection from HSV-2-induced neurologic disease and significantly reduced viral recovery compared to HSV-2 singly-infected controls. Neither protection from mortality nor reduced viral recovery were observed when mice were i) super-infected with HSV-2 on day 27 post Cm; ii) infected with UV-irradiated Cm and super-infected with HSV-2; or iii) azithromycin-treated prior to HSV-2 super-infection. Therefore, protection from HSV-2-induced disease requires active infection with viable chlamydiae and is not observed after chlamydial shedding ceases, either naturally or due to antibiotic treatment. Thus, Chlamydia-induced protection is transient and requires the continued presence of chlamydiae or their components. These data demonstrate that chlamydial pre-infection can alter progression of subsequent HSV-2 infection, with implications for HSV-2 transmission from co-infected humans.
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Affiliation(s)
- Jessica Slade
- Department of Biomedical Sciences, Center for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, United States of America
| | - Jennifer V. Hall
- Department of Biomedical Sciences, Center for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, United States of America
| | - Jennifer Kintner
- Department of Biomedical Sciences, Center for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, United States of America
| | - Robert V. Schoborg
- Department of Biomedical Sciences, Center for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, United States of America
- * E-mail:
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211
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Hsu YP, Meng X, VanNieuwenhze M. Methods for visualization of peptidoglycan biosynthesis. METHODS IN MICROBIOLOGY 2016. [DOI: 10.1016/bs.mim.2016.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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212
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Abstract
The lifestyle of Chlamydiae is unique: the bacteria alternate between two morphologically distinct forms, an infectious non-replicative elementary body (EB), and a replicative, non-infectious reticulate body (RB). This review focuses on recent advances in understanding the structure and function of the infectious form of the best-studied member of the phylum, the human pathogen Chlamydia trachomatis. Once considered as an inert particle of little functional capacity, the EB is now perceived as a sophisticated entity that encounters at least three different environments during each infectious cycle. We review current knowledge on its composition and morphology, and emerging metabolic activities. These features confer resistance to the extracellular environment, the ability to penetrate a host cell and ultimately enable the EB to establish a niche enabling bacterial survival and growth. The bacterial and host molecules involved in these processes are beginning to emerge.
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213
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van Elsland DM, Bos E, de Boer W, Overkleeft HS, Koster AJ, van Kasteren SI. Detection of bioorthogonal groups by correlative light and electron microscopy allows imaging of degraded bacteria in phagocytes. Chem Sci 2016; 7:752-758. [PMID: 28791116 PMCID: PMC5529995 DOI: 10.1039/c5sc02905h] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/21/2015] [Indexed: 01/07/2023] Open
Abstract
The interaction between parasites and phagocytic immune cells is a key inter-species interaction in biology. Normally, phagocytosis results in the killing of invaders, but obligate intracellular parasites hijack the pathway to ensure their survival and replication. The in situ study of these parasites in the phagocytic pathway is very difficult, as genetic modification is often complicated and, if successful, only allows the tracking of pathogen phagocytosis up until the degradation of the engineered reporter constructs. Here we combine bioorthogonal chemistry with correlative light-electron microscopy (CLEM) to follow bacterial processing in the phagolysosomal system. Labelled bacteria are produced using bioorthogonal non-canonical amino tagging (BONCAT), precluding the need for any genetic modification. The bacterial proteome - even during degradation - was then visualised using a novel CLEM-based approach. This allowed us to obtain high resolution information about the subcellular location of the degrading bacteria, even after the proteolytic degradation of reporter constructs. To further explore the potential of CLEM-based imaging of bioorthogonal functionalities, azide-labelled glycans were imaged by this same approach, as well as active-subpopulations of enzymes using a 2-step activity-based protein profiling strategy.
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Affiliation(s)
- Daphne M van Elsland
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Erik Bos
- Department of Molecular Cell Biology , Section Electron Microscopy , Leiden University Medical Center , Leiden , The Netherlands .
| | - Wouter de Boer
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Herman S Overkleeft
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Abraham J Koster
- Department of Molecular Cell Biology , Section Electron Microscopy , Leiden University Medical Center , Leiden , The Netherlands .
| | - Sander I van Kasteren
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
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214
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Abstract
Nearly all bacteria contain a peptidoglycan cell wall. The peptidoglycan precursor molecule is LipidII, containing the basic peptidoglycan building block attached to a lipid. Although the suitability of LipidII as an antibacterial target has long been recognized, progress on elucidating the role(s) of LipidII in bacterial cell biology has been slow. The focus of this review is on exciting new developments, both with respect to antibacterials targeting LipidII as well as the emerging role of LipidII in organizing the membrane and cell wall synthesis. It appears that on both sides of the membrane, LipidII plays crucial roles in organizing cytoskeletal proteins and peptidoglycan synthesis machineries. Finally, the recent discovery of no less than three different categories of LipidII flippases will be discussed.
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Affiliation(s)
- Dirk-Jan Scheffers
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
- * E-mail:
| | - Menno B. Tol
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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215
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Structure of a bacterial type III secretion system in contact with a host membrane in situ. Nat Commun 2015; 6:10114. [PMID: 26656452 PMCID: PMC4682100 DOI: 10.1038/ncomms10114] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/03/2015] [Indexed: 12/16/2022] Open
Abstract
Many bacterial pathogens of animals and plants use a conserved type III secretion system (T3SS) to inject virulence effector proteins directly into eukaryotic cells to subvert host functions. Contact with host membranes is critical for T3SS activation, yet little is known about T3SS architecture in this state or the conformational changes that drive effector translocation. Here we use cryo-electron tomography and sub-tomogram averaging to derive the intact structure of the primordial Chlamydia trachomatis T3SS in the presence and absence of host membrane contact. Comparison of the averaged structures demonstrates a marked compaction of the basal body (4 nm) occurs when the needle tip contacts the host cell membrane. This compaction is coupled to a stabilization of the cytosolic sorting platform–ATPase. Our findings reveal the first structure of a bacterial T3SS from a major human pathogen engaged with a eukaryotic host, and reveal striking ‘pump-action' conformational changes that underpin effector injection. Bacterial type III secretion systems (T3SSs) inject virulence effector proteins into eukaryotic cells and are activated by host membrane contact. Here the authors report the in situ structure of the Chlamydia trachomatis T3SS in the presence or absence of host membrane, and observe compaction of the basal body embedded in the bacterial envelope.
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216
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Henrich E, Ma Y, Engels I, Münch D, Otten C, Schneider T, Henrichfreise B, Sahl HG, Dötsch V, Bernhard F. Lipid Requirements for the Enzymatic Activity of MraY Translocases and in Vitro Reconstitution of the Lipid II Synthesis Pathway. J Biol Chem 2015; 291:2535-46. [PMID: 26620564 DOI: 10.1074/jbc.m115.664292] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 12/19/2022] Open
Abstract
Screening of new compounds directed against key protein targets must continually keep pace with emerging antibiotic resistances. Although periplasmic enzymes of bacterial cell wall biosynthesis have been among the first drug targets, compounds directed against the membrane-integrated catalysts are hardly available. A promising future target is the integral membrane protein MraY catalyzing the first membrane associated step within the cytoplasmic pathway of bacterial peptidoglycan biosynthesis. However, the expression of most MraY homologues in cellular expression systems is challenging and limits biochemical analysis. We report the efficient production of MraY homologues from various human pathogens by synthetic cell-free expression approaches and their subsequent characterization. MraY homologues originating from Bordetella pertussis, Helicobacter pylori, Chlamydia pneumoniae, Borrelia burgdorferi, and Escherichia coli as well as Bacillus subtilis were co-translationally solubilized using either detergent micelles or preformed nanodiscs assembled with defined membranes. All MraY enzymes originating from Gram-negative bacteria were sensitive to detergents and required nanodiscs containing negatively charged lipids for obtaining a stable and functionally folded conformation. In contrast, the Gram-positive B. subtilis MraY not only tolerates detergent but is also less specific for its lipid environment. The MraY·nanodisc complexes were able to reconstitute a complete in vitro lipid I and lipid II forming pipeline in combination with the cell-free expressed soluble enzymes MurA-F and with the membrane-associated protein MurG. As a proof of principle for future screening platforms, we demonstrate the inhibition of the in vitro lipid II biosynthesis with the specific inhibitors fosfomycin, feglymycin, and tunicamycin.
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Affiliation(s)
- Erik Henrich
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany
| | - Yi Ma
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany, the School of Bioscience and Bioengineering, South China University of Technology, 510006 Guangzhou, China,
| | - Ina Engels
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and the German Centre for Infection Research (DZIF), partner site Cologne-Bonn, 53115 Bonn, Germany
| | - Daniela Münch
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and
| | - Christian Otten
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and
| | - Tanja Schneider
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and the German Centre for Infection Research (DZIF), partner site Cologne-Bonn, 53115 Bonn, Germany
| | - Beate Henrichfreise
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and
| | - Hans-Georg Sahl
- the Institute for Pharmaceutical Microbiology, University of Bonn, Germany, and the German Centre for Infection Research (DZIF), partner site Cologne-Bonn, 53115 Bonn, Germany
| | - Volker Dötsch
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany
| | - Frank Bernhard
- From the Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J. W. Goethe-University, 60438 Frankfurt-am-Main, Germany,
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217
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Fura JM, Kearns D, Pires MM. D-Amino Acid Probes for Penicillin Binding Protein-based Bacterial Surface Labeling. J Biol Chem 2015; 290:30540-50. [PMID: 26499795 DOI: 10.1074/jbc.m115.683342] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 02/02/2023] Open
Abstract
Peptidoglycan is an essential and highly conserved mesh structure that surrounds bacterial cells. It plays a critical role in retaining a defined cell shape, and, in the case of pathogenic Gram-positive bacteria, it lies at the interface between bacterial cells and the host organism. Intriguingly, bacteria can metabolically incorporate unnatural D-amino acids into the peptidoglycan stem peptide directly from the surrounding medium, a process mediated by penicillin binding proteins (PBPs). Metabolic peptidoglycan remodeling via unnatural D-amino acids has provided unique insights into peptidoglycan biosynthesis of live bacteria and has also served as the basis of a synthetic immunology strategy with potential therapeutic implications. A striking feature of this process is the vast promiscuity displayed by PBPs in tolerating entirely unnatural side chains. However, the chemical space and physical features of this side chain promiscuity have not been determined systematically. In this report, we designed and synthesized a library of variants displaying diverse side chains to comprehensively establish the tolerability of unnatural D-amino acids by PBPs in both Gram-positive and Gram-negative organisms. In addition, nine Bacillus subtilis PBP-null mutants were evaluated with the goal of identifying a potential primary PBP responsible for unnatural D-amino acid incorporation and gaining insights into the temporal control of PBP activity. We empirically established the scope of physical parameters that govern the metabolic incorporation of unnatural D-amino acids into bacterial peptidoglycan.
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Affiliation(s)
- Jonathan M Fura
- From the Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania and
| | - Daniel Kearns
- the Department of Biology, Indiana University, Bloomington, Indiana
| | - Marcos M Pires
- From the Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania and
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218
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Jacquier N, Frandi A, Viollier PH, Greub G. Disassembly of a Medial Transenvelope Structure by Antibiotics during Intracellular Division. ACTA ACUST UNITED AC 2015; 22:1217-27. [PMID: 26364930 DOI: 10.1016/j.chembiol.2015.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 07/28/2015] [Accepted: 08/01/2015] [Indexed: 10/23/2022]
Abstract
Chlamydiales possess a minimal but functional peptidoglycan precursor biosynthetic and remodeling pathway involved in the assembly of the division septum by an atypical cytokinetic machine and cryptic or modified peptidoglycan-like structure (PGLS). How this reduced cytokinetic machine collectively coordinates the invagination of the envelope has not yet been explored in Chlamydiales. In other Gram-negative bacteria, peptidoglycan provides anchor points that connect the outer membrane to the peptidoglycan during constriction using the Pal-Tol complex. Purifying PGLS and associated proteins from the chlamydial pathogen Waddlia chondrophila, we unearthed the Pal protein as a peptidoglycan-binding protein that localizes to the chlamydial division septum along with other components of the Pal-Tol complex. Together, our PGLS characterization and peptidoglycan-binding assays support the notion that diaminopimelic acid is an important determinant recruiting Pal to the division plane to coordinate the invagination of all envelope layers with the conserved Pal-Tol complex, even during osmotically protected intracellular growth.
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Affiliation(s)
- Nicolas Jacquier
- Department of Laboratories, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne 1011, Switzerland
| | - Antonio Frandi
- Department of Microbiology & Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Geneva 1211, Switzerland
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Geneva 1211, Switzerland.
| | - Gilbert Greub
- Department of Laboratories, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne 1011, Switzerland.
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219
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Gale RT, Brown ED. New chemical tools to probe cell wall biosynthesis in bacteria. Curr Opin Microbiol 2015; 27:69-77. [PMID: 26291270 DOI: 10.1016/j.mib.2015.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/23/2015] [Accepted: 07/30/2015] [Indexed: 12/25/2022]
Abstract
Some of the most successful drugs in the antibiotic pharmacopeia are those that inhibit bacterial cell wall biosynthesis. However, the worldwide spread of bacterial antibiotic resistance has eroded the clinical efficacy of these drugs and the antibiotic pipeline continues to be lean as drug discovery programs struggle to bring new agents to the clinic. Nevertheless, cell wall biogenesis remains a high interest and celebrated target. Recent advances in the preparation of chemical probes and biosynthetic intermediates provide the tools necessary to better understand cell wall assembly. Likewise, these tools offer new opportunities to identify and evaluate novel biosynthetic inhibitors. This review aims to highlight these advancements and to provide context for their utility as innovative new tools to study cell wall biogenesis and for antibacterial drug discovery.
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Affiliation(s)
- Robert T Gale
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Eric D Brown
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5.
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220
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Structural characterization of muropeptides from Chlamydia trachomatis peptidoglycan by mass spectrometry resolves "chlamydial anomaly". Proc Natl Acad Sci U S A 2015; 112:11660-5. [PMID: 26290580 DOI: 10.1073/pnas.1514026112] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The "chlamydial anomaly," first coined by James Moulder, describes the inability of researchers to detect or purify peptidoglycan (PG) from pathogenic Chlamydiae despite genetic and biochemical evidence and antibiotic susceptibility data that suggest its existence. We recently detected PG in Chlamydia trachomatis by a new metabolic cell wall labeling method, however efforts to purify PG from pathogenic Chlamydiae have remained unsuccessful. Pathogenic chlamydial species are known to activate nucleotide-binding oligomerization domain-containing protein 2 (NOD2) innate immune receptors by as yet uncharacterized ligands, which are presumed to be PG fragments (muramyl di- and tripeptides). We used the NOD2-dependent activation of NF-κB by C. trachomatis-infected cell lysates as a biomarker for the presence of PG fragments within specific lysate fractions. We designed a new method of muropeptide isolation consisting of a double filtration step coupled with reverse-phase HPLC fractionation of Chlamydia-infected HeLa cell lysates. Fractions that displayed NOD2 activity were analyzed by electrospray ionization mass spectrometry, confirming the presence of muramyl di- and tripeptides in Chlamydia-infected cell lysate fractions. Moreover, the mass spectrometry data of large muropeptide fragments provided evidence that transpeptidation and transglycosylation reactions occur in pathogenic Chlamydiae. These results reveal the composition of chlamydial PG and disprove the "glycanless peptidoglycan" hypothesis.
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221
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Tian Y, Yu M, Li Z, Han J, Yang L, Han S. Optical Tracking of Phagocytosis with an Activatable Profluorophore Metabolically Incorporated into Bacterial Peptidoglycan. Anal Chem 2015. [DOI: 10.1021/acs.analchem.5b01633] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yunpeng Tian
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network and ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Mingzu Yu
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network and ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Zhu Li
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network and ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Jiahuai Han
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network and ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Liu Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network and ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005, China
| | - Shoufa Han
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, State Key Laboratory for Physical Chemistry of Solid Surfaces, the Key Laboratory for Chemical Biology of Fujian Province, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, and Innovation Center for Cell Signaling Network and ‡State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005, China
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222
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Fura JM, Pires MM. d-amino carboxamide-based recruitment of dinitrophenol antibodies to bacterial surfaces via peptidoglycan remodeling. Biopolymers 2015; 104:351-9. [DOI: 10.1002/bip.22618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/12/2015] [Accepted: 01/14/2015] [Indexed: 12/13/2022]
Affiliation(s)
| | - Marcos M. Pires
- Department of Chemistry; Lehigh University; Bethlehem PA 18015
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223
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Chlamydia trachomatis In Vivo to In Vitro Transition Reveals Mechanisms of Phase Variation and Down-Regulation of Virulence Factors. PLoS One 2015. [PMID: 26207372 PMCID: PMC4514472 DOI: 10.1371/journal.pone.0133420] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Research on the obligate intracellular bacterium Chlamydia trachomatis demands culture in cell-lines, but the adaptive process behind the in vivo to in vitro transition is not understood. We assessed the genomic and transcriptomic dynamics underlying C. trachomatis in vitro adaptation of strains representing the three disease groups (ocular, epithelial-genital and lymphogranuloma venereum) propagated in epithelial cells over multiple passages. We found genetic features potentially underlying phase variation mechanisms mediating the regulation of a lipid A biosynthesis enzyme (CT533/LpxC), and the functionality of the cytotoxin (CT166) through an ON/OFF mechanism. We detected inactivating mutations in CT713/porB, a scenario suggesting metabolic adaptation to the available carbon source. CT135 was inactivated in a tropism-specific manner, with CT135-negative clones emerging for all epithelial-genital populations (but not for LGV and ocular populations) and rapidly increasing in frequency (~23% mutants per 10 passages). RNA-sequencing analyses revealed that a deletion event involving CT135 impacted the expression of multiple virulence factors, namely effectors known to play a role in the C. trachomatis host-cell invasion or subversion (e.g., CT456/Tarp, CT694, CT875/TepP and CT868/ChlaDub1). This reflects a scenario of attenuation of C. trachomatis virulence in vitro, which may take place independently or in a cumulative fashion with the also observed down-regulation of plasmid-related virulence factors. This issue may be relevant on behalf of the recent advances in Chlamydia mutagenesis and transformation where culture propagation for selecting mutants/transformants is mandatory. Finally, there was an increase in the growth rate for all strains, reflecting gradual fitness enhancement over time. In general, these data shed light on the adaptive process underlying the C. trachomatis in vivo to in vitro transition, and indicates that it would be prudent to restrict culture propagation to minimal passages and check the status of the CT135 genotype in order to avoid the selection of CT135-negative mutants, likely originating less virulent strains.
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224
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Randich AM, Brun YV. Molecular mechanisms for the evolution of bacterial morphologies and growth modes. Front Microbiol 2015; 6:580. [PMID: 26106381 PMCID: PMC4460556 DOI: 10.3389/fmicb.2015.00580] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/26/2015] [Indexed: 12/13/2022] Open
Abstract
Bacteria exhibit a rich diversity of morphologies. Within this diversity, there is a uniformity of shape for each species that is replicated faithfully each generation, suggesting that bacterial shape is as selectable as any other biochemical adaptation. We describe the spatiotemporal mechanisms that target peptidoglycan synthesis to different subcellular zones to generate the rod-shape of model organisms Escherichia coli and Bacillus subtilis. We then demonstrate, using the related genera Caulobacter and Asticcacaulis as examples, how the modularity of the core components of the peptidoglycan synthesis machinery permits repositioning of the machinery to achieve different growth modes and morphologies. Finally, we highlight cases in which the mechanisms that underlie morphological evolution are beginning to be understood, and how they depend upon the expansion and diversification of the core components of the peptidoglycan synthesis machinery.
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Affiliation(s)
- Amelia M Randich
- Department of Biology, Indiana University , Bloomington, IN, USA
| | - Yves V Brun
- Department of Biology, Indiana University , Bloomington, IN, USA
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225
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Kamneva OK, Poudel S, Ward NL. Proteins Related to the Type I Secretion System Are Associated with Secondary SecA_DEAD Domain Proteins in Some Species of Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi. PLoS One 2015; 10:e0129066. [PMID: 26030905 PMCID: PMC4452313 DOI: 10.1371/journal.pone.0129066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 05/04/2015] [Indexed: 01/09/2023] Open
Abstract
A number of bacteria belonging to the PVC (Planctomycetes-Verrucomicrobia-Chlamydiae) super-phylum contain unusual ribosome-bearing intracellular membranes. The evolutionary origins and functions of these membranes are unknown. Some proteins putatively associated with the presence of intracellular membranes in PVC bacteria contain signal peptides. Signal peptides mark proteins for translocation across the cytoplasmic membrane in prokaryotes, and the membrane of the endoplasmic reticulum in eukaryotes, by highly conserved Sec machinery. This suggests that proteins might be targeted to intracellular membranes in PVC bacteria via the Sec pathway. Here, we show that canonical signal peptides are significantly over-represented in proteins preferentially present in PVC bacteria possessing intracellular membranes, indicating involvement of Sec translocase in their cellular targeting. We also characterized Sec proteins using comparative genomics approaches, focusing on the PVC super-phylum. While we were unable to detect unique changes in Sec proteins conserved among membrane-bearing PVC species, we identified (1) SecA ATPase domain re-arrangements in some Planctomycetes, and (2) secondary SecA_DEAD domain proteins in the genomes of some Planctomycetes, Verrucomicrobia, Proteobacteria, Nitrospirae and Chlorobi. This is the first report of potentially duplicated SecA in Gram-negative bacteria. The phylogenetic distribution of secondary SecA_DEAD domain proteins suggests that the presence of these proteins is not related to the occurrence of PVC endomembranes. Further genomic analysis showed that secondary SecA_DEAD domain proteins are located within genomic neighborhoods that also encode three proteins possessing domains specific for the Type I secretion system.
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Affiliation(s)
- Olga K. Kamneva
- Department of Biology, Stanford University, Stanford, CA, 94305–5020, United States of America
| | - Saroj Poudel
- Computer Science Department, Montana State University, Bozeman, MT, 59717, United States of America
| | - Naomi L. Ward
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, United States of America
- Department of Botany, University of Wyoming, Laramie, WY, 82071, United States of America
- Program in Ecology, University of Wyoming, Laramie, WY, 82071, United States of America
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226
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Jeske O, Schüler M, Schumann P, Schneider A, Boedeker C, Jogler M, Bollschweiler D, Rohde M, Mayer C, Engelhardt H, Spring S, Jogler C. Planctomycetes do possess a peptidoglycan cell wall. Nat Commun 2015; 6:7116. [PMID: 25964217 PMCID: PMC4432640 DOI: 10.1038/ncomms8116] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/07/2015] [Indexed: 11/28/2022] Open
Abstract
Most bacteria contain a peptidoglycan (PG) cell wall, which is critical for
maintenance of shape and important for cell division. In contrast, Planctomycetes
have been proposed to produce a proteinaceous cell wall devoid of PG. The apparent
absence of PG has been used as an argument for the putative planctomycetal ancestry
of all bacterial lineages. Here we show, employing multiple bioinformatic methods,
that planctomycetal genomes encode proteins required for PG synthesis. Furthermore,
we biochemically demonstrate the presence of the sugar and the peptide components of
PG in Planctomycetes. In addition, light and electron microscopic experiments reveal
planctomycetal PG sacculi that are susceptible to lysozyme treatment. Finally,
cryo-electron tomography demonstrates that Planctomycetes possess a typical PG cell
wall and that their cellular architecture is thus more similar to that of other
Gram-negative bacteria. Our findings shed new light on the cellular architecture and
cell division of the maverick Planctomycetes. Planctomycetes appear to differ from all other bacteria in their
cellular organization and their apparent lack of a peptidoglycan (PG) cell wall. Here
Jeske et al. show that Planctomycetes do possess a typical PG cell wall and that
their cellular architecture resembles that of Gram-negative bacteria.
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Affiliation(s)
- Olga Jeske
- Independent Junior Research Group Microbial Cell Biology and Genetics, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
| | - Margarete Schüler
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Peter Schumann
- Department of Microbiology, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
| | - Alexander Schneider
- Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Christian Boedeker
- Independent Junior Research Group Microbial Cell Biology and Genetics, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
| | - Mareike Jogler
- Independent Junior Research Group Microbial Cell Biology and Genetics, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
| | - Daniel Bollschweiler
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Manfred Rohde
- Research Group Molecular Mechanisms of Streptococci, Helmholtz Center for Infection Research GmbH, Inhoffenstraße 7, Braunschweig 38124, Germany
| | - Christoph Mayer
- Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Harald Engelhardt
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Stefan Spring
- Department of Microbiology, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
| | - Christian Jogler
- Independent Junior Research Group Microbial Cell Biology and Genetics, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
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227
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van Teeseling MCF, Mesman RJ, Kuru E, Espaillat A, Cava F, Brun YV, VanNieuwenhze MS, Kartal B, van Niftrik L. Anammox Planctomycetes have a peptidoglycan cell wall. Nat Commun 2015; 6:6878. [PMID: 25962786 PMCID: PMC4432595 DOI: 10.1038/ncomms7878] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/09/2015] [Indexed: 12/11/2022] Open
Abstract
Planctomycetes are intriguing microorganisms that apparently lack peptidoglycan, a structure that controls the shape and integrity of almost all bacterial cells. Therefore, the planctomycetal cell envelope is considered exceptional and their cell plan uniquely compartmentalized. Anaerobic ammonium-oxidizing (anammox) Planctomycetes play a key role in the global nitrogen cycle by releasing fixed nitrogen back to the atmosphere as N2. Here using a complementary array of state-of-the-art techniques including continuous culturing, cryo-transmission electron microscopy, peptidoglycan-specific probes and muropeptide analysis, we show that the anammox bacterium Kuenenia stuttgartiensis contains peptidoglycan. On the basis of the thickness, composition and location of peptidoglycan in K. stuttgartiensis, we propose to redefine Planctomycetes as Gram-negative bacteria. Our results demonstrate that Planctomycetes are not an exception to the universal presence of peptidoglycan in bacteria. Planctomycetes are unusual bacteria with complex intracellular compartments and an apparent lack of peptidoglycan in their cell walls. Here, van Teeseling et al. show that the cell wall of an anammox planctomycete does contain peptidoglycan, and propose to redefine planctomycetes as Gram-negative bacteria.
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Affiliation(s)
- Muriel C F van Teeseling
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Rob J Mesman
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Erkin Kuru
- Interdisciplinary Biochemistry Program, Indiana University, Bloomington, Indiana 47405, USA
| | - Akbar Espaillat
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå SE-90187, Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Umeå University, Umeå SE-90187, Sweden
| | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | | | - Boran Kartal
- 1] Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen 6525AJ, The Netherlands [2] Department of Biochemistry and Microbiology, Laboratory of Microbiology, Gent University, Gent 9000, Belgium
| | - Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen 6525AJ, The Netherlands
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228
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Wolff BJ, Morrison SS, Pesti D, Ganakammal SR, Srinivasamoorthy G, Changayil S, Weil MR, MacCannell D, Rowe L, Frace M, Ritchie BW, Dean D, Winchell JM. Chlamydia psittaci comparative genomics reveals intraspecies variations in the putative outer membrane and type III secretion system genes. MICROBIOLOGY-SGM 2015; 161:1378-91. [PMID: 25887617 PMCID: PMC4635502 DOI: 10.1099/mic.0.000097] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Chlamydia psittaci is an obligate intracellular bacterium that can cause significant disease among a broad range of hosts. In humans, this organism may cause psittacosis, a respiratory disease that can spread to involve multiple organs, and in rare untreated cases may be fatal. There are ten known genotypes based on sequencing the major outer-membrane protein gene, ompA, of C. psittaci. Each genotype has overlapping host preferences and virulence characteristics. Recent studies have compared C. psittaci among other members of the Chlamydiaceae family and showed that this species frequently switches hosts and has undergone multiple genomic rearrangements. In this study, we sequenced five genomes of C. psittaci strains representing four genotypes, A, B, D and E. Due to the known association of the type III secretion system (T3SS) and polymorphic outer-membrane proteins (Pmps) with host tropism and virulence potential, we performed a comparative analysis of these elements among these five strains along with a representative genome from each of the remaining six genotypes previously sequenced. We found significant genetic variation in the Pmps and tbl3SS genes that may partially explain differences noted in C. psittaci host infection and disease.
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Affiliation(s)
- Bernard J Wolff
- 1Infectious Diseases Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA 2Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shatavia S Morrison
- 2Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Denise Pesti
- 1Infectious Diseases Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Satishkumar Ranganathan Ganakammal
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ganesh Srinivasamoorthy
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shankar Changayil
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - M Ryan Weil
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Duncan MacCannell
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lori Rowe
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael Frace
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Branson W Ritchie
- 1Infectious Diseases Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Deborah Dean
- 4Children's Hospital Oakland Research Institute, Oakland, CA 5UCSF and UC Berkeley Joint Graduate Program in Bioengineering, Oakland, CA
| | - Jonas M Winchell
- 2Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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229
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Otten C, De Benedetti S, Gaballah A, Bühl H, Klöckner A, Brauner J, Sahl HG, Henrichfreise B. Co-solvents as stabilizing agents during heterologous overexpression in Escherichia coli - application to chlamydial penicillin-binding protein 6. PLoS One 2015; 10:e0122110. [PMID: 25849314 PMCID: PMC4388811 DOI: 10.1371/journal.pone.0122110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/17/2015] [Indexed: 01/29/2023] Open
Abstract
Heterologous overexpression of foreign proteins in Escherichia coli often leads to insoluble aggregates of misfolded inactive proteins, so-called inclusion bodies. To solve this problem use of chaperones or in vitro refolding procedures are the means of choice. These methods are time consuming and cost intensive, due to additional purification steps to get rid of the chaperons or the process of refolding itself. We describe an easy to use lab-scale method to avoid formation of inclusion bodies. The method systematically combines use of co-solvents, usually applied for in vitro stabilization of biologicals in biopharmaceutical formulation, and periplasmic expression and can be completed in one week using standard equipment in any life science laboratory. Demonstrating the unique power of our method, we overproduced and purified for the first time an active chlamydial penicillin-binding protein, demonstrated its function as penicillin sensitive DD-carboxypeptidase and took a major leap towards understanding the "chlamydial anomaly."
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Affiliation(s)
- Christian Otten
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
- * E-mail: (BH); (CO)
| | | | - Ahmed Gaballah
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Henrike Bühl
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Anna Klöckner
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Jarryd Brauner
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Hans-Georg Sahl
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Beate Henrichfreise
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
- * E-mail: (BH); (CO)
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230
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Jacquier N, Viollier PH, Greub G. The role of peptidoglycan in chlamydial cell division: towards resolving the chlamydial anomaly. FEMS Microbiol Rev 2015; 39:262-75. [PMID: 25670734 DOI: 10.1093/femsre/fuv001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Chlamydiales are obligate intracellular bacteria including some important pathogens causing trachoma, genital tract infections and pneumonia, among others. They share an atypical division mechanism, which is independent of an FtsZ homologue. However, they divide by binary fission, in a process inhibited by penicillin derivatives, causing the formation of an aberrant form of the bacteria, which is able to survive in the presence of the antibiotic. The paradox of penicillin sensitivity of chlamydial cells in the absence of detectable peptidoglycan (PG) was dubbed the chlamydial anomaly, since no PG modified by enzymes (Pbps) that are the usual target of penicillin could be detected in Chlamydiales. We review here the recent advances in this field with the first direct and indirect evidences of PG-like material in both Chlamydiaceae and Chlamydia-related bacteria. Moreover, PG biosynthesis is required for proper localization of the newly described septal proteins RodZ and NlpD. Taken together, these new results set the stage for a better understanding of the role of PG and septal proteins in the division mechanism of Chlamydiales and illuminate the long-standing chlamydial anomaly. Moreover, understanding the chlamydial division mechanism is critical for the development of new antibiotics for the treatment of chlamydial chronic infections.
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Affiliation(s)
- Nicolas Jacquier
- Institute of Microbiology, University Hospital Center and University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Patrick H Viollier
- Department of Microbiology & Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine / CMU, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, CH-1011 Lausanne, Switzerland
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231
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Jiang C, Caccamo PD, Brun YV. Mechanisms of bacterial morphogenesis: evolutionary cell biology approaches provide new insights. Bioessays 2015; 37:413-25. [PMID: 25664446 DOI: 10.1002/bies.201400098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
How Darwin's "endless forms most beautiful" have evolved remains one of the most exciting questions in biology. The significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. While our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity are largely unknown. The emerging field of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. This relatively novel approach provides hypotheses and insights into cell biological mechanisms, such as morphogenesis, and their evolution that would have been difficult to obtain by studying only model organisms. We discuss the necessary steps, challenges, and impact of integrating "evolutionary thinking" into bacterial cell biology in the genomic era.
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Affiliation(s)
- Chao Jiang
- Department of Biology, Indiana University, Bloomington, IN, USA
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232
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Siegrist MS, Swarts BM, Fox DM, Lim SA, Bertozzi CR. Illumination of growth, division and secretion by metabolic labeling of the bacterial cell surface. FEMS Microbiol Rev 2015; 39:184-202. [PMID: 25725012 DOI: 10.1093/femsre/fuu012] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The cell surface is the essential interface between a bacterium and its surroundings. Composed primarily of molecules that are not directly genetically encoded, this highly dynamic structure accommodates the basic cellular processes of growth and division as well as the transport of molecules between the cytoplasm and the extracellular milieu. In this review, we describe aspects of bacterial growth, division and secretion that have recently been uncovered by metabolic labeling of the cell envelope. Metabolite derivatives can be used to label a variety of macromolecules, from proteins to non-genetically-encoded glycans and lipids. The embedded metabolite enables precise tracking in time and space, and the versatility of newer chemoselective detection methods offers the ability to execute multiple experiments concurrently. In addition to reviewing the discoveries enabled by metabolic labeling of the bacterial cell envelope, we also discuss the potential of these techniques for translational applications. Finally, we offer some guidelines for implementing this emerging technology.
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Affiliation(s)
- M Sloan Siegrist
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Benjamin M Swarts
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Douglas M Fox
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Shion An Lim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, University of California, Berkeley, CA 94720, USA Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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233
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Kuru E, Tekkam S, Hall E, Brun YV, VanNieuwenhze MS. Synthesis of fluorescent D-amino acids and their use for probing peptidoglycan synthesis and bacterial growth in situ. Nat Protoc 2015; 10:33-52. [PMID: 25474031 PMCID: PMC4300143 DOI: 10.1038/nprot.2014.197] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fluorescent D-amino acids (FDAAs) are efficiently incorporated into the peptidoglycans (PGs) of diverse bacterial species at the sites of PG biosynthesis, allowing specific and covalent probing of bacterial growth with minimal perturbation. Here we provide a protocol for the synthesis of four FDAAs emitting light in blue (HCC-amino-D-alanine, HADA), green (NBD-amino-D-alanine, NADA, and fluorescein-D-lysine, FDL) or red (TAMRA-D-lysine, TDL) and for their use in PG labeling of live bacteria. Our modular synthesis protocol gives easy access to a library of different FDAAs made with commercially available fluorophores and diamino acid starting materials. Molecules can be synthesized in a typical chemistry laboratory in 2-3 d using standard chemical transformations. The simple labeling procedure involves the addition of the FDAAs to a bacterial sample for the desired labeling duration and stopping further label incorporation by fixing the cells with cold 70% (vol/vol) ethanol or by washing away excess dye. We discuss several scenarios for the use of these labels in fluorescence microscopy applications, including short or long labeling durations, and the combination of different labels in pure culture (e.g., for 'virtual time-lapse' microscopy) or in situ labeling of complex environmental samples. Depending on the experiment, FDAA labeling can take as little as 30 s for a rapidly growing species such as Escherichia coli.
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Affiliation(s)
- Erkin Kuru
- Indiana University, Bloomington, IN 47405
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234
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Kemege KE, Hickey JM, Barta ML, Wickstrum J, Balwalli N, Lovell S, Battaile KP, Hefty PS. Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB. Mol Microbiol 2014; 95:365-82. [PMID: 25382739 DOI: 10.1111/mmi.12855] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2014] [Indexed: 11/28/2022]
Abstract
Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non-canonical mechanisms may be employed. The rod-shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies herein expand on those observations through protein structure, mutagenesis and cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient Escherichia coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia.
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Affiliation(s)
- Kyle E Kemege
- Department of Molecular Biosciences, University of Kansas, Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
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235
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Ojkic N, López-Garrido J, Pogliano K, Endres RG. Bistable forespore engulfment in Bacillus subtilis by a zipper mechanism in absence of the cell wall. PLoS Comput Biol 2014; 10:e1003912. [PMID: 25356555 PMCID: PMC4214620 DOI: 10.1371/journal.pcbi.1003912] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/16/2014] [Indexed: 12/22/2022] Open
Abstract
To survive starvation, the bacterium Bacillus subtilis forms durable spores. The initial step of sporulation is asymmetric cell division, leading to a large mother-cell and a small forespore compartment. After division is completed and the dividing septum is thinned, the mother cell engulfs the forespore in a slow process based on cell-wall degradation and synthesis. However, recently a new cell-wall independent mechanism was shown to significantly contribute, which can even lead to fast engulfment in 60 of the cases when the cell wall is completely removed. In this backup mechanism, strong ligand-receptor binding between mother-cell protein SpoIIIAH and forespore-protein SpoIIQ leads to zipper-like engulfment, but quantitative understanding is missing. In our work, we combined fluorescence image analysis and stochastic Langevin simulations of the fluctuating membrane to investigate the origin of fast bistable engulfment in absence of the cell wall. Our cell morphologies compare favorably with experimental time-lapse microscopy, with engulfment sensitive to the number of SpoIIQ-SpoIIIAH bonds in a threshold-like manner. By systematic exploration of model parameters, we predict regions of osmotic pressure and membrane-surface tension that produce successful engulfment. Indeed, decreasing the medium osmolarity in experiments prevents engulfment in line with our predictions. Forespore engulfment may thus not only be an ideal model system to study decision-making in single cells, but its biophysical principles are likely applicable to engulfment in other cell types, e.g. during phagocytosis in eukaryotes. When the bacterium B. subtilis runs out of food, it undergoes a fundamental development process by which it forms durable spores. Sporulation is initiated by asymmetric cell division after which the larger mother cell engulfs the smaller forespore, followed by spore maturation and release. This survival strategy is so robust that engulfment even proceeds when cells are deprived of their protective cell wall. Under these severe perturbations, 60 of the mother cells still engulf their forespores in only 10 of the normal engulfment time, while the remaining 40 of mother cells withdraw from engulfment. This all-or-none outcome of engulfment suggests decision-making, which was recently also identified in other types of engulfment, e.g. during phagocytosis when immune cells engulf and destroy pathogens. Here, we developed a biophysical model to explain fast bistable forespore engulfment in absence of the cell wall and energy sources. Our discovered principles may prove very general, thus predicting key ingredients of successful engulfment across all kingdoms of life.
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Affiliation(s)
- Nikola Ojkic
- Department of Life Sciences, Imperial College, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom
- * E-mail:
| | - Javier López-Garrido
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Robert G. Endres
- Department of Life Sciences, Imperial College, London, United Kingdom
- Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, United Kingdom
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236
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Aistleitner K, Anrather D, Schott T, Klose J, Bright M, Ammerer G, Horn M. Conserved features and major differences in the outer membrane protein composition of chlamydiae. Environ Microbiol 2014; 17:1397-413. [DOI: 10.1111/1462-2920.12621] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 09/06/2014] [Indexed: 12/28/2022]
Affiliation(s)
- Karin Aistleitner
- Department of Microbiology and Ecosystem Science University of Vienna Vienna Austria
| | - Dorothea Anrather
- Department of Mass Spectrometry Facility Max F. Perutz Laboratories University of Vienna Vienna Austria
| | - Thomas Schott
- Department of Microbiology and Ecosystem Science University of Vienna Vienna Austria
| | - Julia Klose
- Department of Limnology and Oceanography University of Vienna Vienna Austria
| | - Monika Bright
- Department of Limnology and Oceanography University of Vienna Vienna Austria
| | - Gustav Ammerer
- Department of Biochemistry and Cell Biology Max F. Perutz Laboratories University of Vienna Vienna Austria
| | - Matthias Horn
- Department of Microbiology and Ecosystem Science University of Vienna Vienna Austria
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237
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Qiao Y, Lebar MD, Schirner K, Schaefer K, Tsukamoto H, Kahne D, Walker S. Detection of lipid-linked peptidoglycan precursors by exploiting an unexpected transpeptidase reaction. J Am Chem Soc 2014; 136:14678-81. [PMID: 25291014 PMCID: PMC4210121 DOI: 10.1021/ja508147s] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Penicillin-binding
proteins (PBPs) are involved in the synthesis
and remodeling of bacterial peptidoglycan (PG). Staphylococcus
aureus expresses four PBPs. Genetic studies in S.
aureus have implicated PBP4 in the formation of highly cross-linked
PG, but biochemical studies have not reached a consensus on its primary
enzymatic activity. Using synthetic Lipid II, we show here that PBP4
preferentially acts as a transpeptidase (TP) in vitro. Moreover, it is the PBP primarily responsible for incorporating
exogenous d-amino acids into cellular PG, implying that it
also has TP activity in vivo. Notably, PBP4 efficiently
exchanges d-amino acids not only into PG polymers but also
into the PG monomers Lipid I and Lipid II. This is the first demonstration
that any TP domain of a PBP can activate the PG monomer building blocks.
Exploiting the promiscuous TP activity of PBP4, we developed a simple,
highly sensitive assay to detect cellular pools of lipid-linked PG
precursors, which are of notoriously low abundance. This method, which
addresses a longstanding problem, is useful for assessing how genetic
and pharmacological perturbations affect precursor levels, and may
facilitate studies to elucidate antibiotic mechanism of action.
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Affiliation(s)
- Yuan Qiao
- Chemical Biology Program, Harvard University , Cambridge, Massachusetts 02138, United States
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238
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Kouidmi I, Levesque RC, Paradis-Bleau C. The biology of Mur ligases as an antibacterial target. Mol Microbiol 2014; 94:242-53. [DOI: 10.1111/mmi.12758] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Imène Kouidmi
- Department of Microbiology, Infectiology and Immunology; Université de Montreal; Montreal Quebec Canada
| | - Roger C. Levesque
- Institut de biologie intégrative et des systèmes; Université Laval; Montreal Quebec Canada
| | - Catherine Paradis-Bleau
- Department of Microbiology, Infectiology and Immunology; Université de Montreal; Montreal Quebec Canada
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239
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Cadby IT, Lovering AL. Molecular surveillance of the subtle septum: discovering a new mode of peptidoglycan synthesis in streptococci. Mol Microbiol 2014; 94:1-4. [PMID: 25135390 DOI: 10.1111/mmi.12756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2014] [Indexed: 11/29/2022]
Abstract
The process of septation requires precise temporal and spatial organization of penicillin binding proteins (PBPs) and associated proteins for the deposition of new cell wall material. In most bacteria, the filamentous protein FtsZ organises PBPs into assemblies at the midcell which then constrict inwards as peptidoglycan is synthesised, eventually closing the septa. Tsui et al. (2014), through the use of fluorescent d-amino acids and high resolution microscopy, report that PBP2x of Streptococcus pneumoniae is directed to a discrete location within the septal aperture during the later stages of cell division. Once at this new site, PBP2x catalyses the de novo synthesis of peptidoglycan, which is imaged by the authors as a central 'spot', distinct from material made by other PBPs at the outer ring. This discovery, which represents a novel mode of cell wall assembly, was made in a directed capsular knockout of strain D39, thereby avoiding potential mechanistic complications in commonly used laboratory strain R6. These findings prompt not only a partial rethink of septum formation in S. pneumoniae, but consideration of the modes of PBP localization and the subtleties that can influence phenotypic study.
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Affiliation(s)
- Ian T Cadby
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Birmingham, UK
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240
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Abdelsayed S, Ha Duong N, Hai J, Hémadi M, El Hage Chahine J, Verbeke P, Serradji N. Design and synthesis of 3-isoxazolidone derivatives as new Chlamydia trachomatis inhibitors. Bioorg Med Chem Lett 2014; 24:3854-60. [DOI: 10.1016/j.bmcl.2014.06.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 12/19/2022]
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241
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Shih HW, Kamber DN, Prescher JA. Building better bioorthogonal reactions. Curr Opin Chem Biol 2014; 21:103-11. [DOI: 10.1016/j.cbpa.2014.07.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/25/2014] [Accepted: 07/03/2014] [Indexed: 12/31/2022]
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242
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Lebar MD, May JM, Meeske AJ, Leiman SA, Lupoli TJ, Tsukamoto H, Losick R, Rudner DZ, Walker S, Kahne D. Reconstitution of peptidoglycan cross-linking leads to improved fluorescent probes of cell wall synthesis. J Am Chem Soc 2014; 136:10874-7. [PMID: 25036369 PMCID: PMC4132960 DOI: 10.1021/ja505668f] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
The
peptidoglycan precursor, Lipid II, produced in the model Gram-positive
bacterium Bacillus subtilis differs from Lipid II
found in Gram-negative bacteria such as Escherichia coli by a single amidation on the peptide side chain. How this difference
affects the cross-linking activity of penicillin-binding proteins
(PBPs) that assemble peptidoglycan in cells has not been investigated
because B. subtilis Lipid II was not previously available.
Here we report the synthesis of B. subtilis Lipid
II and its use by purified B. subtilis PBP1 and E. coli PBP1A. While enzymes from both organisms assembled B. subtilis Lipid II into glycan strands, only the B. subtilis enzyme cross-linked the strands. Furthermore, B. subtilis PBP1 catalyzed the exchange of both d-amino acids and d-amino carboxamides into nascent peptidoglycan,
but the E. coli enzyme only exchanged d-amino
acids. We exploited these observations to design a fluorescent d-amino carboxamide probe to label B. subtilis PG in vivo and found that this probe labels the cell wall dramatically
better than existing reagents.
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Affiliation(s)
- Matthew D Lebar
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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243
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Fura JM, Sabulski MJ, Pires MM. D-amino acid mediated recruitment of endogenous antibodies to bacterial surfaces. ACS Chem Biol 2014; 9:1480-9. [PMID: 24870969 DOI: 10.1021/cb5002685] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The number of antibiotic resistant bacterial strains has been continuously increasing over the last few decades. Nontraditional routes to combat bacteria may offer an attractive alternative to the ongoing problem of drug discovery in this field. Herein, we describe the initial framework toward the development of bacterial d-amino acid antibody recruitment therapy (DART). DART represents a promising antibiotic strategy by exploiting the promiscuity of bacteria to incorporate unnatural d-amino acids and subsequently recruit antibodies to the bacterial surface. The conjugation of 2,4-dinitrophenyl (DNP) to various d-amino acids led to the discovery of a d-amino acid that specifically tags the surface of Bacillus subtilis and Staphylococcus aureus for the recruitment of anti-DNP antibodies (a highly abundant antibody in human serum). This system represents a novel strategy as an antibacterial therapy that targets planktonic Gram-positive bacteria.
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Affiliation(s)
- Jonathan M. Fura
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Mary J. Sabulski
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Marcos M. Pires
- Department
of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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244
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FtsZ-independent septal recruitment and function of cell wall remodelling enzymes in chlamydial pathogens. Nat Commun 2014; 5:4200. [PMID: 24953095 PMCID: PMC4083446 DOI: 10.1038/ncomms5200] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/22/2014] [Indexed: 11/08/2022] Open
Abstract
The nature and assembly of the chlamydial division septum is poorly defined due to the paucity of a detectable peptidoglycan (PG)-based cell wall, the inhibition of constriction by penicillin and the presence of coding sequences for cell wall precursor and remodelling enzymes in the reduced chlamydial (pan-)genome. Here we show that the chlamydial amidase (AmiA) is active and remodels PG in Escherichia coli. Moreover, forward genetics using an E. coli amidase mutant as entry point reveals that the chlamydial LysM-domain protein NlpD is active in an E. coli reporter strain for PG endopeptidase activity (ΔnlpI). Immunolocalization unveils NlpD as the first septal (cell-wall-binding) protein in Chlamydiae and we show that its septal sequestration depends on prior cell wall synthesis. Since AmiA assembles into peripheral clusters, trimming of a PG-like polymer or precursors occurs throughout the chlamydial envelope, while NlpD targets PG-like peptide crosslinks at the chlamydial septum during constriction.
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245
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Klöckner A, Otten C, Derouaux A, Vollmer W, Bühl H, De Benedetti S, Münch D, Josten M, Mölleken K, Sahl HG, Henrichfreise B. AmiA is a penicillin target enzyme with dual activity in the intracellular pathogen Chlamydia pneumoniae. Nat Commun 2014; 5:4201. [PMID: 24953137 PMCID: PMC4083426 DOI: 10.1038/ncomms5201] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/22/2014] [Indexed: 11/09/2022] Open
Abstract
Intracellular Chlamydiaceae do not need to resist osmotic challenges and a functional cell wall was not detected in these pathogens. Nevertheless, a recent study revealed evidence for circular peptidoglycan-like structures in Chlamydiaceae and penicillin inhibits cytokinesis, a phenomenon known as the chlamydial anomaly. Here, by characterizing a cell wall precursor-processing enzyme, we provide insights into the mechanisms underlying this mystery. We show that AmiA from Chlamydia pneumoniae separates daughter cells in an Escherichia coli amidase mutant. Contrary to homologues from free-living bacteria, chlamydial AmiA uses lipid II as a substrate and has dual activity, acting as an amidase and a carboxypeptidase. The latter function is penicillin sensitive and assigned to a penicillin-binding protein motif. Consistent with the lack of a regulatory domain in AmiA, chlamydial CPn0902, annotated as NlpD, is a carboxypeptidase, rather than an amidase activator, which is the case for E. coli NlpD. Functional conservation of AmiA implicates a role in cytokinesis and host response modulation. Penicillin inhibits growth of chlamydial pathogens despite their lack of a conventional peptidoglycan cell wall. Here the authors report that the chlamydial amidase, AmiA, which can rescue cell division defects of an E. coli amiA mutant, has dual activity as a penicillin sensitive, lipid II-targetting carboxypeptidase.
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Affiliation(s)
- Anna Klöckner
- 1] Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology, University of Bonn, 53115 Bonn, Germany [2]
| | - Christian Otten
- 1] Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology, University of Bonn, 53115 Bonn, Germany [2]
| | - Adeline Derouaux
- 1] The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK [2]
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Henrike Bühl
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology, University of Bonn, 53115 Bonn, Germany
| | - Stefania De Benedetti
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology, University of Bonn, 53115 Bonn, Germany
| | - Daniela Münch
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology, University of Bonn, 53115 Bonn, Germany
| | - Michaele Josten
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology, University of Bonn, 53115 Bonn, Germany
| | - Katja Mölleken
- Institute of Functional Microbial Genomics, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Hans-Georg Sahl
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology, University of Bonn, 53115 Bonn, Germany
| | - Beate Henrichfreise
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology, University of Bonn, 53115 Bonn, Germany
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246
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Frohlich KM, Hua Z, Quayle AJ, Wang J, Lewis ME, Chou CW, Luo M, Buckner LR, Shen L. Membrane vesicle production by Chlamydia trachomatis as an adaptive response. Front Cell Infect Microbiol 2014; 4:73. [PMID: 24959424 PMCID: PMC4050530 DOI: 10.3389/fcimb.2014.00073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/19/2014] [Indexed: 01/08/2023] Open
Abstract
Bacteria have evolved specific adaptive responses to cope with changing environments. These adaptations include stress response phenotypes with dynamic modifications of the bacterial cell envelope and generation of membrane vesicles (MVs). The obligate intracellular bacterium, Chlamydia trachomatis, typically has a biphasic lifestyle, but can enter into an altered growth state typified by morphologically aberrant chlamydial forms, termed persistent growth forms, when induced by stress in vitro. How C. trachomatis can adapt to a persistent growth state in host epithelial cells in vivo is not well understood, but is an important question, since it extends the host-bacterial relationship in vitro and has thus been indicated as a survival mechanism in chronic chlamydial infections. Here, we review recent findings on the mechanistic aspects of bacterial adaptation to stress with a focus on how C. trachomatis remodels its envelope, produces MVs, and the potential important consequences of MV production with respect to host-pathogen interactions. Emerging data suggest that the generation of MVs may be an important mechanism for C. trachomatis intracellular survival of stress, and thus may aid in the establishment of a chronic infection in human genital epithelial cells.
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Affiliation(s)
- Kyla M Frohlich
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, LA, USA
| | - Ziyu Hua
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, LA, USA ; Department of Neonatology, Ministry of Education Key Laboratory of Child Development and Disorder, The Children's Hospital, Chongqing Medical University Chongqing, China
| | - Alison J Quayle
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, LA, USA
| | - Jin Wang
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, LA, USA
| | - Maria E Lewis
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, LA, USA
| | - Chau-wen Chou
- Department of Chemistry, University of Georgia Athens, GA, USA
| | - Miao Luo
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, LA, USA
| | - Lyndsey R Buckner
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, LA, USA
| | - Li Shen
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New Orleans, LA, USA
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247
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Ollivaux C, Soyez D, Toullec JY. Biogenesis of d
-amino acid containing peptides/proteins: where, when and how? J Pept Sci 2014; 20:595-612. [DOI: 10.1002/psc.2637] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Céline Ollivaux
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227; Integrative Biology of Marine Models, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
- CNRS, UMR 8227; Integrative Biology of Marine Models, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
| | - Daniel Soyez
- Sorbonne Universités, UPMC Univ Paris 06, ER3; Biogenèse des signaux peptidiques; 7 Quai Saint Bernard F-75251 Paris cedex 05 France
- CNRS, ER3; Biogenèse des signaux peptidiques; 7 Quai Saint Bernard F-75251 Paris cedex 05 France
| | - Jean-Yves Toullec
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144; Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
- CNRS, UMR 7144; Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff; CS 90074, F-29688 Roscoff cedex France
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248
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Abstract
Getting visible: A new method to label bacterial cell walls shows the presence of functional peptidoglycan in the important pathogen Chlamydia trachomatis. This might clarify the long-standing paradox of the "chlamydial anomaly".
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Affiliation(s)
- Tamimount Mohammadi
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht (The Netherlands)
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249
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Bachmann NL, Polkinghorne A, Timms P. Chlamydia genomics: providing novel insights into chlamydial biology. Trends Microbiol 2014; 22:464-72. [PMID: 24882432 DOI: 10.1016/j.tim.2014.04.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/18/2014] [Accepted: 04/28/2014] [Indexed: 12/12/2022]
Abstract
Chlamydiaceae are obligate intracellular pathogens that have successfully evolved to colonize a diverse range of hosts. There are currently 11 described species of Chlamydia, most of which have a significant impact on the health of humans or animals. Expanding chlamydial genome sequence information has revolutionized our understanding of chlamydial biology, including aspects of their unique lifecycle, host-pathogen interactions, and genetic differences between Chlamydia strains associated with different host and tissue tropisms. This review summarizes the major highlights of chlamydial genomics and reflects on the considerable impact these have had on understanding the biology of chlamydial pathogens and the changing nature of genomics tools in the 'post-genomics' era.
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Affiliation(s)
- Nathan L Bachmann
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia.
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250
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Alvarez L, Espaillat A, Hermoso JA, de Pedro MA, Cava F. Peptidoglycan remodeling by the coordinated action of multispecific enzymes. Microb Drug Resist 2014; 20:190-8. [PMID: 24799190 DOI: 10.1089/mdr.2014.0047] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The peptidoglycan (PG) cell wall constitutes the main defense barrier of bacteria against environmental insults and acts as communication interface. The biochemistry of this macromolecule has been well characterized throughout the years but recent discoveries have unveiled its chemical plasticity under environmental stresses. Non-canonical D-amino acids (NCDAA) are produced and released to the extracellular media by diverse bacteria. Such molecules govern cell wall adaptation to challenging environments through their incorporation into the polymer, a widespread capability among bacteria that reveals the inherent catalytic plasticity of the enzymes involved in the cell wall metabolism. Here, we analyze the recent structural and biochemical characterization of Bsr, a new family of broad spectrum racemases able to generate a wide range of NCDAA. We also discuss the necessity of a coordinated action of PG multispecific enzymes to generate adequate levels of modification in the murein sacculus. Finally, we also highlight how this catalytic plasticity of NCDAA-incorporating enzymes has allowed the development of new revolutionary methodologies for the study of PG modes of growth and in vivo dynamics.
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Affiliation(s)
- Laura Alvarez
- 1 Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University , Umeå, Sweden
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