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Gurung JM, Amer AAA, Chen S, Diepold A, Francis MS. Type III secretion by Yersinia pseudotuberculosis is reliant upon an authentic N-terminal YscX secretor domain. Mol Microbiol 2022; 117:886-906. [PMID: 35043994 PMCID: PMC9303273 DOI: 10.1111/mmi.14880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
Abstract
YscX was discovered as an essential part of the Yersinia type III secretion system about 20 years ago. It is required for substrate secretion and is exported itself. Despite this central role, its precise function and mode of action remains unknown. In order to address this knowledge gap, this present study refocused attention on YscX to build on the recent advances in the understanding of YscX function. Our experiments identified a N-terminal secretion domain in YscX promoting its secretion, with the first five codons constituting a minimal signal capable of promoting secretion of the signalless β-lactamase reporter. Replacing the extreme YscX N-terminus with known secretion signals of other Ysc-Yop substrates revealed that the YscX N-terminal segment contains non-redundant information needed for YscX function. Further, both in cis deletion of the YscX N-terminus in the virulence plasmid and ectopic expression of epitope tagged YscX variants again lead to stable YscX production but not type III secretion of Yop effector proteins. Mislocalisation of the needle components, SctI and SctF, accompanied this general defect in Yops secretion. Hence, a coupling exists between YscX secretion permissiveness and the assembly of an operational secretion system.
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Affiliation(s)
- Jyoti M Gurung
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Ayad A A Amer
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Shiyun Chen
- Wuhan Institute of Virology, The Chinese Academy of Sciences, Wuhan, China
| | - Andreas Diepold
- Max Planck Institute for Terrestrial Microbiology, Department of Ecophysiology, Marburg, Germany
| | - Matthew S Francis
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
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2
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Umrekar TR, Cohen E, Drobnič T, Gonzalez-Rodriguez N, Beeby M. CryoEM of bacterial secretion systems: A primer for microbiologists. Mol Microbiol 2020; 115:366-382. [PMID: 33140482 DOI: 10.1111/mmi.14637] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
"CryoEM" has come of age, enabling considerable structural insights into many facets of molecular biology. Here, we present a primer for microbiologists to understand the capabilities and limitations of two complementary cryoEM techniques for studying bacterial secretion systems. The first, single particle analysis, determines the structures of purified protein complexes to resolutions sufficient for molecular modeling, while the second, electron cryotomography and subtomogram averaging, tends to determine more modest resolution structures of protein complexes in intact cells. We illustrate these abilities with examples of insights provided into how secretion systems work by cryoEM, with a focus on type III secretion systems.
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Affiliation(s)
| | - Eli Cohen
- Department of Life Sciences, Imperial College London, London, UK
| | - Tina Drobnič
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, UK
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3
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Muthuramalingam M, Middaugh CR, Picking WD. The cytoplasmic portion of the T3SS inner membrane ring components sort into distinct families based on biophysical properties. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:787-793. [PMID: 31195141 DOI: 10.1016/j.bbapap.2019.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/04/2019] [Accepted: 06/07/2019] [Indexed: 11/30/2022]
Abstract
Type III secretion systems are used by many Gram-negative bacteria to inject effector proteins into eukaryotic cells to subvert their normal activities. Structurally conserved portions of the type III secretion apparatus include a: basal body located within the bacterial envelope; an exposed needle with tip complex that delivers effectors across the target cell membrane; and cytoplasmic sorting platform that selects cargo and powers secretion. While structurally conserved, the individual proteins that make up this nanomachine are typically not interchangeable though they do tend to fall into families. Here we selected a single domain from the inner membrane ring of the basal body from six different type III secretion systems (called SctD using a proposed unifying nomenclature). The selected domain creates an integral interface between the basal body and the sorting platform. Therefore, it represents a pivotal point between two distinct assemblies. All six protein domains possess a structural motif called a forkhead-associated-like (FHA-like) domain but differ greatly in their sequences and solution behaviors. These differences are used here to define family boundaries for these FHA-like domains. The data parallel, though not precisely, family boundaries defined by other proteins within the apparatus and by phylogenetic analysis. Ultimately, differences in the families are likely to reflect differences in the activities of these type III secretion systems or the host niches in which these pathogens are found.
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Affiliation(s)
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, United States of America
| | - William D Picking
- Higuchi Biosciences Center, University of Kansas, Lawrence, KS 66047, United States of America; Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, United States of America.
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4
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Abstract
Type III secretion systems (T3SSs) afford Gram-negative bacteria an intimate means of altering the biology of their eukaryotic hosts--the direct delivery of effector proteins from the bacterial cytoplasm to that of the eukaryote. This incredible biophysical feat is accomplished by nanosyringe "injectisomes," which form a conduit across the three plasma membranes, peptidoglycan layer, and extracellular space that form a barrier to the direct delivery of proteins from bacterium to host. The focus of this chapter is T3SS function at the structural level; we will summarize the core findings that have shaped our understanding of the structure and function of these systems and highlight recent developments in the field. In turn, we describe the T3SS secretory apparatus, consider its engagement with secretion substrates, and discuss the posttranslational regulation of secretory function. Lastly, we close with a discussion of the future prospects for the interrogation of structure-function relationships in the T3SS.
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5
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Abrusci P, McDowell MA, Lea SM, Johnson S. Building a secreting nanomachine: a structural overview of the T3SS. Curr Opin Struct Biol 2014; 25:111-7. [PMID: 24704748 PMCID: PMC4045390 DOI: 10.1016/j.sbi.2013.11.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/05/2013] [Accepted: 11/06/2013] [Indexed: 12/21/2022]
Abstract
To fulfill complex biological tasks, such as locomotion and protein translocation, bacteria assemble macromolecular nanomachines. One such nanodevice, the type III secretion system (T3SS), has evolved to provide a means of transporting proteins from the bacterial cytoplasm across the periplasmic and extracellular spaces. T3SS can be broadly classified into two highly homologous families: the flagellar T3SS which drive cell motility, and the non-flagellar T3SS (NF-T3SS) that inject effector proteins into eukaryotic host cells, a trait frequently associated with virulence. Although the structures and symmetries of ancillary components of the T3SS have diversified to match requirements of different species adapted to different niches, recent genetic, molecular and structural studies demonstrate that these systems are built by arranging homologous modular protein assemblies.
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Affiliation(s)
- Patrizia Abrusci
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Melanie A McDowell
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Susan M Lea
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, United Kingdom.
| | - Steven Johnson
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, United Kingdom
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6
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Burkinshaw BJ, Strynadka NCJ. Assembly and structure of the T3SS. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1649-63. [PMID: 24512838 DOI: 10.1016/j.bbamcr.2014.01.035] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/27/2014] [Accepted: 01/29/2014] [Indexed: 02/06/2023]
Abstract
The Type III Secretion System (T3SS) is a multi-mega Dalton apparatus assembled from more than twenty components and is found in many species of animal and plant bacterial pathogens. The T3SS creates a contiguous channel through the bacterial and host membranes, allowing injection of specialized bacterial effector proteins directly to the host cell. In this review, we discuss our current understanding of T3SS assembly and structure, as well as highlight structurally characterized Salmonella effectors. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Brianne J Burkinshaw
- Department of Biochemistry and Molecular Biology, Center for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, Center for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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Barison N, Gupta R, Kolbe M. A sophisticated multi-step secretion mechanism: how the type 3 secretion system is regulated. Cell Microbiol 2013; 15:1809-17. [PMID: 23927570 DOI: 10.1111/cmi.12178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 11/28/2022]
Abstract
Many Gram-negative pathogens utilize type 3 secretion systems (T3SSs) for a successful infection. The T3SS is a large macromolecular complex which spans both bacterial membranes and delivers effector proteins into the host cell. The infection requires spatiotemporal control of diverse sets of secreted effectors and various mechanisms have evolved to regulate T3SS in response to external stimuli. This review will describe mechanisms that may control type 3 secretion, revealing a multi-step regulatory strategy. We then propose an updated model of T3SS that illustrates different stages of secretion and integrates the most recent structural and functional data.
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Affiliation(s)
- Nicola Barison
- Max-Planck-Institute for Infection Biology, Cellular Microbiology, Charitéplatz 1, 10117, Berlin, Germany
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Kudryashev M, Stenta M, Schmelz S, Amstutz M, Wiesand U, Castaño-Díez D, Degiacomi MT, Münnich S, Bleck CK, Kowal J, Diepold A, Heinz DW, Dal Peraro M, Cornelis GR, Stahlberg H. In situ structural analysis of the Yersinia enterocolitica injectisome. eLife 2013; 2:e00792. [PMID: 23908767 PMCID: PMC3728920 DOI: 10.7554/elife.00792] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/27/2013] [Indexed: 12/20/2022] Open
Abstract
Injectisomes are multi-protein transmembrane machines allowing pathogenic bacteria to
inject effector proteins into eukaryotic host cells, a process called type III
secretion. Here we present the first three-dimensional structure of Yersinia
enterocolitica and Shigella flexneri injectisomes in
situ and the first structural analysis of the Yersinia injectisome.
Unexpectedly, basal bodies of injectisomes inside the bacterial cells showed length
variations of 20%. The in situ structures of the Y. enterocolitica
and S. flexneri injectisomes had similar dimensions and were
significantly longer than the isolated structures of related injectisomes. The
crystal structure of the inner membrane injectisome component YscD appeared elongated
compared to a homologous protein, and molecular dynamics simulations documented its
elongation elasticity. The ring-shaped secretin YscC at the outer membrane was
stretched by 30–40% in situ, compared to its isolated liposome-embedded
conformation. We suggest that elasticity is critical for some two-membrane spanning
protein complexes to cope with variations in the intermembrane distance. DOI:http://dx.doi.org/10.7554/eLife.00792.001 Humans and other animals can use the five senses—touch, taste, sight, smell,
and hearing—to interpret the world around them. Single-celled organisms,
however, must rely on molecular cues to understand their immediate surroundings. In
particular, bacteria gather information about external conditions, including
potential hosts nearby, by secreting protein sensors that can relay messages back to
the cell. Bacteria export these sensors via secretion systems that enable the organism both to
receive information about the environment and to invade a host cell. A total of seven
separate secretion systems, known as types I–VII, have been identified. These
different secretion systems handle distinct cargoes, allowing the bacterial cell to
respond to a range of feedback from the external milieu. The type III secretion system, also known as the ‘injectisome’, is
found in bacterial species that are enclosed by two membranes separated by a
periplasmic space. The injectisome comprises different components that combine to
form the basal body, which spans the inner and outer membranes, and a projection from
the basal body, called the hollow needle, that mediates the export of cargo from a
bacterium to its host or the local environment. The distance between the inner and outer membranes may vary across species or
according to environmental conditions, so the basal body must be able to accommodate
these changes. However, no mechanism has yet been established that might introduce
such elasticity into the injectisome. Now, Kudryashev et al. have generated
three-dimensional structures for the injectisomes of two species of bacteria,
Shigella flexneri and Yersinia enterocolitica,
and shown that the size of the basal body can fluctuate by up to 20%. Kudryashev et al. imaged whole injectisomes in these two species and found that the
height of the basal body was proportional to the distance between the inner and outer
membranes. To probe how this could occur, the properties of two proteins that are
important components of the basal body were studied in greater detail. YscD, a
protein that extends across the periplasmic space, was crystallized and its structure
was then determined and used to develop a computer model to assess its
compressibility: this model indicated that YscD could stretch or contract by up to
50% of its total length. The outer membrane component YscC also appeared elastic:
when the protein was isolated and introduced into synthetic membranes, its length was
reduced 30–40% relative to that observed in intact bacterial membranes. A further experiment confirmed the adaptability of the basal body: when the
separation of the membranes was deliberately increased by placing bacteria in a
high-salt medium, the basal body extended approximately 10% in length. Cumulatively,
therefore, these experiments suggest that the in-built flexibility of the basal body
of the injectisome allows bacteria to adjust to environmental changes while
maintaining their sensory abilities and host-invasion potential. DOI:http://dx.doi.org/10.7554/eLife.00792.002
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Affiliation(s)
- Mikhail Kudryashev
- Center for Cellular Imaging and NanoAnalytics (C-CINA) , Biozentrum, University of Basel , Basel , Switzerland
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9
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Bergeron JRC, Worrall LJ, Sgourakis NG, DiMaio F, Pfuetzner RA, Felise HB, Vuckovic M, Yu AC, Miller SI, Baker D, Strynadka NCJ. A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly. PLoS Pathog 2013; 9:e1003307. [PMID: 23633951 PMCID: PMC3635987 DOI: 10.1371/journal.ppat.1003307] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 03/02/2013] [Indexed: 12/22/2022] Open
Abstract
The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed of a “basal body”, a lock-nut structure spanning both bacterial membranes, and a “needle” that protrudes away from the bacterial surface. A hollow channel spans throughout the apparatus, permitting the translocation of effector proteins from the bacterial cytosol to the host plasma membrane. The basal body is composed largely of three membrane-embedded proteins that form oligomerized concentric rings. Here, we report the crystal structures of three domains of the prototypical Salmonella SPI-1 basal body, and use a new approach incorporating symmetric flexible backbone docking and EM data to produce a model for their oligomeric assembly. The obtained models, validated by biochemical and in vivo assays, reveal the molecular details of the interactions driving basal body assembly, and notably demonstrate a conserved oligomerization mechanism. Gram-negative bacteria such as E. coli, Salmonella, Shigella, Pseudomonas aeruginosa, and Yersinia pestis are responsible for a wide range of diseases, from pneumonia to lethal diarrhea and plague. A common trait shared by these bacteria is their capacity to inject toxins directly inside the cells of infected individuals, thanks to a syringe-shaped “nano-machine” called the Type III Secretion System injectisome. These toxins lead to modifications of the host cell, allowing the bacteria to replicate efficiently and/or to evade the immune system, and are necessary to establish an infection. As a consequence, the injectisome is an important potential target for the development of novel therapeutics against bacterial infection. In this study, we focus on the basal body, an essential region of the injectisome that forms the continuous hollow channel across both membranes of the bacteria. We have used an array of biophysical methods to obtain an atomic model of the basal body. This model provides new insights as to how the basal body assembles at the surface of bacteria, and could be used for the design of novel antibiotics.
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Affiliation(s)
- Julien R. C. Bergeron
- Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nikolaos G. Sgourakis
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Richard A. Pfuetzner
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Heather B. Felise
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angel C. Yu
- Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel I. Miller
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
- * E-mail: (DB); (NCJS)
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology, and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail: (DB); (NCJS)
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10
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Protein export according to schedule: architecture, assembly, and regulation of type III secretion systems from plant- and animal-pathogenic bacteria. Microbiol Mol Biol Rev 2012; 76:262-310. [PMID: 22688814 DOI: 10.1128/mmbr.05017-11] [Citation(s) in RCA: 304] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Flagellar and translocation-associated type III secretion (T3S) systems are present in most gram-negative plant- and animal-pathogenic bacteria and are often essential for bacterial motility or pathogenicity. The architectures of the complex membrane-spanning secretion apparatuses of both systems are similar, but they are associated with different extracellular appendages, including the flagellar hook and filament or the needle/pilus structures of translocation-associated T3S systems. The needle/pilus is connected to a bacterial translocon that is inserted into the host plasma membrane and mediates the transkingdom transport of bacterial effector proteins into eukaryotic cells. During the last 3 to 5 years, significant progress has been made in the characterization of membrane-associated core components and extracellular structures of T3S systems. Furthermore, transcriptional and posttranscriptional regulators that control T3S gene expression and substrate specificity have been described. Given the architecture of the T3S system, it is assumed that extracellular components of the secretion apparatus are secreted prior to effector proteins, suggesting that there is a hierarchy in T3S. The aim of this review is to summarize our current knowledge of T3S system components and associated control proteins from both plant- and animal-pathogenic bacteria.
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Structure and interactions of the cytoplasmic domain of the Yersinia type III secretion protein YscD. J Bacteriol 2012; 194:5949-58. [PMID: 22942247 DOI: 10.1128/jb.00513-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The virulence of a large number of Gram-negative bacterial pathogens depends on the type III secretion (T3S) system, which transports select bacterial proteins into host cells. An essential component of the Yersinia T3S system is YscD, a single-pass inner membrane protein. We report here the 2.52-Å resolution structure of the cytoplasmic domain of YscD, called YscDc. The structure confirms that YscDc consists of a forkhead-associated (FHA) fold, which in many but not all cases specifies binding to phosphothreonine. YscDc, however, lacks the structural properties associated with phosphothreonine binding and thus most likely interacts with partners in a phosphorylation-independent manner. Structural comparison highlighted two loop regions, L3 and L4, as potential sites of interactions. Alanine substitutions at L3 and L4 had no deleterious effects on protein structure or stability but abrogated T3S in a dominant negative manner. To gain insight into the function of L3 and L4, we identified proteins associated with YscD by affinity purification coupled to mass spectrometry. The lipoprotein YscJ was found associated with wild-type YscD, as was the effector YopH. Notably, the L3 and L4 substitution mutants interacted with more YopH than did wild-type YscD. These substitution mutants also interacted with SycH (the specific chaperone for YopH), the putative C-ring component YscQ, and the ruler component YscP, whereas wild-type YscD did not. These results suggest that substitutions in the L3 and L4 loops of YscD disrupted the dissociation of SycH from YopH, leading to the accumulation of a large protein complex that stalled the T3S apparatus.
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