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Ochoa JM, Mijares O, Acosta AA, Escoto X, Leon-Rivera N, Marshall JD, Sawaya MR, Yeates TO. Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments. Acta Crystallogr F Struct Biol Commun 2021; 77:275-285. [PMID: 34473104 PMCID: PMC8411931 DOI: 10.1107/s2053230x21007470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/21/2021] [Indexed: 11/08/2023] Open
Abstract
Bacterial microcompartments are large supramolecular structures comprising an outer proteinaceous shell that encapsulates various enzymes in order to optimize metabolic processes. The outer shells of bacterial microcompartments are made of several thousand protein subunits, generally forming hexameric building blocks based on the canonical bacterial microcompartment (BMC) domain. Among the diverse metabolic types of bacterial microcompartments, the structures of those that use glycyl radical enzymes to metabolize choline have not been adequately characterized. Here, six structures of hexameric shell proteins from type I and type II choline-utilization microcompartments are reported. Sequence and structure analysis reveals electrostatic surface properties that are shared between the four types of shell proteins described here.
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Affiliation(s)
- Jessica M. Ochoa
- UCLA Molecular Biology Institute, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Oscar Mijares
- Whittier College, 13406 East Philadelphia Street, Whittier, CA 90602, USA
| | - Andrea A. Acosta
- Whittier College, 13406 East Philadelphia Street, Whittier, CA 90602, USA
| | - Xavier Escoto
- Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Nancy Leon-Rivera
- Whittier College, 13406 East Philadelphia Street, Whittier, CA 90602, USA
| | - Joanna D. Marshall
- Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- UCLA–DOE Institute of Genomics and Proteomics, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Todd O. Yeates
- UCLA Molecular Biology Institute, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- UCLA–DOE Institute of Genomics and Proteomics, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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Tomoyasu T, Tabata A, Imaki H, Tsuruno K, Miyazaki A, Sonomoto K, Whiley RA, Nagamune H. Role of Streptococcus intermedius DnaK chaperone system in stress tolerance and pathogenicity. Cell Stress Chaperones 2012; 17:41-55. [PMID: 21822788 PMCID: PMC3227844 DOI: 10.1007/s12192-011-0284-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 07/04/2011] [Accepted: 07/13/2011] [Indexed: 01/13/2023] Open
Abstract
Streptococcus intermedius is a facultatively anaerobic, opportunistic pathogen that causes purulent infections and abscess formation. The DnaK chaperone system has been characterized in several pathogenic bacteria and seems to have important functions in stress resistance and pathogenicity. However, the role of DnaK in S. intermedius remains unclear. Therefore, we constructed a dnaK knockout mutant that exhibited slow growth, thermosensitivity, accumulation of GroEL in the cell, and reduced cytotoxicity to HepG2 cells. The level of secretion of a major pathogenic factor, intermedilysin, was not affected by dnaK mutation. We further examined the function and property of the S. intermedius DnaK chaperone system by using Escherichia coli ΔdnaK and ΔrpoH mutant strains. S. intermedius DnaK could not complement the thermosensitivity of E. coli ΔdnaK mutant. However, the intact S. intermedius DnaK chaperone system could complement the thermosensitivity and acid sensitivity of E. coli ΔdnaK mutant. The S. intermedius DnaK chaperone system could regulate the activity and stability of the heat shock transcription factor σ(32) in E. coli, although S. intermedius does not utilize σ(32) for heat shock transcription. The S. intermedius DnaK chaperone system was also able to efficiently eliminate the aggregated proteins from ΔrpoH mutant cells. Overall, our data showed that the S. intermedius DnaK chaperone system has important functions in quality control of cellular proteins but has less participation in the modulation of expression of pathogenic factors.
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Affiliation(s)
- Toshifumi Tomoyasu
- Department of Biological Science and Technology, Institute of Technology and Science, The University of Tokushima Graduate School, 2 chome, Minami-josanjima, Tokushima, 770-8506 Japan
- Department of Resource Circulation Engineering, Center for Frontier Research of Engineering, The University of Tokushima Graduate School, 2 chome, Minami-josanjima, Tokushima, 770-8506 Japan
| | - Atsushi Tabata
- Department of Biological Science and Technology, Institute of Technology and Science, The University of Tokushima Graduate School, 2 chome, Minami-josanjima, Tokushima, 770-8506 Japan
| | - Hidenori Imaki
- Department of Biological Science and Technology, Institute of Technology and Science, The University of Tokushima Graduate School, 2 chome, Minami-josanjima, Tokushima, 770-8506 Japan
| | - Keigo Tsuruno
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Aya Miyazaki
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Kenji Sonomoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Robert Alan Whiley
- Department of Clinical and Diagnostic Oral Sciences, Institute of Dentistry, Bart’s and The London School of Medicine and Dentistry, Queen Mary University of London, Turner Street, London, E1 2 AD UK
| | - Hideaki Nagamune
- Department of Biological Science and Technology, Institute of Technology and Science, The University of Tokushima Graduate School, 2 chome, Minami-josanjima, Tokushima, 770-8506 Japan
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Liu D, Yumoto H, Murakami K, Hirota K, Kayama S, Taniguchi T, Yamamoto A, Ono T, Matsuo T, Miyake Y. Heterologous expression ofa histone-like protein from Streptococcus intermedius in Escherichia coli alters the nucleoid structure and inhibits the growth of E. coli. FEMS Microbiol Lett 2008; 288:68-75. [PMID: 18761672 DOI: 10.1111/j.1574-6968.2008.01327.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Escherichia coli failed to survive after transformation with a Streptococcus intermedius histone-like protein gene (Si-hlp) and its promoter-harbored plasmid. The promoter function of Si-hlp in E. coli was determined using enhanced green fluorescence protein (egfp) gene as a reporter. The inhibitory effect of Si-HLP on E. coli viability was verified by a tetracycline-inducible gene expression system. Further study suggested that Si-HLP may alter the bacterial nucleoid structure, leading to the growth inhibition of E. coli.
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Heuck AP, Savva CG, Holzenburg A, Johnson AE. Conformational changes that effect oligomerization and initiate pore formation are triggered throughout perfringolysin O upon binding to cholesterol. J Biol Chem 2007; 282:22629-37. [PMID: 17553799 DOI: 10.1074/jbc.m703207200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pore formation by the cholesterol-dependent cytolysins (CDCs) requires the presence of cholesterol in the target membrane. Cholesterol was long thought to be the cellular receptor for these toxins, but not all CDCs require cholesterol for binding. Intermedilysin, secreted by Streptococcus intermedius, only binds to membranes containing the human protein CD59 but forms pores only if the membrane contains sufficient cholesterol. In contrast, perfringolysin O (PFO), secreted by Clostridium perfringens, only binds to membranes containing substantial amounts of cholesterol. Given that different steps in the assembly of various CDC pores require cholesterol, here we have analyzed to what extent cholesterol molecules, by themselves, can modulate the conformational changes associated with PFO oligomerization and pore formation. PFO binds to cholesterol when dispersed in aqueous solution, and this binding triggers the distant rearrangement of a beta-strand that exposes an oligomerization interface. Moreover, upon binding to cholesterol, PFO forms a prepore complex, unfolds two amphipathic transmembrane beta-hairpins, and positions their nonpolar surfaces so they associate with the hydrophobic cholesterol surface. The interaction of PFO with cholesterol is therefore sufficient to initiate an irreversible sequence of coupled conformational changes that extend throughout the toxin molecule.
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Affiliation(s)
- Alejandro P Heuck
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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Soltani CE, Hotze EM, Johnson AE, Tweten RK. Specific protein-membrane contacts are required for prepore and pore assembly by a cholesterol-dependent cytolysin. J Biol Chem 2007; 282:15709-16. [PMID: 17412689 PMCID: PMC3746338 DOI: 10.1074/jbc.m701173200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Three short hydrophobic loops and a conserved undecapeptide at the tip of domain 4 (D4) of the cholesterol-dependent cytolysins (CDCs) mediate the binding of the CDC monomers to cholesterol-rich cell membranes. But intermedilysin (ILY), from Streptococcus intermedius, does not bind to cholesterol-rich membranes unless they contain the human protein CD59. This observation suggested that the D4 loops, which include loops L1-L3 and the undecapeptide, of ILY were no longer required for its cell binding. However, we show here that membrane insertion of the D4 loops is required for the cytolysis by ILY. Receptor binding triggers changes in the structure of ILY that are necessary for oligomerization, but membrane insertion of the D4 loops is critical for oligomer assembly and pore formation. Defects that prevent membrane insertion of the undecapeptide also block assembly of the prepore oligomer, while defects in the membrane insertion of the L1-L3 loops prevent the conversion of the prepore oligomer to the pore complex. These studies reveal that pore formation by ILY, and probably other CDCs, is affected by an intricate and coupled sequence of interactions between domain 4 and the membrane.
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Affiliation(s)
- Casie E. Soltani
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104
| | - Eileen M. Hotze
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104
| | - Arthur E. Johnson
- Department of Molecular and Cellular Medicine, Texas A&M University System Health Science Center, College Station, Texas 77843-1114
- Departments of Chemistry and of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Rodney K. Tweten
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104
- To whom correspondence should be addressed: Microbiology & Immunology, BMSB-1053, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104. Tel.: 405-271-1205; Fax: 405-271-3117;
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Taylor MB, Oh JHL, Kang KL, Chow VTK. Intermedilysin release byStreptococcus intermedius: effects of various antibacterial drugs at sub-MIC levels. FEMS Microbiol Lett 2005; 243:379-84. [PMID: 15686838 DOI: 10.1016/j.femsle.2004.12.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Revised: 12/19/2004] [Accepted: 12/24/2004] [Indexed: 11/22/2022] Open
Abstract
Intermedilysin is a cytolytic toxin produced by Streptococcus intermedius, a pathogen of humans. In vitro studies showed that exposure of S. intermedius to sub-minimum inhibitory concentration (MIC) levels (1/2 MIC) of protein-inhibiting antibiotics and nucleic acid-inhibiting antibiotics decreased intermedilysin release by S. intermedius. The most potent antibiotic was clindamycin. On the other hand, exposure to cell wall-inhibiting antibiotics generally showed insignificant changes in intermedilysin release at sub-MIC concentrations. Investigations into possible mechanisms underlying this sub-MIC effect with clindamycin showed that there was selective decrease in biosynthesis and release of toxin after exposure to 1/2 MIC condition. However, no significant differences in the mRNA levels of the intermedilysin gene were observed.
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Affiliation(s)
- Mark B Taylor
- Department of Microbiology, National University of Singapore, Blk MD4, 5 Science Drive 2, Singapore 117597, Singapore.
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Nagamune H, Ohkura K, Sukeno A, Cowan G, Mitchell TJ, Ito W, Ohnishi O, Hattori K, Yamato M, Hirota K, Miyake Y, Maeda T, Kourai H. The human-specific action of intermedilysin, a homolog of streptolysin O, is dictated by domain 4 of the protein. Microbiol Immunol 2005; 48:677-92. [PMID: 15383705 DOI: 10.1111/j.1348-0421.2004.tb03479.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Intermedilysin is a pore-forming cytolysin belonging to the streptolysin O gene family known as the 'Cholesterol-binding/dependent cytolysins' and is unique within the family in that it is highly humanspecific. This specificity suggests interaction with a component of human cells other than cholesterol, the proposed receptor for the other toxins of the gene family. Indeed, intermedilysin showed no significant degree of affinity to free or liposome-embedded cholesterol. Characterization of intermedilysin undecapeptide mutants revealed that this lack of affinity to cholesterol was a result of the substitutions of intermedilysin in this region. Absorption assays with erythrocyte membranes from various animals, competitive inhibition with domain 4 of intermedilysin and liposome-binding assays of streptolysin O and intermedilysin indicated that cell membrane binding is the human-specific step of intermedilysin action, that the host cell membrane-binding site is located within domain 4 in common with other members of the family and that the receptor for this toxin is not cholesterol. The species specificity of undecapeptide mutants of intermedilysin and streptolysin O and chimeric mutants between intermedilysin and streptolysin O, and intermedilysin and pneumolysin indicated that domain 4 of intermedilysin determines the human-specific action step and the cell-binding site of domain 4 lies within the 56 amino acids of the C-terminal, excluding the undecapeptide region.
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Affiliation(s)
- Hideaki Nagamune
- Department of Biological Science and Technology, Faculty of Engineering, The University of Tokushima, #1, 2-chrome, Minamijosanjima-cho, Tokushima, Tokushima 770-8506, Japan.
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Otten JE, Wiedmann-Al-Ahmad M, Jahnke H, Pelz K. Bacterial colonization on different suture materials—A potential risk for intraoral dentoalveolar surgery. J Biomed Mater Res B Appl Biomater 2005; 74:627-35. [PMID: 15889436 DOI: 10.1002/jbm.b.30250] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this in vivo and in vitro study on resorbable (Monocryl and nonresorbable (Deknalon) monofilament sutures used in intraoral dentoalveolar surgery the bacterial colonization was compared. For the in vivo study the sutures were applied in 11 patients during dental surgery. Eight days postoperative the sutures were removed and the adhered bacteria were isolated and identified by biochemistry, morphology, antibiotic susceptibility, and gas chromatography. The colonization was studied by scanning electron microscopy. Aerobic and anaerobic bacteria were isolated in nearly equal colony-forming units (cfu) on each suture. In comparison with Monocryl about 15% more aerobic and anaerobic strains were isolated on Deknalon. Regarding the pathogens only, about three times more anaerobic strains were isolated on both sutures in total. Additionally, more pathogens were found on Deknalon than on Monocryl (aerobic >40%, anaerobic >25%). The variety of bacteria correspond with purulent infections, not with normal oral flora. Intraindividual comparisons of cfu showed differences in dependence of the patient as described for subgingivale plaques. For the in vitro study the sutures were incubated with Streptococcus intermedius and Prevotella intermedia for 0.5 h. Scanning electron microscopy was performed to examine qualitatively the level of bacterial adherence. After 0.5 h the bacteria adhered very well. The colonization rate of Streptococcus intermedius on both sutures was similar. Coccoid bacteria within biofilms were seen. The growth of Prevotella intermedia was much better on Deknalon than on Monocryl. The risk of bacteremia at the time of suture removal is discussed.
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Affiliation(s)
- J-E Otten
- Klinik und Poliklinik für Mund-, Kiefer- und Gesichtschirurgie, Albert-Ludwigs-Universität Freiburg, Germany.
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Takao A, Nagamune H, Maeda N. Identification of the anginosus group within the genus Streptococcus using polymerase chain reaction. FEMS Microbiol Lett 2004; 233:83-9. [PMID: 15043873 DOI: 10.1016/j.femsle.2004.01.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Revised: 01/26/2004] [Accepted: 01/26/2004] [Indexed: 10/26/2022] Open
Abstract
The aim of this study was to establish an identification method for the anginosus group within the genus Streptococcus by polymerase chain reaction (PCR). Using a primer pair based on the group-specific sequences of penicillin-binding protein 2B (pbp2b) gene, a 275-bp fragment was amplified from each species in the group but no size-matched products were obtained in other streptococci. Further identification in the species or subspecies level was possible by a multiplex PCR with primers for the 16S ribosomal RNA gene of Streptococcus anginosus, the hyaluronate lyase genes both of Streptococcus intermedius and Streptococcus constellatus subsp. constellatus, and the intermedilysin (ily) gene of S. intermedius. In the case ofStreptococcus constellatus subsp. pharyngis, the amplified fragment from the S. intermedius-type hyaluronate lyase gene was obtained, while that from the ily gene was not. These results also indicate that two different hyaluronate lyase genes are distributed among the anginosus group.
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Affiliation(s)
- Ayuko Takao
- Department of Oral Bacteriology, School of Dental Medicine, Tsurumi University, 2-1-3 Tsurumi, Tsurumi-ku, Yokohama 230-8501, Japan.
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Polekhina G, Giddings KS, Tweten RK, Parker MW. Crystallization and preliminary X-ray analysis of the human-specific toxin intermedilysin. Acta Crystallogr D Biol Crystallogr 2004; 60:347-9. [PMID: 14747721 DOI: 10.1107/s0907444903027240] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Accepted: 11/27/2003] [Indexed: 11/11/2022]
Abstract
Intermedilysin is a human-specific toxin from Streptococcus intermedius, which is part of normal human oral flora. The bacterium is an opportunistic pathogen with a tendency for deep-seated infection in the brain and liver. Intermedilysin belongs to the cholesterol-dependent cytolysin (CDCs) family of toxins, which have been identified in several different bacteria including the serious human pathogens S. pneumoniae and Clostridium perfringens. Intermedilysin, however, is the only member that shows exclusive specificity for human cells. The toxin has a couple of non-conservative amino-acid substitutions in a tryptophan-rich region of the molecule (Cys to Ala and Trp to Pro), the most conserved region amongst the CDCs. Mutations in this region are known to render other CDCs inactive. In order to investigate the structure-function relationships of the unusual features of intermedilysin, which will help us to understand the molecular mechanism of the toxin family in general, recombinant intermedilysin has been crystallized. The crystals belong to an orthorhombic space group and contain two molecules per asymmetric unit. Diffraction data were collected to 2.3 A using synchrotron radiation.
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Affiliation(s)
- Galina Polekhina
- Biota Structural Biology Laboratory, St Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia.
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