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Guo E, Chou SZ, Lara-Tejero M, Galan JE. Cryo-EM structure of the bacterial effector protein SipA bound to F-actin reveals a unique mechanism for filament stabilization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572903. [PMID: 38187563 PMCID: PMC10769390 DOI: 10.1101/2023.12.21.572903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The bacterial pathogen Salmonella spp. modulates cellular processes by delivering effector proteins through its type III secretion systems. Among these effectors, SipA facilitates bacterial invasion and promotes intestinal inflammation. The mechanisms by which this effector carries out these functions are incompletely understood although SipA's ability to modulate actin dynamics is central to some of these activities. Here we report the cryo-EM structure of SipA bound to filamentous actin. We show that this effector stabilizes actin filaments through unique interactions of its carboxy terminal domain with four actin subunits. Furthermore, our structure-function studies revealed that SipA's actin-binding activity is independent from its ability to stimulate intestinal inflammation. Overall, these studies illuminate critical aspects of Salmonella pathogenesis, and provide unique insight into the mechanisms by which a bacterial effector modulates actin dynamics.
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Zhang C, Yao D, Su Z, Chen H, Hao P, Liao Y, Guo Y, Yang D. Copper/Zinc-Modified Palygorskite Protects Against Salmonella Typhimurium Infection and Modulates the Intestinal Microbiota in Chickens. Front Microbiol 2021; 12:739348. [PMID: 34956111 PMCID: PMC8696032 DOI: 10.3389/fmicb.2021.739348] [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: 07/13/2021] [Accepted: 11/04/2021] [Indexed: 12/26/2022] Open
Abstract
Palygorskite (Pal), a clay nanoparticle, has been demonstrated to be a vehicle for drug delivery. Copper has antibacterial properties, and zinc is an essential micronutrient for intestinal health in animals and humans. However, whether copper/zinc-modified Pal (Cu/Zn-Pal) can protect chickens from Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) infection remains unclear. In this study, three complexes (Cu/Zn-Pal-1, Cu/Zn-Pal-2, and Cu/Zn-Pal-3) were prepared, and Cu/Zn-Pal-1 was shown to be the most effective at inhibiting the growth of S. Typhimurium in vitro, whereas natural Pal alone had no inhibitory effect. In vivo, Cu/Zn-Pal-1 reduced S. Typhimurium colonization in the intestine of infected chickens and relieved S. Typhimurium-induced organ and intestinal mucosal barrier damage. Moreover, this reduction in Salmonella load attenuated intestinal inflammation and the oxidative stress response in challenged chickens. Additionally, Cu/Zn-Pal-1 modulated the intestinal microbiota in infected chickens, which was characterized by the reduced abundance of Firmicutes and the increased abundance of Proteobacteria and Bacteroidetes. Our results indicated that the Cu/Zn-Pal-1 complex may be an effective feed supplement for reducing S. Typhimurium colonization of the gut.
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Affiliation(s)
- Chaozheng Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Dawei Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zenan Su
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Huan Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Pan Hao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yun Liao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yiwen Guo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Deji Yang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis. Infect Immun 2021; 90:e0033421. [PMID: 34780277 PMCID: PMC9119117 DOI: 10.1128/iai.00334-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To identify sequences with a role in microbial pathogenesis, we assessed the adequacy of their annotation by existing controlled vocabularies and sequence databases. Our goal was to regularize descriptions of microbial pathogenesis for improved integration with bioinformatic applications. Here, we review the challenges of annotating sequences for pathogenic activity. We relate the categorization of more than 2,750 sequences of pathogenic microbes through a controlled vocabulary called Functions of Sequences of Concern (FunSoCs). These allow for an ease of description by both humans and machines. We provide a subset of 220 fully annotated sequences in the supplemental material as examples. The use of this compact (∼30 terms), controlled vocabulary has potential benefits for research in microbial genomics, public health, biosecurity, biosurveillance, and the characterization of new and emerging pathogens.
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Shatila F, Yalçın HT, Özyurt C, Evran S, Çakır B, Yaşa İ, Nalbantsoy A. Single-stranded DNA (ssDNA) Aptamer targeting SipA protein inhibits Salmonella Enteritidis invasion of intestinal epithelial cells. Int J Biol Macromol 2020; 148:518-524. [PMID: 31953175 DOI: 10.1016/j.ijbiomac.2020.01.132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
Salmonella Enteritidis is an important pathogen that can invade the intestinal cells of its host causing salmonellosis. SipA protein, an effector protein secreted by T3SS, maintains invasion of host cells more efficient. Thus, inhibitory aptamers against SipA protein were developed using magnetic bead-based Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method. The enriched sequences were obtained after 9 SELEX rounds. Among which, an aptamer namely Apt17 displayed Kd values equivalent to 114.9 and 63.4 nM at 27 °C and 37 °C, respectively. The effect of Apt17 on adhesion and invasion of Caco-2 cells by the tested strains was determined. While the adhesion and invasion of Salmonella Enteritidis TM 6 were inhibited by 70% and 37.7%, those of Salmonella Enteritidis TM 68 were inhibited by 45.71% and 39.5% respectively. These results represent a corner stone for future studies that could aim to develop putative inhibitors against Salmonellosis.
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Affiliation(s)
- Fatima Shatila
- Department of Biology, Faculty of Science, Ege University, Bornova, Izmir 35100, Turkey.
| | - H Tansel Yalçın
- Department of Biology, Faculty of Science, Ege University, Bornova, Izmir 35100, Turkey.
| | - Canan Özyurt
- Department of Chemistry and Chemical Processing Technologies, Lapseki Vocational School, Canakkale Onsekiz Mart University, Canakkale, Lapseki, Turkey
| | - Serap Evran
- Department of Biochemistry, Faculty of Science, Ege University, Bornova, Izmir 35100, Turkey
| | - Büşra Çakır
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir 35100, Turkey
| | - İhsan Yaşa
- Department of Biology, Faculty of Science, Ege University, Bornova, Izmir 35100, Turkey
| | - Ayşe Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir 35100, Turkey
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YshB Promotes Intracellular Replication and Is Required for Salmonella Virulence. J Bacteriol 2019; 201:JB.00314-19. [PMID: 31182500 DOI: 10.1128/jb.00314-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/07/2019] [Indexed: 11/20/2022] Open
Abstract
Salmonella virulence requires the initial invasion of host cells, followed by modulation of the intracellular environment for survival and replication. In an effort to characterize the role of small RNAs in Salmonella pathogenesis, we inadvertently identified a 5-kDa protein named YshB that is involved in the intracellular survival of Salmonella We show here that yshB expression is upregulated upon entry into macrophages. When yshB expression is upregulated before bacterial entry, invasion efficiency is inhibited. Lack of YshB resulted in reduced bacterial survival within the macrophages and led to reduced virulence in a mouse model of infection.IMPORTANCE Salmonella gastroenteritis is one of the most common causes of foodborne disease, possibly affecting millions of people globally each year. Here we characterize the role of a novel small protein, YshB, in mediating Salmonella intracellular survival. This elucidation adds to the body of knowledge regarding how this bacterium achieves intracellular survival.
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Zhang K, Riba A, Nietschke M, Torow N, Repnik U, Pütz A, Fulde M, Dupont A, Hensel M, Hornef M. Minimal SPI1-T3SS effector requirement for Salmonella enterocyte invasion and intracellular proliferation in vivo. PLoS Pathog 2018. [PMID: 29522566 PMCID: PMC5862521 DOI: 10.1371/journal.ppat.1006925] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Effector molecules translocated by the Salmonella pathogenicity island (SPI)1-encoded type 3 secretion system (T3SS) critically contribute to the pathogenesis of human Salmonella infection. They facilitate internalization by non-phagocytic enterocytes rendering the intestinal epithelium an entry site for infection. Their function in vivo has remained ill-defined due to the lack of a suitable animal model that allows visualization of intraepithelial Salmonella. Here, we took advantage of our novel neonatal mouse model and analyzed various bacterial mutants and reporter strains as well as gene deficient mice. Our results demonstrate the critical but redundant role of SopE2 and SipA for enterocyte invasion, prerequisite for transcriptional stimulation and mucosal translocation in vivo. In contrast, the generation of a replicative intraepithelial endosomal compartment required the cooperative action of SipA and SopE2 or SipA and SopB but was independent of SopA or host MyD88 signaling. Intraepithelial growth had no critical influence on systemic spread. Our results define the role of SPI1-T3SS effector molecules during enterocyte invasion and intraepithelial proliferation in vivo providing novel insight in the early course of Salmonella infection. Non-typhoidal Salmonella represent a major causative agent of gastroenteritis worldwide. Hallmark of the pathogenesis is their ability to actively invade the intestinal epithelium by virtue of their type 3 secretion system that delivers bacterial virulence factors directly into the host cell cytosol. The role of these virulence factors during enterocyte entry and intraepithelial growth has only been investigated in vitro since the previously established in vivo models in small animals did not allow visualization of intraepithelial Salmonella. However, immortalized cell lines lack the overlaying mucus layer, final cell lineage differentiation, apical-basolateral polarization as well as continuous migration along the crypt villus axis and thus the role of virulence factors during the Salmonella infection in vivo has remained largely undefined. Here, we took advantage of our novel neonatal mouse infection model and for the first time systematically analyzed the importance of Salmonella virulence factors for enterocyte invasion and intraepithelial growth.
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Affiliation(s)
- Kaiyi Zhang
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Ambre Riba
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Monika Nietschke
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Natalia Torow
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Urska Repnik
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Andreas Pütz
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Marcus Fulde
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Aline Dupont
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Michael Hensel
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Mathias Hornef
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
- * E-mail:
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Keestra-Gounder AM, Tsolis RM. NOD1 and NOD2: Beyond Peptidoglycan Sensing. Trends Immunol 2017; 38:758-767. [PMID: 28823510 DOI: 10.1016/j.it.2017.07.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 02/06/2023]
Abstract
NOD1 and NOD2 are pattern recognition receptors of the innate immune system with well-established roles in sensing fragments of bacterial peptidoglycan. In addition to their role as microbial sensors, recent evidence indicates that nucleotide-binding oligomerization domains (NODs) can also recognize a broader array of danger signals. Indeed, recent work has expanded the roles of NOD1 and NOD2 to encompass not only sensing of infections with viruses and parasites but also perceiving perturbations of cellular processes such as regulation of the actin cytoskeleton and maintenance of endoplasmic reticulum homeostasis. This review will comment on recent progress and point out emerging questions in these areas.
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Affiliation(s)
| | - Renée M Tsolis
- Department of Medical Microbiology and Immunology, University of California at Davis, School of Medicine, Davis, CA USA.
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Young AM, Palmer AE. Methods to Illuminate the Role of Salmonella Effector Proteins during Infection: A Review. Front Cell Infect Microbiol 2017; 7:363. [PMID: 28848721 PMCID: PMC5554337 DOI: 10.3389/fcimb.2017.00363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 07/27/2017] [Indexed: 12/19/2022] Open
Abstract
Intracellular bacterial pathogens like Salmonella enterica use secretion systems, such as the Type III Secretion System, to deliver virulence factors into host cells in order to invade and colonize these cells. Salmonella virulence factors include a suite of effector proteins that remodel the host cell to facilitate bacterial internalization, replication, and evasion of host immune surveillance. A number of diverse and innovative approaches have been used to identify and characterize the role of effector proteins during infection. Recent techniques for studying infection using single cell and animal models have illuminated the contribution of individual effector proteins in infection. This review will highlight the techniques applied to study Salmonella effector proteins during infection. It will describe how different approaches have revealed mechanistic details for effectors in manipulating host cellular processes including: the dynamics of effector translocation into host cells, cytoskeleton reorganization, membrane trafficking, gene regulation, and autophagy.
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Affiliation(s)
- Alexandra M Young
- Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado BoulderBoulder, CO, United States
| | - Amy E Palmer
- Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado BoulderBoulder, CO, United States
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InvS Coordinates Expression of PrgH and FimZ and Is Required for Invasion of Epithelial Cells by Salmonella enterica serovar Typhimurium. J Bacteriol 2017; 199:JB.00824-16. [PMID: 28439039 DOI: 10.1128/jb.00824-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/20/2017] [Indexed: 11/20/2022] Open
Abstract
Deep sequencing has revolutionized our understanding of the bacterial RNA world and has facilitated the identification of 280 small RNAs (sRNAs) in Salmonella Despite the suspicions that sRNAs may play important roles in Salmonella pathogenesis, the functions of most sRNAs remain unknown. To advance our understanding of RNA biology in Salmonella virulence, we searched for sRNAs required for bacterial invasion into nonphagocytic cells. After screening 75 sRNAs, we discovered that the ablation of InvS caused a significant decrease of Salmonella invasion into epithelial cells. A proteomic analysis showed that InvS modulated the levels of several type III secreted Salmonella proteins. The level of PrgH, a type III secretion apparatus protein, was significantly lower in the absence of InvS, consistent with the known roles of PrgH in effector secretion and bacterial invasion. We discovered that InvS modulates fimZ expression and hence flagellar gene expression and motility. We propose that InvS coordinates the increase of PrgH and decrease in FimZ that promote efficient Salmonella invasion into nonphagocytic cells.IMPORTANCE Salmonellosis continues to be the most common foodborne infection reported by the CDC in the United States. Central to Salmonella pathogenesis is the ability to invade nonphagocytic cells and to replicate inside host cells. Invasion genes are known to be regulated by protein transcriptional networks, but little is known about the role played by small RNAs (sRNAs) in this process. We have identified a novel sRNA, InvS, that is involved in Salmonella invasion. Our result will likely provide an opportunity to better understand the fundamental question of how Salmonella regulates invasion gene expression and may inform strategies for therapeutic intervention.
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Lhocine N, Arena ET, Bomme P, Ubelmann F, Prévost MC, Robine S, Sansonetti PJ. Apical invasion of intestinal epithelial cells by Salmonella typhimurium requires villin to remodel the brush border actin cytoskeleton. Cell Host Microbe 2015; 17:164-77. [PMID: 25600187 PMCID: PMC4346658 DOI: 10.1016/j.chom.2014.12.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 09/16/2014] [Accepted: 12/04/2014] [Indexed: 01/16/2023]
Abstract
Salmonella invasion of intestinal epithelial cells requires extensive, though transient, actin modifications at the site of bacterial entry. The actin-modifying protein villin is present in the brush border where it participates in the constitution of microvilli and in epithelial restitution after damage through its actin-severing activity. We investigated a possible role for villin in Salmonella invasion. The absence of villin, which is normally located at the bacterial entry site, leads to a decrease in Salmonella invasion. Villin is necessary for early membrane-associated processes and for optimal ruffle assembly by balancing the steady-state level of actin. The severing activity of villin is important for Salmonella invasion in vivo. The bacterial phosphatase SptP tightly regulates villin phosphorylation, while the actin-binding effector SipA protects F-actin and counterbalances villin-severing activity. Thus, villin plays an important role in establishing the balance between actin polymerization and actin severing to facilitate the initial steps of Salmonella entry. The host actin-binding protein villin is required for Salmonella apical invasion Villin plays a role in Salmonella ruffle formation and actin dynamics Villin-severing activity promotes Salmonella invasion in cells and in vivo The bacterial effectors SipA and SptP regulate villin activities
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Affiliation(s)
- Nouara Lhocine
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France; INSERM U786, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - Ellen T Arena
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France; INSERM U786, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - Perrine Bomme
- Plateforme de Microscopie Ultrastructurale, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - Florent Ubelmann
- Unité Mixte de Recherche 144, Institut Curie, 75248 Paris Cedex 05, France; Centro de Estudos de Doenças Crónicas (CEDOC), Faculdade de Ciencias Médicas, Universidade Nova de Lisboa, 1169-056, Portugal
| | - Marie-Christine Prévost
- Plateforme de Microscopie Ultrastructurale, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - Sylvie Robine
- Unité Mixte de Recherche 144, Institut Curie, 75248 Paris Cedex 05, France
| | - Philippe J Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France; INSERM U786, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France; Collège de France, 11 Place Marcelin Berthelot, 75005 Paris, France.
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