1
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Campanacci V, Gigant B. The C-terminus of stathmin-like proteins governs the stability of their complexes with tubulin. Biochem Biophys Res Commun 2023; 682:244-249. [PMID: 37826947 DOI: 10.1016/j.bbrc.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
Microtubule dynamics is modulated by many cellular factors including stathmin family proteins. Vertebrate stathmins sequester two αβ-tubulin heterodimers into a tight complex that cannot be incorporated in microtubules. Stathmins are regulated at the expression level during development and among tissues; they are also regulated by phosphorylation. Here, we study the dissociation kinetics of tubulin:stathmin assemblies in presence of different tubulin-binding proteins and identify a critical role of the C-terminus of the stathmin partner. Destabilizing this C-terminal region may represent an additional regulatory mechanism of the interaction with tubulin of stathmin proteins.
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Affiliation(s)
- Valérie Campanacci
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Benoît Gigant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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2
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Abstract
Type III secretion systems (T3SSs) are utilized by Gram-negative pathogens to enhance their pathogenesis. This secretion system is associated with the delivery of effectors through a needle-like structure from the bacterial cytosol directly into a target eukaryotic cell. These effector proteins then manipulate specific eukaryotic cell functions to benefit pathogen survival within the host. The obligate intracellular pathogens of the family Chlamydiaceae have a highly evolutionarily conserved nonflagellar T3SS that is an absolute requirement for their survival and propagation within the host with about one-seventh of the genome dedicated to genes associated with the T3SS apparatus, chaperones, and effectors. Chlamydiae also have a unique biphasic developmental cycle where the organism alternates between an infectious elementary body (EB) and replicative reticulate body (RB). T3SS structures have been visualized on both EBs and RBs. And there are effector proteins that function at each stage of the chlamydial developmental cycle, including entry and egress. This review will discuss the history of the discovery of chlamydial T3SS and the biochemical characterization of components of the T3SS apparatus and associated chaperones in the absence of chlamydial genetic tools. These data will be contextualized into how the T3SS apparatus functions throughout the chlamydial developmental cycle and the utility of heterologous/surrogate models to study chlamydial T3SS. Finally, there will be a targeted discussion on the history of chlamydial effectors and recent advances in the field.
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Affiliation(s)
- Elizabeth A. Rucks
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Durham Research Center II, Omaha, Nebraska, USA
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3
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Navarrete KM, Bumba L, Prudnikova T, Malcova I, Allsop TR, Sebo P, Kamanova J. BopN is a Gatekeeper of the Bordetella Type III Secretion System. Microbiol Spectr 2023; 11:e0411222. [PMID: 37036369 PMCID: PMC10269732 DOI: 10.1128/spectrum.04112-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/17/2023] [Indexed: 04/11/2023] Open
Abstract
The classical Bordetella species infect the respiratory tract of mammals. While B. bronchiseptica causes rather chronic respiratory infections in a variety of mammals, the human-adapted species B. pertussis and B. parapertussisHU cause an acute respiratory disease known as whooping cough or pertussis. The virulence factors include a type III secretion system (T3SS) that translocates effectors BteA and BopN into host cells. However, the regulatory mechanisms underlying the secretion and translocation activity of T3SS in bordetellae are largely unknown. We have solved the crystal structure of BopN of B. pertussis and show that it is similar to the structures of gatekeepers that control access to the T3SS channel from the bacterial cytoplasm. We further found that BopN accumulates at the cell periphery at physiological concentrations of calcium ions (2 mM) that inhibit the secretion of BteA and BopN. Deletion of the bopN gene in B. bronchiseptica increased secretion of the BteA effector into calcium-rich medium but had no effect on secretion of the T3SS translocon components BopD and BopB. Moreover, the ΔbopN mutant secreted approximately 10-fold higher amounts of BteA into the medium of infected cells than the wild-type bacteria, but it translocated lower amounts of BteA into the host cell cytoplasm. These data demonstrate that BopN is a Bordetella T3SS gatekeeper required for regulated and targeted translocation of the BteA effector through the T3SS injectisome into host cells. IMPORTANCE The T3SS is utilized by many Gram-negative bacteria to deliver effector proteins from bacterial cytosol directly into infected host cell cytoplasm in a regulated and targeted manner. Pathogenic bordetellae use the T3SS to inject the BteA and BopN proteins into infected cells and upregulate the production of the anti-inflammatory cytokine interleukin-10 (IL-10) to evade host immunity. Previous studies proposed that BopN acted as an effector in host cells. In this study, we report that BopN is a T3SS gatekeeper that regulates the secretion and translocation activity of Bordetella T3SS.
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Affiliation(s)
- Kevin Munoz Navarrete
- Laboratory of Infection Biology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ladislav Bumba
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tatyana Prudnikova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Ceske Budejovice, Czech Republic
| | - Ivana Malcova
- Laboratory of Infection Biology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tania Romero Allsop
- Laboratory of Infection Biology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Peter Sebo
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Kamanova
- Laboratory of Infection Biology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
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4
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Wevers C, Höhler M, Alcázar-Román AR, Hegemann JH, Fleig U. A Functional Yeast-Based Screen Identifies the Host Microtubule Cytoskeleton as a Target of Numerous Chlamydia pneumoniae Proteins. Int J Mol Sci 2023; 24:ijms24087618. [PMID: 37108781 PMCID: PMC10142024 DOI: 10.3390/ijms24087618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Bacterial pathogens have evolved intricate ways to manipulate the host to support infection. Here, we systematically assessed the importance of the microtubule cytoskeleton for infection by Chlamydiae, which are obligate intracellular bacteria that are of great importance for human health. The elimination of microtubules in human HEp-2 cells prior to C. pneumoniae infection profoundly attenuated the infection efficiency, demonstrating the need for microtubules for the early infection processes. To identify microtubule-modulating C. pneumoniae proteins, a screen in the model yeast Schizosaccharomyces pombe was performed. Unexpectedly, among 116 selected chlamydial proteins, more than 10%, namely, 13 proteins, massively altered the yeast interphase microtubule cytoskeleton. With two exceptions, these proteins were predicted to be inclusion membrane proteins. As proof of principle, we selected the conserved CPn0443 protein, which caused massive microtubule instability in yeast, for further analysis. CPn0443 bound and bundled microtubules in vitro and co-localized partially with microtubules in vivo in yeast and human cells. Furthermore, CPn0443-transfected U2OS cells had a significantly reduced infection rate by C. pneumoniae EBs. Thus, our yeast screen identified numerous proteins encoded using the highly reduced C. pneumoniae genome that modulated microtubule dynamics. Hijacking of the host microtubule cytoskeleton must be a vital part of chlamydial infection.
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Affiliation(s)
- Carolin Wevers
- Eukaryotic Microbiology, Institute of Functional Microbial Genomics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Mona Höhler
- Eukaryotic Microbiology, Institute of Functional Microbial Genomics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Abel R Alcázar-Román
- Eukaryotic Microbiology, Institute of Functional Microbial Genomics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Johannes H Hegemann
- Institute of Functional Microbial Genomics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Ursula Fleig
- Eukaryotic Microbiology, Institute of Functional Microbial Genomics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
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5
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Structural convergence for tubulin binding of CPAP and vinca domain microtubule inhibitors. Proc Natl Acad Sci U S A 2022; 119:e2120098119. [PMID: 35507869 PMCID: PMC9171608 DOI: 10.1073/pnas.2120098119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Microtubules are dynamic assemblies of αβ-tubulin that are involved in key cellular functions, including cell division and intracellular transport. Microtubule dynamics is inhibited by several families of small molecules, some of which are used in oncology. The extent to which these compounds target the binding sites of cellular partners of tubulin remains poorly characterized. We show here that a region of the CPAP protein binds to the so-called vinca domain of β-tubulin in a way very similar to that of peptide-like inhibitors produced by bacteria and fungi. Therefore, our work identifies a structural convergence for tubulin binding between inhibitors and a regulator of microtubule dynamics. Microtubule dynamics is regulated by various cellular proteins and perturbed by small-molecule compounds. To what extent the mechanism of the former resembles that of the latter is an open question. We report here structures of tubulin bound to the PN2-3 domain of CPAP, a protein controlling the length of the centrioles. We show that an α-helix of the PN2-3 N-terminal region binds and caps the longitudinal surface of the tubulin β subunit. Moreover, a PN2-3 N-terminal stretch lies in a β-tubulin site also targeted by fungal and bacterial peptide-like inhibitors of the vinca domain, sharing a very similar binding mode with these compounds. Therefore, our results identify several characteristic features of cellular partners that bind to this site and highlight a structural convergence of CPAP with small-molecule inhibitors of microtubule assembly.
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6
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Huang Y, Wurihan W, Lu B, Zou Y, Wang Y, Weldon K, Fondell JD, Lai Z, Wu X, Fan H. Robust Heat Shock Response in Chlamydia Lacking a Typical Heat Shock Sigma Factor. Front Microbiol 2022; 12:812448. [PMID: 35046926 PMCID: PMC8762339 DOI: 10.3389/fmicb.2021.812448] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
Cells reprogram their transcriptome in response to stress, such as heat shock. In free-living bacteria, the transcriptomic reprogramming is mediated by increased DNA-binding activity of heat shock sigma factors and activation of genes normally repressed by heat-induced transcription factors. In this study, we performed transcriptomic analyses to investigate heat shock response in the obligate intracellular bacterium Chlamydia trachomatis, whose genome encodes only three sigma factors and a single heat-induced transcription factor. Nearly one-third of C. trachomatis genes showed statistically significant (≥1.5-fold) expression changes 30 min after shifting from 37 to 45°C. Notably, chromosomal genes encoding chaperones, energy metabolism enzymes, type III secretion proteins, as well as most plasmid-encoded genes, were differentially upregulated. In contrast, genes with functions in protein synthesis were disproportionately downregulated. These findings suggest that facilitating protein folding, increasing energy production, manipulating host activities, upregulating plasmid-encoded gene expression, and decreasing general protein synthesis helps facilitate C. trachomatis survival under stress. In addition to relieving negative regulation by the heat-inducible transcriptional repressor HrcA, heat shock upregulated the chlamydial primary sigma factor σ66 and an alternative sigma factor σ28. Interestingly, we show for the first time that heat shock downregulates the other alternative sigma factor σ54 in a bacterium. Downregulation of σ54 was accompanied by increased expression of the σ54 RNA polymerase activator AtoC, thus suggesting a unique regulatory mechanism for reestablishing normal expression of select σ54 target genes. Taken together, our findings reveal that C. trachomatis utilizes multiple novel survival strategies to cope with environmental stress and even to replicate. Future strategies that can specifically target and disrupt Chlamydia’s heat shock response will likely be of therapeutic value.
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Affiliation(s)
- Yehong Huang
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Bin Lu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Korri Weldon
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Joseph D Fondell
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States.,Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Xiang Wu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
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7
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Guimarães BG, Golinelli-Pimpaneau B. De novo crystal structure determination of double stranded RNA binding domain using only the sulfur anomalous diffraction in SAD phasing. Curr Res Struct Biol 2021; 3:112-120. [PMID: 34235491 PMCID: PMC8244422 DOI: 10.1016/j.crstbi.2021.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/07/2021] [Accepted: 05/31/2021] [Indexed: 10/25/2022] Open
Abstract
Single-wavelength anomalous dispersion (SAD)-phasing using sulfur as the unique anomalous scatterer is a powerful method to solve the phase problem in protein crystallography. However, it is not yet widely used by non-expert crystallographers. We report here the structure determination of the double stranded RNA binding domain of human dihydrouridine synthase using the sulfur-SAD method and highly redundant data collected at 1.8 Å ("off-edge"), at which the estimated overall anomalous signal was 1.08%. High multiplicity data were collected on a single crystal rotated along the ϕ or ω axis at different κ angles, with the primary beam intensity being attenuated from 50% to 95%, compared to data collection at 0.98 Å, to reduce radiation damage. SHELXD succeeded to locate 14 out 15 sulfur sites only using the data sets recorded with highest beam attenuation, which provided phases sufficient for structure solving. In an attempt to stimulate the use of sulfur-SAD phasing by a broader community of crystallographers, we describe our experimental strategy together with a compilation of previous successful cases, suggesting that sulfur-SAD phasing should be attempted for determining the de novo structure of any protein with average sulfur content diffracting better than 3 Å resolution.
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Affiliation(s)
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, 11 Place Marcelin Berthelot, 75005 Paris, France
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8
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Gazi AD, Kokkinidis M, Fadouloglou VE. α-Helices in the Type III Secretion Effectors: A Prevalent Feature with Versatile Roles. Int J Mol Sci 2021; 22:ijms22115412. [PMID: 34063760 PMCID: PMC8196651 DOI: 10.3390/ijms22115412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Type III Secretion Systems (T3SSs) are multicomponent nanomachines located at the cell envelope of Gram-negative bacteria. Their main function is to transport bacterial proteins either extracellularly or directly into the eukaryotic host cell cytoplasm. Type III Secretion effectors (T3SEs), latest to be secreted T3S substrates, are destined to act at the eukaryotic host cell cytoplasm and occasionally at the nucleus, hijacking cellular processes through mimicking eukaryotic proteins. A broad range of functions is attributed to T3SEs, ranging from the manipulation of the host cell's metabolism for the benefit of the bacterium to bypassing the host's defense mechanisms. To perform this broad range of manipulations, T3SEs have evolved numerous novel folds that are compatible with some basic requirements: they should be able to easily unfold, pass through the narrow T3SS channel, and refold to an active form when on the other side. In this review, the various folds of T3SEs are presented with the emphasis placed on the functional and structural importance of α-helices and helical domains.
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Affiliation(s)
- Anastasia D. Gazi
- Unit of Technology & Service Ultrastructural Bio-Imaging (UTechS UBI), Institut Pasteur, 75015 Paris, France
- Correspondence: (A.D.G.); (V.E.F.)
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion, 70013 Crete, Greece;
- Department of Biology, Voutes University Campus, University of Crete, Heraklion, 70013 Crete, Greece
| | - Vasiliki E. Fadouloglou
- Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Correspondence: (A.D.G.); (V.E.F.)
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9
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Kamanova J. Bordetella Type III Secretion Injectosome and Effector Proteins. Front Cell Infect Microbiol 2020; 10:466. [PMID: 33014891 PMCID: PMC7498569 DOI: 10.3389/fcimb.2020.00466] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
Pertussis, also known as whooping cough, is a resurging acute respiratory disease of humans primarily caused by the Gram-negative coccobacilli Bordetella pertussis, and less commonly by the human-adapted lineage of B. parapertussis HU. The ovine-adapted lineage of B. parapertussis OV infects only sheep, while B. bronchiseptica causes chronic and often asymptomatic respiratory infections in a broad range of mammals but rarely in humans. A largely overlapping set of virulence factors inflicts the pathogenicity of these bordetellae. Their genomes also harbor a pathogenicity island, named bsc locus, that encodes components of the type III secretion injectosome, and adjacent btr locus with the type III regulatory proteins. The Bsc injectosome of bordetellae translocates the cytotoxic BteA effector protein, also referred to as BopC, into the cells of the mammalian hosts. While the role of type III secretion activity in the persistent colonization of the lower respiratory tract by B. bronchiseptica is well recognized, the functionality of the type III secretion injectosome in B. pertussis was overlooked for many years due to the adaptation of laboratory-passaged B. pertussis strains. This review highlights the current knowledge of the type III secretion system in the so-called classical Bordetella species, comprising B. pertussis, B. parapertussis, and B. bronchiseptica, and discusses its functional divergence. Comparison with other well-studied bacterial injectosomes, regulation of the type III secretion on the transcriptional and post-transcriptional level, and activities of BteA effector protein and BopN protein, homologous to the type III secretion gatekeepers, are addressed.
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Affiliation(s)
- Jana Kamanova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
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10
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Context-Dependent Action of Scc4 Reinforces Control of the Type III Secretion System. J Bacteriol 2020; 202:JB.00132-20. [PMID: 32424009 DOI: 10.1128/jb.00132-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/07/2020] [Indexed: 02/03/2023] Open
Abstract
Chlamydia trachomatis Scc4 (formerly CT663) engages the transcription machinery and the pathogenic type III secretion system (T3SS). Both machines are required for Chlamydia infection. These requirements and the limited ability for genetic manipulation in Chlamydia have hampered dissection of Scc4's contributions. Here, by developing bacterial systems that permit the controlled expression and stable maintenance of Scc4, we assess Scc4's effects on chlamydial growth phenotype, secretion, and the patterns of T3SS gene expression. Expressing Scc4 in Escherichia coli lacking a T3SS injectisome causes a growth defect. This deficiency is rescued by overexpressing the β-subunit of RNA polymerase (RNAP) or by exploiting sigma 70 (σ70) (homologous to chlamydial σ66) mutants that strengthen the interaction between σ70 region 4 and the β-flap, confirming Scc4's distinction as a module of RNAP holoenzyme capable of modulating transcription. Yersinia pestis expressing Scc4 sustains a functional T3SS, through which CopN secretion is boosted by cooption of Scc4 and Scc1. Finally, conditional expression of Scc4 in C. trachomatis results in fast expansion of the Chlamydia-containing vacuole and accelerated chlamydial development, coupled to selective up- or downregulation of gene expression from different T3SS genes. This work reveals, for the first time, the context-dependent action of Scc4 linking it to diverse protein networks in bacteria. It establishes that Scc4, when overexpressed, exerts incredible effects on chlamydial development by reinforcing control of the T3SS.IMPORTANCE The T3SS is a key virulence factor required for C. trachomatis infection. The control of the T3SS has not been well studied in this obligate intracellular pathogen. Here, we show that Scc4 plays a major role for precise control of the pathogenic T3SS at the levels of gene expression and effector secretion through genetically separable protein networks, allowing a fast adaptive mode of C. trachomatis development during infection in human epithelial cells.
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11
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Czajka P, Antosiewicz JM, Długosz M. Effects of Hydrodynamic Interactions on the Near-Surface Diffusion of Spheroidal Molecules. ACS OMEGA 2019; 4:17016-17030. [PMID: 31646249 PMCID: PMC6796493 DOI: 10.1021/acsomega.9b02618] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/12/2019] [Indexed: 05/21/2023]
Abstract
We investigated diffusion of spheroidal molecules near a planar surface, accounting for spatially dependent translational and rotational mobilities of molecules resulting from their hydrodynamic interactions with the plane. Rigid-body Brownian dynamics simulations of prolate ellipsoids of revolution of an axial ratio in the range of 1.5 to 3.0, suspended in a viscous fluid, with a no-slip flat boundary confining the suspension were employed. Mobility tensor matrices of molecules were evaluated as functions of spheroids' distance and orientation with respect to the plane. Hydrodynamic interactions with the surface lead to substantial changes of spheroids' translational diffusion coefficients both in the direction perpendicular and parallel to the plane when compared with the values characterizing the bulk diffusion. Moreover, the short-time translational diffusion of molecules, measured in the laboratory frame, both in an unbounded fluid and under the confinement, is non-Gaussian, with much larger deviations from Gaussianity observed in the latter case. In an unbounded fluid, distributions of translational displacements of molecules deviate from those expected for a simple Brownian motion as a result of shape anisotropy. In the presence of the plane, spheroids experience an additional anisotropic drag, and consequently, their mobilities depend on their positions and orientations. Therefore, anomalies in the short-time dynamics observed under confinement can be explained in terms of the so-called diffusing-diffusivity mechanism. Our findings have implications for understanding of a wide range of biological and technological processes that involve diffusion of anisotropic molecules near surfaces of natural and model cell membranes, biosensors and nanosensors, and electrodes.
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Affiliation(s)
- Paweł Czajka
- Faculty
of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Jan M. Antosiewicz
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Maciej Długosz
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
- E-mail: . Phone: +48 22 55 32 229
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12
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Abstract
Nucleation is one of the least understood steps of microtubule dynamics. It is a kinetically unfavorable process that is templated in the cell by the γ-tubulin ring complex or by preexisting microtubules; it also occurs in vitro from pure tubulin. Here we study the nucleation inhibition potency of natural or artificial proteins in connection with their binding mode to the longitudinal surface of α- or β-tubulin. The structure of tubulin-bound CopN, a Chlamydia protein that delays nucleation, suggests that this protein may interfere with two protofilaments at the (+) end of a nucleus. Designed ankyrin repeat proteins that share a binding mode similar to that of CopN also impede nucleation, whereas those that target only one protofilament do not. In addition, an αRep protein predicted to target two protofilaments at the (-) end does not delay nucleation, pointing to different behaviors at both ends of the nucleus. Our results link the interference with protofilaments at the (+) end and the inhibition of nucleation.
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13
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Campanacci V, Urvoas A, Consolati T, Cantos-Fernandes S, Aumont-Nicaise M, Valerio-Lepiniec M, Surrey T, Minard P, Gigant B. Selection and Characterization of Artificial Proteins Targeting the Tubulin α Subunit. Structure 2019; 27:497-506.e4. [PMID: 30661854 PMCID: PMC6408325 DOI: 10.1016/j.str.2018.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/24/2018] [Accepted: 12/03/2018] [Indexed: 11/08/2022]
Abstract
Microtubules are cytoskeletal filaments of eukaryotic cells made of αβ-tubulin heterodimers. Structural studies of non-microtubular tubulin rely mainly on molecules that prevent its self-assembly and are used as crystallization chaperones. Here we identified artificial proteins from an αRep library that are specific to α-tubulin. Turbidity experiments indicate that these αReps impede microtubule assembly in a dose-dependent manner and total internal reflection fluorescence microscopy further shows that they specifically block growth at the microtubule (−) end. Structural data indicate that they do so by targeting the α-tubulin longitudinal surface. Interestingly, in one of the complexes studied, the α subunit is in a conformation that is intermediate between the ones most commonly observed in X-ray structures of tubulin and those seen in the microtubule, emphasizing the plasticity of tubulin. These α-tubulin-specific αReps broaden the range of tools available for the mechanistic study of microtubule dynamics and its regulation. Selection of α-tubulin-specific artificial αRep proteins The αReps inhibit microtubule assembly and specifically block growth at the (−) end The αReps target the longitudinal surface of α-tubulin The αReps are useful tools for the mechanistic study of microtubule dynamics
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Affiliation(s)
- Valérie Campanacci
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Tanja Consolati
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Soraya Cantos-Fernandes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Thomas Surrey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.
| | - Benoît Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.
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14
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Olczak A, Cianci M. The signal-to-noise ratio in SAD experiments. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2017.1386182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Andrzej Olczak
- Institute of General and Ecological Chemistry, Lodz University of Technology, Lodz, Poland
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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15
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Abstract
Chlamydia spp. are important causes of human disease for which no effective vaccine exists. These obligate intracellular pathogens replicate in a specialized membrane compartment and use a large arsenal of secreted effectors to survive in the hostile intracellular environment of the host. In this Review, we summarize the progress in decoding the interactions between Chlamydia spp. and their hosts that has been made possible by recent technological advances in chlamydial proteomics and genetics. The field is now poised to decipher the molecular mechanisms that underlie the intimate interactions between Chlamydia spp. and their hosts, which will open up many exciting avenues of research for these medically important pathogens.
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16
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Shen L, Macnaughtan MA, Frohlich KM, Cong Y, Goodwin OY, Chou CW, LeCour L, Krup K, Luo M, Worthylake DK. Multipart Chaperone-Effector Recognition in the Type III Secretion System of Chlamydia trachomatis. J Biol Chem 2015; 290:28141-28155. [PMID: 26438824 DOI: 10.1074/jbc.m115.670232] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Indexed: 11/06/2022] Open
Abstract
Secretion of effector proteins into the eukaryotic host cell is required for Chlamydia trachomatis virulence. In the infection process, Scc1 and Scc4, two chaperones of the type III secretion (T3S) system, facilitate secretion of the important effector and plug protein, CopN, but little is known about the details of this event. Here we use biochemistry, mass spectrometry, nuclear magnetic resonance spectroscopy, and genetic analyses to characterize this trimolecular event. We find that Scc4 complexes with Scc1 and CopN in situ at the late developmental cycle of C. trachomatis. We show that Scc4 and Scc1 undergo dynamic interactions as part of the unique bacterial developmental cycle. Using alanine substitutions, we identify several amino acid residues in Scc4 that are critical for the Scc4-Scc1 interaction, which is required for forming the Scc4·Scc1·CopN ternary complex. These results, combined with our previous findings that Scc4 plays a role in transcription (Rao, X., Deighan, P., Hua, Z., Hu, X., Wang, J., Luo, M., Wang, J., Liang, Y., Zhong, G., Hochschild, A., and Shen, L. (2009) Genes Dev. 23, 1818-1829), reveal that the T3S process is linked to bacterial transcriptional events, all of which are mediated by Scc4 and its interacting proteins. A model describing how the T3S process may affect gene expression is proposed.
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Affiliation(s)
- Li Shen
- Department of Microbiology, Immunology, and Parasitology.
| | - Megan A Macnaughtan
- Department of Chemistry, Louisiana State University, Baton Range, Louisiana 70803
| | | | - Yanguang Cong
- Department of Microbiology, Immunology, and Parasitology
| | - Octavia Y Goodwin
- Department of Chemistry, Louisiana State University, Baton Range, Louisiana 70803
| | - Chau-Wen Chou
- Department of Chemistry, University of Georgia, Athens, Georgia 30602
| | - Louis LeCour
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112
| | - Kristen Krup
- Department of Microbiology, Immunology, and Parasitology
| | - Miao Luo
- Department of Microbiology, Immunology, and Parasitology
| | - David K Worthylake
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112
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17
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Burkinshaw BJ, Souza SA, Strynadka NCJ. Structural analysis of SepL, an enteropathogenic Escherichia coli type III secretion-system gatekeeper protein. Acta Crystallogr F Struct Biol Commun 2015; 71:1300-8. [PMID: 26457522 PMCID: PMC4601595 DOI: 10.1107/s2053230x15016064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 08/27/2015] [Indexed: 12/26/2022] Open
Abstract
During infection, enteropathogenic Escherichia coli assembles a complex multi-protein type III secretion system that traverses the bacterial membranes and targets the host cell membrane to directly deliver virulence or effector proteins to the host cytoplasm. As this secretion system is composed of more than 20 proteins, many of which form oligomeric associations, its assembly must be tightly regulated. A protein called the gatekeeper, or SepL, ensures that the secretion of the translocon component, which inserts into the host membrane, occurs before the secretion of effectors. The crystal structure of the gatekeeper SepL was determined and compared with the structures of SepL homologues from other bacterial pathogens in order to identify SepL residues that may be critical for its role in type III secretion-system assembly.
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Affiliation(s)
- Brianne J. Burkinshaw
- Department of Biochemistry and Molecular Biology, University of British Columbia, Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Sergio A. Souza
- Department of Biochemistry and Molecular Biology, University of British Columbia, Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, Life Sciences Centre, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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18
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Abstract
UNLABELLED The Scc4 protein (CT663) of the pathogenic bacterium Chlamydia has been described as a type III secretion (T3S) chaperone as well as an inhibitor of RNA polymerase. To examine if these roles are connected, we first investigated physical interactions between Chlamydia trachomatis Scc4 and the T3S chaperone Scc1 and a T3S substrate, CopN. In a yeast 3-hybrid assay, Scc4, Scc1, and CopN were all required to detect an interaction, which suggests that these proteins form a trimolecular complex. We also detected interactions between any two of these three T3S proteins in a pulldown assay using only recombinant proteins. We next determined whether these interactions affected the function of Scc4 as an inhibitor of RNA transcription. Using Escherichia coli as a heterologous in vivo system, we demonstrated that expression of C. trachomatis Scc4 led to a drastic decrease in transcript levels for multiple genes. However, coexpression of Scc4 with Scc1, CopN, or both alleviated Scc4-mediated inhibition of transcription. Scc4 expression also severely impaired E. coli growth, but this growth defect was reversed by coexpression of Scc4 with Scc1, CopN, or both, suggesting that the inhibitory effect of Scc4 on transcription and growth can be antagonized by interactions between Scc4, Scc1, and CopN. These findings suggest that the dual functions of Scc4 may serve as a bridge to link T3S and the regulation of gene expression in Chlamydia. IMPORTANCE This study investigates a novel mechanism for regulating gene expression in the pathogenic bacterium Chlamydia. The Chlamydia type III secretion (T3S) chaperone Scc4 has been shown to inhibit transcription by RNA polymerase. This study describes physical interactions between Scc4 and the T3S proteins Scc1 and CopN. Furthermore, Chlamydia Scc1 and CopN antagonized the inhibitory effects of Scc4 on transcription and growth in a heterologous Escherichia coli system. These results provide evidence that transcription in Chlamydia can be regulated by the T3S system through interactions between T3S proteins.
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19
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Klinke S, Foos N, Rinaldi JJ, Paris G, Goldbaum FA, Legrand P, Guimarães BG, Thompson A. S-SAD phasing of monoclinic histidine kinase from Brucella abortus combining data from multiple crystals and orientations: an example of data-collection strategy and a posteriori analysis of different data combinations. ACTA ACUST UNITED AC 2015; 71:1433-43. [PMID: 26143915 DOI: 10.1107/s1399004715007622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/17/2015] [Indexed: 11/10/2022]
Abstract
The histidine kinase (HK) domain belonging to the light-oxygen-voltage histidine kinase (LOV-HK) from Brucella abortus is a member of the HWE family, for which no structural information is available, and has low sequence identity (20%) to the closest HK present in the PDB. The `off-edge' S-SAD method in macromolecular X-ray crystallography was used to solve the structure of the HK domain from LOV-HK at low resolution from crystals in a low-symmetry space group (P21) and with four copies in the asymmetric unit (∼108 kDa). Data were collected both from multiple crystals (diffraction limit varying from 2.90 to 3.25 Å) and from multiple orientations of the same crystal, using the κ-geometry goniostat on SOLEIL beamline PROXIMA 1, to obtain `true redundancy'. Data from three different crystals were combined for structure determination. An optimized HK construct bearing a shorter cloning artifact yielded crystals that diffracted X-rays to 2.51 Å resolution and that were used for final refinement of the model. Moreover, a thorough a posteriori analysis using several different combinations of data sets allowed us to investigate the impact of the data-collection strategy on the success of the structure determination.
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Affiliation(s)
- Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Nicolas Foos
- Experimental Division, Synchrotron SOLEIL, BP 48, L'Orme des Merisiers, 91192 Gif-sur-Yvette, France
| | - Jimena J Rinaldi
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Gastón Paris
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Pierre Legrand
- Experimental Division, Synchrotron SOLEIL, BP 48, L'Orme des Merisiers, 91192 Gif-sur-Yvette, France
| | - Beatriz G Guimarães
- Experimental Division, Synchrotron SOLEIL, BP 48, L'Orme des Merisiers, 91192 Gif-sur-Yvette, France
| | - Andrew Thompson
- Experimental Division, Synchrotron SOLEIL, BP 48, L'Orme des Merisiers, 91192 Gif-sur-Yvette, France
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20
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Ishida K, Matsuo J, Yamamoto Y, Yamaguchi H. Chlamydia pneumoniae effector chlamydial outer protein N sequesters fructose bisphosphate aldolase A, providing a benefit to bacterial growth. BMC Microbiol 2014; 14:330. [PMID: 25528659 PMCID: PMC4302594 DOI: 10.1186/s12866-014-0330-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/16/2014] [Indexed: 01/13/2023] Open
Abstract
Background Pathogenic chlamydiae are obligate intracellular pathogens and have adapted successfully to human cells, causing sexually transmitted diseases or pneumonia. Chlamydial outer protein N (CopN) is likely a critical effector protein secreted by the type III secretion system in chlamydiae, which manipulates host cells. However, the mechanisms of its action remain to be clarified. In this work, we aimed to identify previously unidentified CopN effector target in host cells. Results We first performed a pull-down assay with recombinant glutathione S-transferase (GST) fusion CopN proteins (GST–CpCopN: Chlamydia pneumoniae TW183, GST–CtCopN: Chlamydia trachomatis D/UW-3/CX) as “bait” and soluble lysates obtained from human immortal epithelial HEp-2 cells as “prey”, followed by SDS-PAGE with mass spectroscopy (MS). We found that a host cell protein specifically bound to GST–CpCopN, but not GST–CtCopN. MS revealed the host protein to be fructose bisphosphate aldolase A (aldolase A), which plays a key role in glycolytic metabolism. We also confirmed the role of aldolase A in chlamydia-infected HEp-2 cells by using two distinct experiments for gene knockdown with an siRNA specific to aldolase A transcripts, and for assessment of glycolytic enzyme gene expression levels. As a result, both the numbers of chlamydial inclusion-forming units and RpoD transcripts were increased in the chlamydia-infected aldolase A knockdown cells, as compared with the wild-type HEp-2 cells. Meanwhile, chlamydial infection tended to enhance expression of aldolase A. Conclusions We discovered that one of the C. pneumoniae CopN targets is the glycolytic enzyme aldolase A. Sequestering aldolase A may be beneficial to bacterial growth in infected host cells.
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Affiliation(s)
- Kasumi Ishida
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, 060-0812, Japan. .,Research Fellow of Japan Society for the Promotion of Science, Tokyo, 102-0083, Japan.
| | - Junji Matsuo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, 060-0812, Japan.
| | - Yoshimasa Yamamoto
- Department of Biomedical Informatics, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan. .,Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Osaka, Japan. .,Osaka Prefectural Institute of Public Health, Higashinari-ku, Osaka, 537-0025, Japan.
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Hokkaido, 060-0812, Japan.
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