1
|
Gershberg J, Morhaim M, Rostrovsky I, Eichler J, Sal-Man N. The sequence of events of enteropathogenic E. coli's type III secretion system translocon assembly. iScience 2024; 27:109108. [PMID: 38375228 PMCID: PMC10875159 DOI: 10.1016/j.isci.2024.109108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/17/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Many bacterial pathogens employ the type III secretion system (T3SS), a specialized complex that transports effector proteins that manipulate various cellular processes. The T3SS forms a translocon pore within the host-cell membrane consisting of two secreted proteins that transition from a soluble state into a transmembrane complex. Still, the exact sequence of events leading to the formation of a membranous functional pore remains uncertain. Here, we utilized the translocon proteins of enteropathogenic E. coli (EPEC) to investigate the sequence of those steps leading to translocon assembly, including self-oligomerization, hetero-oligomerization, interprotein interaction, and membrane insertion. We found that in EPEC, EspD (SctE) plays a dominant role in pore formation as it assembles into an oligomeric state, regardless of pH, membrane contact, or the presence of EspB (SctB). Subsequently, EspB subunits integrate into EspD homo-oligomers to create EspB-EspD hetero-oligomers that adopt a transmembrane orientation to create a functional pore complex.
Collapse
Affiliation(s)
- Jenia Gershberg
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - May Morhaim
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Irina Rostrovsky
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| |
Collapse
|
2
|
Elias-Mordechai M, David N, Oren S, Georgia Pelah M, Jopp J, Fichtman B, Harel A, Berkovich R, Sal-Man N. A single filament biomechanical study of the enteropathogenic Escherichia coli Type III secretion system reveals a high elastic aspect ratio. Nanoscale 2023; 15:15027-15037. [PMID: 37668452 DOI: 10.1039/d3nr01953e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Type III secretion systems (T3SSs) are syringe-like protein complexes used by some of the most harmful bacterial pathogens to infect host cells. While the T3SS filament, a long hollow conduit that bridges between bacteria and host cells, has been characterized structurally, very little is known about its physical properties. These filaments should endure shear and normal stresses imposed by the viscous mucosal flow during infection within the intestinal tract. We used atomic force microscopy (AFM) to probe the longitudinal and radial mechanical response of individual T3SS filaments by pulling on filaments extending directly from bacterial surfaces and later pressing into filaments that were detached from the bacteria. The measured longitudinal elastic moduli were higher by about two orders of magnitude than the radial elastic moduli. These proportions are commensurate with the role of the T3SS filament, which requires horizontal flexibility while maintaining its structural integrity to withstand intense stresses during infection.
Collapse
Affiliation(s)
- Moran Elias-Mordechai
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Nofar David
- Department of Microbiology, Immunology, and Genetics, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Sonia Oren
- Department of Microbiology, Immunology, and Genetics, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Maya Georgia Pelah
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| | - Jürgen Jopp
- The Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Boris Fichtman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ronen Berkovich
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
- The Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Neta Sal-Man
- Department of Microbiology, Immunology, and Genetics, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel.
| |
Collapse
|
3
|
Braverman D, Gershberg J, Sal-Man N. The transmembrane domains of the type III secretion system effector Tir are involved in its secretion and cellular activities. Front Cell Infect Microbiol 2023; 13:1103552. [PMID: 36864885 PMCID: PMC9971567 DOI: 10.3389/fcimb.2023.1103552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction Enteropathogenic Escherichia coli (EPEC) is a diarrheagenic pathogen and one of the major causes of gastrointestinal illness in developing countries. EPEC, similar to many other Gram-negative bacterial pathogens, possesses essential virulence machinery called the type III secretion system (T3SS) that enables the injection of effector proteins from the bacteria into the host cytoplasm. Of these, the translocated intimin receptor (Tir) is the first effector to be injected, and its activity is essential for the formation of attaching and effacing lesions, the hallmark of EPEC colonization. Tir belongs to a unique group of transmembrane domain (TMD)-containing secreted proteins, which have two conflicting destination indications, one for bacterial membrane integration and another for protein secretion. In this study, we examined whether TMDs participate in the secretion, translocation, and function of Tir in host cells. Methods We created Tir TMD variants with the original or alternative TMD sequence. Results We found that the C-terminal TMD of Tir (TMD2) is critical for the ability of Tir to escape integration into the bacterial membrane. However, the TMD sequence was not by itself sufficient and its effect was context-dependent. Moreover, the N-terminal TMD of Tir (TMD1) was important for the postsecretion function of Tir at the host cell. Discussion Taken together, our study further supports the hypothesis that the TMD sequences of translocated proteins encode information crucial for protein secretion and their postsecretion function.
Collapse
Affiliation(s)
- Dor Braverman
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Jenia Gershberg
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | |
Collapse
|
4
|
Gorelik O, Rogad A, Holoidovsky L, Meijler MM, Sal-Man N. Indole intercepts the communication between enteropathogenic E. coli and Vibrio cholerae. Gut Microbes 2022; 14:2138677. [PMID: 36519445 PMCID: PMC9635540 DOI: 10.1080/19490976.2022.2138677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reported numbers of diarrheal samples exhibiting co-infections or multiple infections, with two or more infectious agents, are rising, likely due to advances in bacterial diagnostic techniques. Bacterial species detected in these samples include Vibrio cholerae (V. cholerae) and enteropathogenic Escherichia coli (EPEC), which infect the small intestine and are associated with high mortality rates. It has previously been reported that EPEC exhibit enhanced virulence in the presence of V. cholerae owing to their ability to sense and respond to elevated concentrations of cholera autoinducer 1 (CAI-1), which is the primary quorum-sensing (QS) molecule produced by V. cholerae. In this study, we examined this interspecies bacterial communication in the presence of indole, a major microbiome-derived metabolite found at high concentrations in the human gut. Interestingly, we discovered that although indole did not affect bacterial growth or CAI-1 production, it impaired the ability of EPEC to enhance its virulence activity in response to the presence of V. cholerae. Furthermore, the co-culture of EPEC and V. cholerae in the presence of B. thetaiotaomicron, an indole-producing commensal bacteria, ablated the enhancement of EPEC virulence. Together, these results suggest that microbiome compositions or diets that influence indole gut concentrations may differentially impact the virulence of pathogens and their ability to sense and respond to competing bacteria.
Collapse
Affiliation(s)
- Orna Gorelik
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Alona Rogad
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lara Holoidovsky
- Department of Chemistry, the National Institute for Biotechnology in the Negev Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Michael M. Meijler
- Department of Chemistry, the National Institute for Biotechnology in the Negev Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel,CONTACT Neta Sal-Man The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| |
Collapse
|
5
|
Naor-Hoffmann S, Svetlitsky D, Sal-Man N, Orenstein Y, Ziv-Ukelson M. Predicting the pathogenicity of bacterial genomes using widely spread protein families. BMC Bioinformatics 2022; 23:253. [PMID: 35751023 PMCID: PMC9233384 DOI: 10.1186/s12859-022-04777-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/13/2022] [Indexed: 11/15/2022] Open
Abstract
Background The human body is inhabited by a diverse community of commensal non-pathogenic bacteria, many of which are essential for our health. By contrast, pathogenic bacteria have the ability to invade their hosts and cause a disease. Characterizing the differences between pathogenic and commensal non-pathogenic bacteria is important for the detection of emerging pathogens and for the development of new treatments. Previous methods for classification of bacteria as pathogenic or non-pathogenic used either raw genomic reads or protein families as features. Using protein families instead of reads provided a better interpretability of the resulting model. However, the accuracy of protein-families-based classifiers can still be improved. Results We developed a wide scope pathogenicity classifier (WSPC), a new protein-content-based machine-learning classification model. We trained WSPC on a newly curated dataset of 641 bacterial genomes, where each genome belongs to a different species. A comparative analysis we conducted shows that WSPC outperforms existing models on two benchmark test sets. We observed that the most discriminative protein-family features in WSPC are widely spread among bacterial species. These features correspond to proteins that are involved in the ability of bacteria to survive and replicate during an infection, rather than proteins that are directly involved in damaging or invading the host.
Collapse
Affiliation(s)
- Shaked Naor-Hoffmann
- Department of Computer Science, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Dina Svetlitsky
- Department of Computer Science, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Yaron Orenstein
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Michal Ziv-Ukelson
- Department of Computer Science, Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| |
Collapse
|
6
|
Abstract
The type III secretion system (T3SS) is crucial for the virulence of several pathogenic Escherichia coli species as well as for other gram-negative bacterial strains. Therefore, the ability to monitor this system constitutes a valuable tool for assessing the involvement of different proteins in bacterial virulence, for identifying critical domains and specific mutations, and for evaluating the antivirulence activities of various drugs. The major advantage of the T3SS secretion assay for E. coli over assays for other gram-negative pathogens is that it does not necessarily require specific antibodies. Here, we describe how to grow enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) strains under T3SS-inducing conditions, separate the supernatant fraction from the bacterial pellet, analyze this fraction on sodium dodecyl sulfate (SDS)-polyacrylamide gels, and evaluate the level of T3SS activity. We describe a qualitative analysis using Coomassie staining and a quantitative assay using western blotting.
Collapse
Affiliation(s)
- Bosko Mitrovic
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| |
Collapse
|
7
|
Tseytin I, Lezerovich S, David N, Sal-Man N. Interactions and substrate selectivity within the SctRST complex of the type III secretion system of enteropathogenic Escherichia coli. Gut Microbes 2022; 14:2013763. [PMID: 34965187 PMCID: PMC8726614 DOI: 10.1080/19490976.2021.2013763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 02/04/2023] Open
Abstract
Many bacterial pathogens employ a protein complex, termed the type III secretion system (T3SS), to inject bacterial effectors into host cells. These effectors manipulate various cellular processes to promote bacterial growth and survival. The T3SS complex adopts a nano-syringe shape that is assembled across the bacterial membranes, with an extracellular needle extending toward the host cell membrane. The assembly of the T3SS is initiated by the association of three proteins, known as SctR, SctS, and SctT, which create an entry portal to the translocation channel within the bacterial inner membrane. Using the T3SS of enteropathogenic Escherichia coli, we investigated, by mutational and functional analyses, the role of two structural construction sites formed within the SctRST complex and revealed that they are mutation-resistant components that are likely to act as seals preventing leakage of ions and metabolites rather than as substrate gates. In addition, we identified two residues in the SctS protein, Pro23, and Lys54, that are critical for the proper activity of the T3SS. We propose that Pro23 is critical for the physical orientation of the SctS transmembrane domains that create the tip of the SctRST complex and for their positioning with regard to other T3SS substructures. Surprisingly, we found that SctS Lys54, which was previously suggested to mediate the SctS self-oligomerization, is critical for T3SS activity due to its essential role in SctS-SctT hetero-interactions.
Collapse
Affiliation(s)
- Irit Tseytin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shir Lezerovich
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Nofar David
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| |
Collapse
|
8
|
Mitrović B, Lezerovich S, Sal-Man N. The Role of the Membrane-Associated Domain of the Export Apparatus Protein, EscV (SctV), in the Activity of the Type III Secretion System. Front Microbiol 2021; 12:719469. [PMID: 34413845 PMCID: PMC8369761 DOI: 10.3389/fmicb.2021.719469] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
Diarrheal diseases remain a major public health concern worldwide. Many of the causative bacterial pathogens that cause these diseases have a specialized protein complex, the type III secretion system (T3SS), which delivers effector proteins directly into host cells. These effectors manipulate host cell processes for the benefit of the infecting bacteria. The T3SS structure resembles a syringe anchored within the bacterial membrane, projecting toward the host cell membrane. The entry port of the T3SS substrates, called the export apparatus, is formed by five integral membrane proteins. Among the export apparatus proteins, EscV is the largest, and as it forms a nonamer, it constitutes the largest portion of the export apparatus complex. While there are considerable data on the soluble cytoplasmic domain of EscV, our knowledge of its membrane-associated section and its transmembrane domains (TMDs) is still very limited. In this study, using an isolated genetic reporter system, we found that TMD5 and TMD6 of EscV mediate strong self-oligomerization. Substituting these TMDs within the full-length protein with a random hydrophobic sequence resulted in a complete loss of function of the T3SS, further suggesting that the EscV TMD5 and TMD6 sequences have a functional role in addition to their structural role as membrane anchors. As we observed only mild reduction in the ability of the TMD-exchanged variants to integrate into the full or intermediate T3SS complexes, we concluded that EscV TMD5 and TMD6 are not crucial for the global assembly or stability of the T3SS complex but are rather involved in promoting the necessary TMD–TMD interactions within the complex and the overall TMD orientation to allow channel opening for the entry of T3SS substrates.
Collapse
Affiliation(s)
- Boško Mitrović
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Shir Lezerovich
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| |
Collapse
|
9
|
Abstract
Many bacterial pathogens utilize a specialized secretion system, termed type III secretion system (T3SS), to translocate effector proteins into host cells and establish bacterial infection. The T3SS is anchored within the bacterial membranes and contains a long needle/filament that extends toward the host-cell and forms, at its distal end, a pore complex within the host membrane. The T3SS pore complex consists of two bacterial proteins, termed SctB and SctE, which have conflicting targeting indications; a signal sequence that targets to secretion to the extracellular environment via the T3SS, and transmembrane domains (TMDs) that target to membrane localization. In this study, we investigate whether the TMD sequences of SctB and SctE have special features that differentiate them from classical TMDs and allow them to escape bacterial membrane integration. For this purpose, we exchanged the SctB and SctE native TMDs for alternative hydrophobic sequences and found that the TMD sequences of SctB and SctE dictate membrane destination (bacterial versus host membrane). Moreover, we examined the role of the SctB TMD sequence in the activity of the full-length protein, post secretion, and found that the TMD does not serve only as a hydrophobic segment, but is also involved in the ability of the protein to translocate itself and other proteins into and across the host cell membrane.
Collapse
Affiliation(s)
- Jenia Gershberg
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dor Braverman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| |
Collapse
|
10
|
Hillman Y, Gershberg J, Lustiger D, Even D, Braverman D, Dror Y, Ashur I, Vernick S, Sal-Man N, Wine Y. Monoclonal Antibody-Based Biosensor for Point-of-Care Detection of Type III Secretion System Expressing Pathogens. Anal Chem 2020; 93:928-935. [DOI: 10.1021/acs.analchem.0c03621] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yaron Hillman
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Green building, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Jenia Gershberg
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva 8410501, Israel
| | - Dan Lustiger
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Green building, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Dan Even
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Green building, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Dor Braverman
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva 8410501, Israel
| | - Yael Dror
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Green building, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Idan Ashur
- Institute of Agricultural Engineering, Agricultural Research Organization, Volcani Center, 68 Hamaccabim Rd, Rishon Lezion 5025001, Israel
| | - Sefi Vernick
- Institute of Agricultural Engineering, Agricultural Research Organization, Volcani Center, 68 Hamaccabim Rd, Rishon Lezion 5025001, Israel
| | - Neta Sal-Man
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva 8410501, Israel
| | - Yariv Wine
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Green building, Tel-Aviv University, Tel Aviv 6997801, Israel
| |
Collapse
|
11
|
Barash E, Sal-Man N, Sabato S, Ziv-Ukelson M. BacPaCS-Bacterial Pathogenicity Classification via Sparse-SVM. Bioinformatics 2020; 35:2001-2008. [PMID: 30407484 DOI: 10.1093/bioinformatics/bty928] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 08/30/2018] [Accepted: 11/07/2018] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION Bacterial infections are a major cause of illness worldwide. However, most bacterial strains pose no threat to human health and may even be beneficial. Thus, developing powerful diagnostic bioinformatic tools that differentiate pathogenic from commensal bacteria are critical for effective treatment of bacterial infections. RESULTS We propose a machine-learning approach for classifying human-hosted bacteria as pathogenic or non-pathogenic based on their genome-derived proteomes. Our approach is based on sparse Support Vector Machines (SVM), which autonomously selects a small set of genes that are related to bacterial pathogenicity. We implement our approach as a tool-'Bacterial Pathogenicity Classification via sparse-SVM' (BacPaCS)-which is fully automated and handles datasets significantly larger than those previously used. BacPaCS shows high accuracy in distinguishing pathogenic from non-pathogenic bacteria, in a clinically relevant dataset, comprising only human-hosted bacteria. Among the genes that received the highest positive weight in the resulting classifier, we found genes that are known to be related to bacterial pathogenicity, in addition to novel candidates, whose involvement in bacterial virulence was never reported. AVAILABILITY AND IMPLEMENTATION The code and the resulting model are available at: https://github.com/barashe/bacpacs. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Eran Barash
- Department of Computer Science, Faculty of Natural Sciences
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, BeerSheva, Israel
| | - Sivan Sabato
- Department of Computer Science, Faculty of Natural Sciences
| | | |
Collapse
|
12
|
Tseytin I, Mitrovic B, David N, Langenfeld K, Zarivach R, Diepold A, Sal-Man N. The Role of the Small Export Apparatus Protein, SctS, in the Activity of the Type III Secretion System. Front Microbiol 2019; 10:2551. [PMID: 31798543 PMCID: PMC6863770 DOI: 10.3389/fmicb.2019.02551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022] Open
Abstract
Many gram-negative pathogens utilize a protein complex, termed the type III secretion system (T3SS), to inject virulence factors from their cytoplasm directly into the host cell. An export apparatus that is formed by five putative integral membrane proteins (SctR/S/T/U/V), resides at the center of the T3SS complex. In this study, we characterized the smallest export apparatus protein, SctS, which contains two putative transmembrane domains (PTMD) that dynamically extract from the inner membrane and adopt a helix-turn-helix structure upon assembly of the T3SS. Replacement of each SctS PTMD with an alternative hydrophobic sequence resulted in abolishment of the T3SS activity, yet SctS self- and hetero-interactions as well as the overall assembly of the T3SS complex were unaffected. Our findings suggest that SctS PTMDs are not crucial for the interactions or the assembly of the T3SS base complex but rather that they are involved in adjusting the orientation of the export apparatus relative to additional T3SS sub-structures, such as the cytoplasmic- and the inner-membrane rings. This ensures the fittings between the dynamic and static components of the T3SS and supports the functionality of the T3SS complex.
Collapse
Affiliation(s)
- Irit Tseytin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Bosko Mitrovic
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Nofar David
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Katja Langenfeld
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Raz Zarivach
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| |
Collapse
|
13
|
Gorelik O, Levy N, Shaulov L, Yegodayev K, Meijler MM, Sal-Man N. Vibrio cholerae autoinducer-1 enhances the virulence of enteropathogenic Escherichia coli. Sci Rep 2019; 9:4122. [PMID: 30858454 PMCID: PMC6411865 DOI: 10.1038/s41598-019-40859-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 02/25/2019] [Indexed: 12/19/2022] Open
Abstract
Diarrhoea is the second leading cause of death in children under the age of five. The bacterial species, Vibrio cholerae and enteropathogenic Escherichia coli (EPEC), are among the main pathogens that cause diarrhoeal diseases, which are associated with high mortality rates. These two pathogens have a common infection site-the small intestine. While it is known that both pathogens utilize quorum sensing (QS) to determine their population size, it is not yet clear whether potential bacterial competitors can also use this information. In this study, we examined the ability of EPEC to determine V. cholerae population sizes and to modulate its own virulence mechanisms accordingly. We found that EPEC virulence is enhanced in response to elevated concentrations of cholera autoinducer-1 (CAI-1), even though neither a CAI-1 synthase nor CAI-1 receptors have been reported in E. coli. This CAI-1 sensing and virulence upregulation response may facilitate the ability of EPEC to coordinate successful colonization of a host co-infected with V. cholerae. To the best of our knowledge, this is the first observed example of 'eavesdropping' between two bacterial pathogens that is based on interspecies sensing of a QS molecule.
Collapse
Affiliation(s)
- Orna Gorelik
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Niva Levy
- The Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lihi Shaulov
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ksenia Yegodayev
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael M Meijler
- The Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| |
Collapse
|
14
|
Levy-Tzedek S, Moran GS, Alon U, Sal-Man N. Peer power: A women's peer-mentoring program at the workplace: example from the academia. EMBO Rep 2018; 19:embr.201847246. [PMID: 30396884 DOI: 10.15252/embr.201847246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Shelly Levy-Tzedek
- Department of Physical Therapy, Recanati School for Community Health Professions, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Galia S Moran
- The Charlotte B. and Jack J. Spitzer Department of Social Work, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| |
Collapse
|
15
|
Nadler H, Shaulov L, Blitsman Y, Mordechai M, Jopp J, Sal-Man N, Berkovich R. Deciphering the Mechanical Properties of Type III Secretion System EspA Protein by Single Molecule Force Spectroscopy. Langmuir 2018; 34:6261-6270. [PMID: 29726683 DOI: 10.1021/acs.langmuir.8b01198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacterial pathogens inject virulence factors into host cells during bacterial infections using type III secretion systems. In enteropathogenic Escherichia coli, this system contains an external filament, formed by a self-oligomerizing protein called E. coli secreted protein A (EspA). The EspA filament penetrates the thick viscous mucus layer to facilitate the attachment of the bacteria to the gut-epithelium. To do that, the EspA filament requires noteworthy mechanical endurance considering the mechanical shear stresses found within the intestinal tract. To date, the mechanical properties of the EspA filament and the structural and biophysical knowledge of monomeric EspA are very limited, mostly due to the strong tendency of the protein to self-oligomerize. To overcome this limitation, we employed a single molecule force spectroscopy (SMFS) technique and studied the mechanical properties of EspA. Force extension dynamic of (I91)4-EspA-(I91)4 chimera revealed two structural unfolding events occurring at low forces during EspA unfolding, thus indicating no unique mechanical stability of the monomeric protein. SMFS examination of purified monomeric EspA protein, treated by a gradually refolding protocol, exhibited similar mechanical properties as the EspA protein within the (I91)4-EspA-(I91)4 chimera. Overall, our results suggest that the mechanical integrity of the EspA filament likely originates from the interactions between EspA monomers and not from the strength of an individual monomer.
Collapse
Affiliation(s)
- Hila Nadler
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Lihi Shaulov
- Department of Microbiology, Immunology and Genetics , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Yossi Blitsman
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Moran Mordechai
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Jürgen Jopp
- The Ilse Katz Institute for Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Neta Sal-Man
- Department of Microbiology, Immunology and Genetics , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Ronen Berkovich
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
- The Ilse Katz Institute for Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| |
Collapse
|
16
|
Sal-Man N, Gerber D, Shai Y. Proline localized to the interaction interface can mediate self-association of transmembrane domains. Biochim Biophys Acta 2014; 1838:2313-8. [PMID: 24841754 DOI: 10.1016/j.bbamem.2014.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/01/2014] [Accepted: 05/09/2014] [Indexed: 01/11/2023]
Abstract
Assembly of transmembrane domains (TMDs) is a critical step in the function of membrane proteins. In recent years, the role of specific amino acids in TMD-TMD interactions has been better characterized, with more emphasis on polar and aromatic residues. Despite the high abundance of proline residues in TMDs, contribution of proline to TMD-TMD association has not been intensively studied. Here, we evaluated statistically the frequency of appearance, and experimentally the contribution of proline, compared to other hydrophobic amino acids (Gly, Ala, Val, Leu, Ile, and Met), with regard to TMD-TMD self-assembly. Our model system is the assembly motif ((22)QxxS(25)) found previously in TMDs of the Escherichia coli aspartate receptor (Tar-1). Statistically, our data revealed that all different motifs, except PxxS (P/S), have frequencies similar to their theoretical random expectancy within a database of 41916 sequences of TMDs, while PxxS motif is underrepresented. Experimentally, using the ToxR assembly system, the SDS-gel running pattern of biotin-conjugated TMD peptides, and FRET experiments between fluorescence-labeled peptides, we found that only the P/S motif preserves the dimerization ability of wild-type Tar-1 TMD. Although proline is known as a helix breaker in solution, Circular Dichroism spectroscopy revealed that the secondary structure of the P/S and the wild-type peptides are similar. All together, these data suggest that proline can stabilize TM self-assembly when localized to the interaction interface of a transmembrane oligomer. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.
Collapse
Affiliation(s)
- Neta Sal-Man
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel; Department of Microbiology and Immunology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| | - Doron Gerber
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel; The Mina & Everard Goodman Faculty of Life Sciences, The Nanotechnology Institute, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yechiel Shai
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
17
|
Sal-Man N, Deng W, Finlay BB. Characterization of rOrf8/EscI of the enteropathogenic Escherichia coli as an inner rod protein. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.604.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Neta Sal-Man
- Department of Biochemistry and Molecular BiologyUniversity of British ColumbiaVancouverBCCanada
| | - Wanyin Deng
- Department of Biochemistry and Molecular BiologyUniversity of British ColumbiaVancouverBCCanada
| | - B. Brett Finlay
- Department of Biochemistry and Molecular BiologyUniversity of British ColumbiaVancouverBCCanada
| |
Collapse
|
18
|
Fink A, Sal-Man N, Gerber D, Shai Y. Transmembrane domains interactions within the membrane milieu: principles, advances and challenges. Biochim Biophys Acta 2011; 1818:974-83. [PMID: 22155642 DOI: 10.1016/j.bbamem.2011.11.029] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 11/17/2011] [Accepted: 11/22/2011] [Indexed: 11/17/2022]
Abstract
Protein-protein interactions within the membrane are involved in many vital cellular processes. Consequently, deficient oligomerization is associated with known diseases. The interactions can be partially or fully mediated by transmembrane domains (TMD). However, in contrast to soluble regions, our knowledge of the factors that control oligomerization and recognition between the membrane-embedded domains is very limited. Due to the unique chemical and physical properties of the membrane environment, rules that apply to interactions between soluble segments are not necessarily valid within the membrane. This review summarizes our knowledge on the sequences mediating TMD-TMD interactions which include conserved motifs such as the GxxxG, QxxS, glycine and leucine zippers, and others. The review discusses the specific role of polar, charged and aromatic amino acids in the interface of the interacting TMD helices. Strategies to determine the strength, dynamics and specificities of these interactions by experimental (ToxR, TOXCAT, GALLEX and FRET) or various computational approaches (molecular dynamic simulation and bioinformatics) are summarized. Importantly, the contribution of the membrane environment to the TMD-TMD interaction is also presented. Studies utilizing exogenously added TMD peptides have been shown to influence in vivo the dimerization of intact membrane proteins involved in various diseases. The chirality independent TMD-TMD interactions allows for the design of novel short d- and l-amino acids containing TMD peptides with advanced properties. Overall these studies shed light on the role of specific amino acids in mediating the assembly of the TMDs within the membrane environment and their contribution to protein function. This article is part of a Special Issue entitled: Protein Folding in Membranes.
Collapse
Affiliation(s)
- Avner Fink
- Department of Biological Chemistry, the Weizmann Institute of Science, Rehovot, 76100 Israel
| | | | | | | |
Collapse
|
19
|
Abstract
Evaluation of: Akopyan K, Edgren T, Wang-Edgren H et al.: Translocation of surface-localized effectors in type III secretion. Proc. Natl Acad. Sci. USA 108(4), 1639–1644 (2011). Type III secretion systems suppress host immune response and modify cell-signaling and regulation pathways by translocation of virulence proteins, called effectors, from the bacteria into the cytosol of the target cells. The common belief was that effectors translocate by a single step mechanism through a continuous channel built up by type III secretion systems. In this article, Akopyan et al. propose an alternative, and possibly parallel, two-step model to translocate effectors into target cells. According to their model, effectors first localized on the surface of the bacterial membrane, followed by a type III secretion system-dependent entry into the host cell.
Collapse
Affiliation(s)
- Neta Sal-Man
- The University of British Columbia, Michael Smith Laboratories, Vancouver, Canada
| | - Matthew A Croxen
- The University of British Columbia, Michael Smith Laboratories, Vancouver, Canada
| | | |
Collapse
|
20
|
Sal-Man N, Biemans-Oldehinkel E, Finlay BB. Structural microengineers: pathogenic Escherichia coli redesigns the actin cytoskeleton in host cells. Structure 2009; 17:15-9. [PMID: 19141278 DOI: 10.1016/j.str.2008.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [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] [Received: 10/23/2008] [Revised: 12/01/2008] [Accepted: 12/08/2008] [Indexed: 11/18/2022]
Abstract
Several virulent bacteria have the ability to manipulate the host cell actin cytoskeleton as part of their pathogenic strategy. These pathogens subvert the host cell actin polymerization machinery for various purposes including motility within host cells, cell-to-cell spread, and to prevent phagocytic engulfment by professional phagocytes. In contrast to intracellular pathogens, pathogenic Escherichia coli (including both enterohemorrhagic and enteropathogenic E. coli) subvert actin polymerization from an extracellular position to facilitate adherence. This review summarizes recent data on the mechanisms by which pathogenic E. coli hijack members of the Wiskott-Aldrich syndrome protein family to manipulate actin polymerization within host cells, including the novel, and surprisingly simple, mechanism recently revealed for the EspFu effector.
Collapse
Affiliation(s)
- Neta Sal-Man
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | | | | |
Collapse
|
21
|
Abstract
Aromatic residues have been previously shown to mediate the self-assembly of different soluble proteins through pi-pi interactions (McGaughey, G. B., Gagne, M., and Rappe, A. K. (1998) J. Biol. Chem. 273, 15458-15463). However, their role in transmembrane (TM) assembly is not yet clear. In this study, we performed statistical analysis of the frequency of occurrence of aromatic pairs in a bacterial TM data base that provided an initial indication that the appearance of a specific aromatic pattern, Aromatic-XX-Aromatic, is not coincidental, similar to the well characterized QXXS motif. The QXXS motif was previously shown to be both critical and sufficient for stabilizing TM self-assembly. Using the ToxR system, we monitored the dimerization propensities of TM domains that contain mutations of interacting residues to aromatic amino acids and demonstrated that aromatic residues can adequately stabilize self-association. Importantly, we have provided an example of a natural TM domain, the cholera toxin secretion protein EpsM, whose TM self-assembly is mediated by an aromatic motif (WXXW). This is, in fact, the first evidence that aromatic residues are involved in the dimerization of a wild type TM domain. The association mediated by aromatic residues was found to be sensitive to the TM sequence, suggesting that aromatic residue motifs can provide a general means for specificity in TM assembly. Molecular dynamics provided a structural explanation for this backbone sequence sensitivity.
Collapse
Affiliation(s)
- Neta Sal-Man
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | |
Collapse
|
22
|
Kristian SA, Timmer AM, Liu GY, Lauth X, Sal-Man N, Rosenfeld Y, Shai Y, Gallo RL, Nizet V. Impairment of innate immune killing mechanisms by bacteriostatic antibiotics. FASEB J 2007; 21:1107-16. [PMID: 17215486 DOI: 10.1096/fj.06-6802com] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [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: 11/11/2022]
Abstract
Antibiotics are designed to support host defense in controlling infection. Here we describe a paradoxical inhibitory effect of bacteriostatic antibiotics on key mediators of mammalian innate immunity. When growth of species including Escherichia coli and Staphylococcus aureus is suppressed by chloramphenicol or erythromycin, the susceptibility of the bacteria to cathelicidin antimicrobial peptides or serum complement was markedly diminished. Survival of the bacteria in human whole blood, human wound fluid, or a mouse wound infection model was in turn increased after antibiotic-induced bacteriostasis. These findings provide a further rationale against the indiscriminate use of antibiotics.
Collapse
Affiliation(s)
- Sascha A Kristian
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0687, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Sal-Man N, Gerber D, Shai Y. The Identification of a Minimal Dimerization Motif QXXS That Enables Homo- and Hetero-association of Transmembrane Helices in Vivo. J Biol Chem 2005; 280:27449-57. [PMID: 15911619 DOI: 10.1074/jbc.m503095200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [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: 11/06/2022] Open
Abstract
Assembly of transmembrane (TM) domains is a critical step in the function of membrane proteins, and therefore, determining the amino acid motifs that mediate this process is important. Studies along this line have shown that the GXXXG motif is involved in TM assembly. In this study we characterized the minimal dimerization motif in the bacterial Tar-1 homodimer TM domain, which does not contain a GXXXG sequence. We found that a short polar motif QXXS is sufficient to induce stable TM-TM interactions. Statistical analysis revealed that this motif appears to be significantly over-represented in a bacterial TM data base compared with its theoretical expectancy, suggesting a general role for this motif in TM assembly. A truncated short TM peptide (9 residues) that contains the QXXS motif interacted slightly with the wild-type Tar-1. However, the same short TM peptide regained wild-type-like activity when conjugated to an octanoyl aliphatic moiety. Biophysical studies indicated that this modification compensated for the missing hydrophobicity, stabilized alpha-helical structure, and enabled insertion of the peptide into the membrane core. These findings serve as direct evidence that even a short peptide containing a minimal recognition motif is sufficient to inhibit the proper assembly of TM domains. Interestingly, electron microscopy revealed that above the critical micellar concentration, the TM lipopeptide forms a network of nanofibers, which can serve for the slow release of the active lipopeptide.
Collapse
Affiliation(s)
- Neta Sal-Man
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | |
Collapse
|
24
|
Sal-Man N, Shai Y. Arginine mutations within a transmembrane domain of Tar, an Escherichia coli aspartate receptor, can drive homodimer dissociation and heterodimer association in vivo. Biochem J 2005; 385:29-36. [PMID: 15330757 PMCID: PMC1134670 DOI: 10.1042/bj20041022] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [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: 11/17/2022]
Abstract
The interactions between the TM (transmembrane) domains of many membrane proteins are important for their proper functioning. Mutations of residues into positively charged ones within TM domains were reported to be involved in many genetic diseases, possibly because these mutations affect the self- and/or hetero-assembly of the corresponding proteins. To our knowledge, despite significant progress in understanding the role of various amino acids in TM-TM interactions in vivo, the direct effect of positively charged residues on these interactions has not been studied. To address this issue, we employed the N-terminal TM domain of the aspartate receptor (Tar-1) as a dimerization model system. We expressed within the ToxR TM assembly system several Tar-1 constructs that dimerize via polar- or non-polar amino acid motifs, and mutated these by replacement with a single arginine residue. Our results have revealed that a mutation in each of the motifs significantly reduced the ability of the TMs to dimerize. Furthermore, a Tar-1 construct that contained two arginine residues was unable to correctly integrate itself into the membrane. Nevertheless, an exogenous synthetic Tar-1 peptide containing these two arginine residues was able to inhibit in vivo the marked dimerization of a mutant Tar-1 construct that contained two glutamate residues at similar positions. This indicates that hetero-assembly of TM domains can be mediated by the interaction of two oppositely charged residues, probably by formation of ion pairs. This study broadens our knowledge regarding the effect of positively charged residues on TM-TM interactions in vivo, and provides a potential therapeutic approach to inhibit uncontrolled dimerization of TM domains caused by mutations of polar amino acids.
Collapse
Affiliation(s)
- Neta Sal-Man
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Yechiel Shai
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel
- The Harold S. and Harriet B. Brady Professorial Chair in Cancer Research, and the author to whom correspondence should be addressed (email )
| |
Collapse
|
25
|
Sal-Man N, Gerber D, Shai Y. Hetero-assembly between all-L- and all-D-amino acid transmembrane domains: forces involved and implication for inactivation of membrane proteins. J Mol Biol 2005; 344:855-64. [PMID: 15533450 DOI: 10.1016/j.jmb.2004.09.066] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2004] [Revised: 09/22/2004] [Accepted: 09/23/2004] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions within the membrane, partially or fully mediated by transmembrane (TM) domains, are involved in many vital cellular processes. Since the unique feature of the membrane environment enables protein-protein assembly that otherwise is not energetically favored in solution, the structural restrictions involved in the assembly of soluble proteins are not necessarily valid for the assembly of TM domains. Here we used the N-terminal TM domain (Tar-1) of the Escherichia coli aspartate receptor as a model system for examining the stereospecificity of TM-TM interactions in vitro and in vivo in isolated systems, and in the context of the full receptor. For this propose, we synthesized Tar-1 all-l and all-d amino acid TM peptides, a mutant TM peptide and an unrelated TM peptide. The data revealed: (i) Tar-1 all-d specifically associated with Tar-1 all-l within a model lipid membrane, as determined by using fluorescence energy transfer experiments; (ii) Tar-1 all-l and all-d, but not the control peptides, demonstrated a dose-dependant dominant negative effect on the Tar-1 TM homodimerization in the bacterial ToxR assembly system, suggesting a wild-type-like interaction; and most interestingly, (iii) both Tar-1 all-l and all-d showed a remarkable ability to inhibit the chemotaxis response of the full-length receptor, in vivo. Peptide binding to the bacteria was confirmed through confocal imaging, and Western blotting confirmed that ToxR Tar-1 chimera protein levels are not affected by the presence of the exogenous peptides. These findings present the first evidence that an all-d TM domain peptide acts in vivo similarly to its parental all-l peptide and suggest that the dimerization of the TM domains is mainly mediated by side-chain interactions, rather than geometrically fitted conformations. In addition, the study provides a new approach for modifying the function of membrane proteins by proteolysis-free peptides.
Collapse
Affiliation(s)
- Neta Sal-Man
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | | | | |
Collapse
|
26
|
Gerber D, Sal-Man N, Shai Y. Structural Adaptation of the Glycophorin A Transmembrane Homodimer to d-Amino Acid Modifications. J Mol Biol 2004; 339:243-50. [PMID: 15123435 DOI: 10.1016/j.jmb.2004.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [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: 02/04/2004] [Revised: 03/05/2004] [Accepted: 03/05/2004] [Indexed: 11/24/2022]
Abstract
Protein-protein recognition is an essential process in life. The chemistry of these kind of interactions is predominantly stereospecific (i.e. receptor-ligand, antibody-hapten binding). Here, we investigated whether the hydrophobic nature of the membrane affects this stereospecificity. To this end, we synthesized a diastereomer analogue (2D-GPA) of the glycophorin A transmembrane helix, with two l-valine residues replaced by their d-enantiomer. This ensures a disruption of the secondary structure. We investigated the ability of the diastereomer peptide to recognize the GPA chimera in the ToxR homodimer reporting system, in vivo. The peptide demonstrated a dose-dependent dominant negative effect on the GPA transmembrane in the bacterial ToxR system, suggesting a wild-type like interaction. This result was corroborated in vitro by fluorescence energy transfer between 2D-GPA and all-l GPA. Peptide binding to the bacteria was confirmed through confocal imaging, and Western blot confirmed that ToxR GPA receptor levels are not affected by the presence of the exogenous peptide. In order to understand the structural basis for heterodimer formation, homodimer and heterodimer structures, based on the NMR 3D structure of GPA, were subjected to a molecular dynamics simulation. The resulting heterodimer structure maintained most of the original inter-helical interactions, and its structure is similar to that of the homodimer. We postulate that the need to satisfy all H-bonds can compensate for the structural strain induced by the presence of the d-amino acid residues.
Collapse
Affiliation(s)
- Doron Gerber
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | |
Collapse
|
27
|
Abstract
Protein assembly is a critical process involved in a wide range of cellular events and occurs through extracellular and/or transmembrane domains (TMs). Previous studies demonstrated that a GXXXG motif is crucial for homodimer formation. Here we selected the TMs of ErbB1 and ErbB2 as a model since these receptors function both as homodimers and as heterodimers. Both TMs contain two GXXXG-like motifs located at the C and N termini. The C-terminal motifs were implicated previously in homodimer formation, but the role of the N-terminal motifs was not clear. We used the ToxR system and expressed the TMs of both ErbB1 and ErbB2 containing only the N-terminal GXXXG motifs. The data revealed that the ErbB2 but not the ErbB1 construct formed homodimers. Importantly, a synthetic ErbB1 TM peptide was able to form a heterodimer with ErbB2, by displacing the ErbB2 TM homodimer. The specificity of the interaction was demonstrated by using three controls: (i) Two single mutations within the GXXXG-like motif of the ErbB1 peptide reduced or preserved its activity, in agreement with similar mutations in glycophorin A. (ii) A TM peptide of the bacterial Tar receptor did not assemble with the ErbB2 construct. (iii) The ErbB1 peptide had no effect on the dimerization of a construct containing the TM-1 domain of the Tar receptor. Fluorescence microscopy demonstrated that all the peptides localized on the membrane. Furthermore, incubation with the peptides had no effect on bacterial growth and protein expression levels. Our results suggest that the N-terminal GXXXG-like motif of the ErbB1 TM plays a role in heterodimerization with the ErbB2 transmembrane domain. To our knowledge, this is the first demonstration of a transmembrane domain with two distinct recognition motifs, one for homodimerization and the other for heterodimerization.
Collapse
Affiliation(s)
- Doron Gerber
- Weizmann Institute of Science, Rehovot, 76100 Israel
| | | | | |
Collapse
|
28
|
Sal-Man N, Gerber D, Shai Y. The Composition Rather than Position of Polar Residues (QxxS) Drives Aspartate Receptor Transmembrane Domain Dimerization in Vivo. Biochemistry 2004; 43:2309-13. [PMID: 14979727 DOI: 10.1021/bi0356294] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [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: 11/28/2022]
Abstract
Transmembrane (TM) helix association is an important process affecting the function of many integral membrane proteins. Consequently, aberrations in this process are associated with diseases. Unfortunately, our knowledge of the factors that control this oligomerization process in the membrane milieu is limited at best. Previous studies have shown a role for polar residues in the assembly of synthetic peptides in vitro and the association of de novo-designed TM helices in vivo. Here we examined, for the first time, the involvement of polar residues in the dimerization of a biological TM domain in its natural environment. We analyzed both the involvement of polar residues in the dimerization process and whether their influence is position-dependent. For this purpose, we used the TM domain of the Escherichia coli aspartate receptor (Tar) and 10 single and double mutants. Polar to nonpolar mutations in the sequence demonstrated the role of the QxxS motif in the dimerization of the Tar TM domain. Moreover, creating a GxxxG motif, instead of the polar motif, almost completely abolished dimerization. Swapping positions between two wild-type polar residues did not affect dimerization, implying a similar contribution from both positions. Interestingly, mutants that contain two identical strong polar residues, EE and QQ, demonstrated a substantially higher level of dimerization than a QE mutant, although all three TM domains contain two strong polar residues. This result suggests that, in addition to the polarity of the residues, the formation of symmetric bonds also plays a role in dimer stability. The results of this study may facilitate a rational modulation of membrane protein function for therapeutic purposes.
Collapse
Affiliation(s)
- Neta Sal-Man
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel
| | | | | |
Collapse
|
29
|
Schwarz M, Sal-Man N, Zamir A, Pick U. A transferrin-like protein that does not bind iron is induced by iron deficiency in the alga Dunaliella salina. Biochim Biophys Acta 2003; 1649:190-200. [PMID: 12878038 DOI: 10.1016/s1570-9639(03)00185-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron deficiency induces two major transferrin-like proteins in the plasma membrane (Pm) of the halotolerant alga Dunaliella salina. TTf, a 150-kDa protein, previously identified as a salt-induced triplicated transferrin, having iron-binding characteristics resembling animal transferrins, and a 100-kDa protein designated idi-100 (for iron-deficiency-induced 100 kDa protein). According to the predicted amino acid sequence of idi-100, it is only 30% identical to TTf and differs from it in having two, rather than three, homologous internal repeats and in a lower conservation of canonical iron/bicarbonate binding residues. Both are localized in the outer surface of the membrane; however, TTf can be dissociated from the membrane by treatment with EDTA, whereas release of idi-100 requires detergents. The accumulation of idi-100 under iron deficiency lags behind that of TTf and in contrast to TTf, it is not induced by high salinity, suggesting that induction of idi-100 requires lower Fe threshold levels than that of TTf. In contrast to TTf, idi-100 does not bind Fe; however, there are indications for interactions with bicarbonate ions. These results suggest that despite their common resemblance to transferrins, their similar subcellular localization and their induction by iron deficiency, idi-100 and TTf fulfill different functions.
Collapse
Affiliation(s)
- Michal Schwarz
- The Department of Biological Chemistry, Weizmann Institute of Science, PO Box 26, 76100 Rehovot, Israel
| | | | | | | |
Collapse
|
30
|
Abstract
Membrane-active peptides comprise a large group of toxins used in the defense and offense systems of all organisms including plants and humans. They act on diverse targets including microorganisms and mammalian cells, but the factors that determine their target cell selectivity are not yet clear. Here, we tested the role of peptide length and preassembly on the ability of diastereomeric cationic antimicrobial peptides to discriminate among bacteria, erythrocytes, and fungal cells, by using peptides with variable lengths (13, 16, and 19 amino acids long) and their covalently linked pentameric bundles. All the bundles expressed similar potent antifungal activity (minimal inhibitory concentration of 0.2-0.3 microM) and high antimicrobial activity. Hemolytic activity was also observed at concentrations higher than those required for antifungal activity. In contrast, all the monomers showed length-dependent antimicrobial activity, were less active toward bacteria and fungi, and were devoid of hemolytic activity. BIAcore biosensor experiments revealed a approximately 300-fold increase in peptide-membrane binding affinity between the 13- and 19-residue monomers toward zwitterionic (egg phosphatidylcholine (PC)/egg spingomyelin (SM)/cholesterol) vesicles. All the monomeric peptides display a similar high affinity to negatively charged (E. coli phosphatidylethanolamine (PE)/egg phosphatidylglycerol (PG)) vesicles regardless of their length. In contrast, irrespective of the size of the monomeric subunit, all the bundles bind irreversibly and strongly disrupt both PC/SM/cholesterol and PE/PG membranes. Attenuated total reflectance Fourier-transform infrared spectroscopy revealed that peptide assembly also affects structure as observed by an increased alpha-helical and beta-sheet content in membranes and enhances acyl chain disruption of PC/cholesterol. The correlation between the antibacterial activity and ability to depolarize the transmembrane potential of E. coli spheroplasts, as well as the ability to induce calcein release from vesicles, suggests that the bacterial membrane is their target. The data demonstrate that preassembly of cationic diastereomeric antimicrobial peptides is an essential factor in their membrane targeting.
Collapse
Affiliation(s)
- Neta Sal-Man
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | |
Collapse
|