1
|
White SH. Fifty Years of Biophysics at the Membrane Frontier. Annu Rev Biophys 2023; 52:21-67. [PMID: 36791747 DOI: 10.1146/annurev-biophys-051622-112341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The author first describes his childhood in the South and the ways in which it fostered the values he has espoused throughout his life, his development of a keen fascination with science, and the influences that supported his progress toward higher education. His experiences in ROTC as a student, followed by two years in the US Army during the Vietnam War, honed his leadership skills. The bulk of the autobiography is a chronological journey through his scientific career, beginning with arrival at the University of California, Irvine in 1972, with an emphasis on the postdoctoral students and colleagues who have contributed substantially to each phase of his lab's progress. White's fundamental findings played a key role in the development of membrane biophysics, helping establish it as fertile ground for research. A story gradually unfolds that reveals the deeply collaborative and painstakingly executed work necessary for a successful career in science.
Collapse
Affiliation(s)
- Stephen H White
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California, USA;
| |
Collapse
|
2
|
Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
Collapse
Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| |
Collapse
|
3
|
Lee B, Wang T. A Modular Scaffold for Controlling Transcriptional Activation via Homomeric Protein-Protein Interactions. ACS Synth Biol 2022; 11:3198-3206. [PMID: 36215660 DOI: 10.1021/acssynbio.2c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein-protein interactions (PPIs) have been extensively utilized in synthetic biology to construct artificial gene networks. However, synthetic regulation of gene expression by PPIs in E. coli has largely relied upon repressors, and existing PPI-controlled transcriptional activators have generally been employed with heterodimeric interactions. Here we report a highly modular, PPI-dependent transcriptional activator, cCadC, that was designed to be compatible with homomeric interactions. We describe the process of engineering cCadC from a transmembrane protein into a soluble cytosolic regulator. We then show that gene transcription by cCadC can be controlled by homomeric PPIs and furthermore discriminates between dimeric and higher-order interactions. Finally, we demonstrate that cCadC activity can be placed under small molecule regulation using chemically induced dimerization or ligand dependent stabilization. This work should greatly expand the scope of PPIs that can be employed in artificial gene circuits in E. coli and complements the existing repertoire of tools for transcriptional regulation in synthetic biology.
Collapse
Affiliation(s)
- ByungUk Lee
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Tina Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
4
|
Chang HJ, Zúñiga A, Conejero I, Voyvodic PL, Gracy J, Fajardo-Ruiz E, Cohen-Gonsaud M, Cambray G, Pageaux GP, Meszaros M, Meunier L, Bonnet J. Programmable receptors enable bacterial biosensors to detect pathological biomarkers in clinical samples. Nat Commun 2021; 12:5216. [PMID: 34471137 PMCID: PMC8410942 DOI: 10.1038/s41467-021-25538-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial biosensors, or bactosensors, are promising agents for medical and environmental diagnostics. However, the lack of scalable frameworks to systematically program ligand detection limits their applications. Here we show how novel, clinically relevant sensing modalities can be introduced into bactosensors in a modular fashion. To do so, we have leveraged a synthetic receptor platform, termed EMeRALD (Engineered Modularized Receptors Activated via Ligand-induced Dimerization) which supports the modular assembly of sensing modules onto a high-performance, generic signaling scaffold controlling gene expression in E. coli. We apply EMeRALD to detect bile salts, a biomarker of liver dysfunction, by repurposing sensing modules from enteropathogenic Vibrio species. We improve the sensitivity and lower the limit-of-detection of the sensing module by directed evolution. We then engineer a colorimetric bactosensor detecting pathological bile salt levels in serum from patients having undergone liver transplant, providing an output detectable by the naked-eye. The EMeRALD technology enables functional exploration of natural sensing modules and rapid engineering of synthetic receptors for diagnostics, environmental monitoring, and control of therapeutic microbes.
Collapse
Affiliation(s)
- Hung-Ju Chang
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Ana Zúñiga
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Ismael Conejero
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
- Neuropsychiatry: Epidemiological and Clinical Research, Inserm Unit 1061, Montpellier, France
- Department of Psychiatry, CHU Nimes, University of Montpellier, Montpellier, France
| | - Peter L Voyvodic
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Jerome Gracy
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Elena Fajardo-Ruiz
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Martin Cohen-Gonsaud
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Guillaume Cambray
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France
| | - Georges-Philippe Pageaux
- Department of Hepatogastroenterology, Hepatology and Liver Transplantation Unit, Saint Eloi Hospital, University of Montpellier, Montpellier, France
| | - Magdalena Meszaros
- Department of Hepatogastroenterology, Hepatology and Liver Transplantation Unit, Saint Eloi Hospital, University of Montpellier, Montpellier, France
| | - Lucy Meunier
- Department of Hepatogastroenterology, Hepatology and Liver Transplantation Unit, Saint Eloi Hospital, University of Montpellier, Montpellier, France
| | - Jerome Bonnet
- Centre de Biologie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France.
| |
Collapse
|
5
|
Martini L, Brameyer S, Hoyer E, Jung K, Gerland U. Dynamics of chromosomal target search by a membrane-integrated one-component receptor. PLoS Comput Biol 2021; 17:e1008680. [PMID: 33539417 PMCID: PMC7888679 DOI: 10.1371/journal.pcbi.1008680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/17/2021] [Accepted: 01/07/2021] [Indexed: 12/03/2022] Open
Abstract
Membrane proteins account for about one third of the cellular proteome, but it is still unclear how dynamic they are and how they establish functional contacts with cytoplasmic interaction partners. Here, we consider a membrane-integrated one-component receptor that also acts as a transcriptional activator, and analyze how it kinetically locates its specific binding site on the genome. We focus on the case of CadC, the pH receptor of the acid stress response Cad system in E. coli. CadC is a prime example of a one-component signaling protein that directly binds to its cognate target site on the chromosome to regulate transcription. We combined fluorescence microscopy experiments, mathematical analysis, and kinetic Monte Carlo simulations to probe this target search process. Using fluorescently labeled CadC, we measured the time from activation of the receptor until successful binding to the DNA in single cells, exploiting that stable receptor-DNA complexes are visible as fluorescent spots. Our experimental data indicate that CadC is highly mobile in the membrane and finds its target by a 2D diffusion and capture mechanism. DNA mobility is constrained due to the overall chromosome organization, but a labeled DNA locus in the vicinity of the target site appears sufficiently mobile to randomly come close to the membrane. Relocation of the DNA target site to a distant position on the chromosome had almost no effect on the mean search time, which was between four and five minutes in either case. However, a mutant strain with two binding sites displayed a mean search time that was reduced by about a factor of two. This behavior is consistent with simulations of a coarse-grained lattice model for the coupled dynamics of DNA within a cell volume and proteins on its surface. The model also rationalizes the experimentally determined distribution of search times. Overall our findings reveal that DNA target search does not present a much bigger kinetic challenge for membrane-integrated proteins than for cytoplasmic proteins. More generally, diffusion and capture mechanisms may be sufficient for bacterial membrane proteins to establish functional contacts with cytoplasmic targets. Adaptation to changing environments is vital to bacteria and is enabled by sophisticated signal transduction systems. While signal transduction by two-component systems is well studied, the signal transduction of membrane-integrated one-component systems, where one protein performs both sensing and response regulation, are insufficiently understood. How can a membrane-integrated protein bind to specific sites on the genome to regulate transcription? Here, we study the kinetics of this process, which involves both protein diffusion within the membrane and conformational fluctuations of the genomic DNA. A well-suited model system for this question is CadC, the signaling protein of the E. coli Cad system involved in pH stress response. Fluorescently labeled CadC forms visible spots in single cells upon stable DNA-binding, marking the end of the protein-DNA search process. Moreover, the start of the search is triggered by a medium shift exposing cells to pH stress. We probe the underlying mechanism by varying the number and position of DNA target sites. We combine these experiments with mathematical analysis and kinetic Monte Carlo simulations of lattice models for the search process. Our results suggest that CadC diffusion in the membrane is pivotal for this search, while the DNA target site is just mobile enough to reach the membrane.
Collapse
Affiliation(s)
- Linda Martini
- Physics of Complex Biosystems, Technical University of Munich, Garching, Germany
| | - Sophie Brameyer
- Microbiology, Ludwig-Maximilians-University Munich, Martinsried, Germany
| | - Elisabeth Hoyer
- Microbiology, Ludwig-Maximilians-University Munich, Martinsried, Germany
| | - Kirsten Jung
- Microbiology, Ludwig-Maximilians-University Munich, Martinsried, Germany
- * E-mail: (KJ); (UG)
| | - Ulrich Gerland
- Physics of Complex Biosystems, Technical University of Munich, Garching, Germany
- * E-mail: (KJ); (UG)
| |
Collapse
|
6
|
Graf von Armansperg B, Koller F, Gericke N, Hellwig M, Jagtap PKA, Heermann R, Hennig J, Henle T, Lassak J. Transcriptional regulation of the N ε -fructoselysine metabolism in Escherichia coli by global and substrate-specific cues. Mol Microbiol 2020; 115:175-190. [PMID: 32979851 DOI: 10.1111/mmi.14608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022]
Abstract
Thermally processed food is an important part of the human diet. Heat-treatment, however, promotes the formation of so-called Amadori rearrangement products, such as fructoselysine. The gut microbiota including Escherichia coli can utilize these compounds as a nutrient source. While the degradation route for fructoselysine is well described, regulation of the corresponding pathway genes frlABCD remained poorly understood. Here, we used bioinformatics combined with molecular and biochemical analyses and show that fructoselysine metabolism in E. coli is tightly controlled at the transcriptional level. The global regulator CRP (CAP) as well as the alternative sigma factor σ32 (RpoH) contribute to promoter activation at high cAMP-levels and inside warm-blooded hosts, respectively. In addition, we identified and characterized a transcriptional regulator FrlR, encoded adjacent to frlABCD, as fructoselysine-6-phosphate specific repressor. Our study provides profound evidence that the interplay of global and substrate-specific regulation is a perfect adaptation strategy to efficiently utilize unusual substrates within the human gut environment.
Collapse
Affiliation(s)
| | - Franziska Koller
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Gericke
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Hellwig
- Chair of Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | | | - Ralf Heermann
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thomas Henle
- Chair of Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| |
Collapse
|
7
|
Brameyer S, Hoyer E, Bibinger S, Burdack K, Lassak J, Jung K. Molecular design of a signaling system influences noise in protein abundance under acid stress in different γ-Proteobacteria. J Bacteriol 2020; 202:JB.00121-20. [PMID: 32482722 PMCID: PMC8404709 DOI: 10.1128/jb.00121-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/22/2020] [Indexed: 12/16/2022] Open
Abstract
Bacteria have evolved different signaling systems to sense and adapt to acid stress. One of these systems, the CadABC-system, responds to a combination of low pH and lysine availability. In Escherichia coli, the two signals are sensed by the pH sensor and transcription activator CadC and the co-sensor LysP, a lysine-specific transporter. Activated CadC promotes the transcription of the cadBA operon, which codes for the lysine decarboxylase CadA and the lysine/cadaverine antiporter CadB. The copy number of CadC is controlled translationally. Using a bioinformatics approach, we identified the presence of CadC with ribosomal stalling motifs together with LysP in species of the Enterobacteriaceae family. In contrast, we identified CadC without stalling motifs in species of the Vibrionaceae family, but the LysP co-sensor was not identified. Therefore, we compared the output of the Cad system in single cells of the distantly related organisms E. coli and V. campbellii using fluorescently-tagged CadB as the reporter. We observed a heterogeneous output in E. coli, and all the V. campbellii cells produced CadB. The copy number of the pH sensor CadC in E. coli was extremely low (≤4 molecules per cell), but it was 10-fold higher in V. campbellii An increase in the CadC copy number in E. coli correlated with a decrease in heterogeneous behavior. This study demonstrated how small changes in the design of a signaling system allow a homogeneous output and, thus, adaptation of Vibrio species that rely on the CadABC-system as the only acid resistance system.Importance Acid resistance is an important property of bacteria, such as Escherichia coli, to survive acidic environments like the human gastrointestinal tract. E. coli possess both passive and inducible acid resistance systems to counteract acidic environments. Thus, E. coli evolved sophisticated signaling systems to sense and appropriately respond to environmental acidic stress by regulating the activity of its three inducible acid resistance systems. One of these systems is the Cad system that is only induced under moderate acidic stress in a lysine-rich environment by the pH-responsive transcriptional regulator CadC. The significance of our research is in identifying the molecular design of the Cad systems in different Proteobacteria and their target expression noise at single cell level during acid stress conditions.
Collapse
Affiliation(s)
- Sophie Brameyer
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Elisabeth Hoyer
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Sebastian Bibinger
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Korinna Burdack
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| |
Collapse
|
8
|
Yeo WS, Anokwute C, Marcadis P, Levitan M, Ahmed M, Bae Y, Kim K, Kostrominova T, Liu Q, Bae T. A Membrane-Bound Transcription Factor is Proteolytically Regulated by the AAA+ Protease FtsH in Staphylococcus aureus. J Bacteriol 2020; 202:e00019-20. [PMID: 32094161 PMCID: PMC7148131 DOI: 10.1128/jb.00019-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
In bacteria, chromosomal DNA resides in the cytoplasm, and most transcription factors are also found in the cytoplasm. However, some transcription factors, called membrane-bound transcription factors (MTFs), reside in the cytoplasmic membrane. Here, we report the identification of a new MTF in the Gram-positive pathogen Staphylococcus aureus and its regulation by the protease FtsH. The MTF, named MbtS (membrane-bound transcription factor of Staphylococcus aureus), is encoded by SAUSA300_2640 and predicted to have an N-terminal DNA binding domain and three transmembrane helices. The MbtS protein was degraded by membrane vesicles containing FtsH or by the purified FtsH. MbtS bound to an inverted repeat sequence in its promoter region, and the DNA binding was essential for its transcription. Transcriptional comparison between the ftsH deletion mutant and the ftsH mbtS double mutant showed that MbtS could alter the transcription of over 200 genes. Although the MbtS protein was not detected in wild-type (WT) cells grown in a liquid medium, the protein was detected in some isolated colonies on an agar plate. In a murine model of a skin infection, the disruption of mbtS increased the lesion size. Based on these results, we concluded that MbtS is a new S. aureus MTF whose activity is proteolytically regulated by FtsH.IMPORTANCEStaphylococcus aureus is an important pathogenic bacterium causing various diseases in humans. In the bacterium, transcription is typically regulated by the transcription factors located in the cytoplasm. In this study, we report an atypical transcription factor identified in S. aureus Unlike most other transcription factors, the newly identified transcription factor is located in the cytoplasmic membrane, and its activity is proteolytically controlled by the membrane-bound AAA+ protease FtsH. The newly identified MTF, named MbtS, has the potential to regulate the transcription of over 200 genes. This study provides a molecular mechanism by which a protease affects bacterial transcription and illustrates the diversity of the bacterial transcriptional regulation.
Collapse
Affiliation(s)
- Won-Sik Yeo
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana, USA
| | - Chiamara Anokwute
- Department of Biology, Indiana University Northwest, Gary, Indiana, USA
| | - Philip Marcadis
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana, USA
| | - Marcus Levitan
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Mahmoud Ahmed
- Department of Biology, Indiana University Northwest, Gary, Indiana, USA
| | - Yeun Bae
- Department of Psychology, Indiana University, Bloomington, Indiana, USA
| | - Kyeongkyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Tatiana Kostrominova
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine-Northwest, Gary, Indiana, USA
| | - Qian Liu
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana, USA
| |
Collapse
|
9
|
Alvarado A, Behrens W, Josenhans C. Protein Activity Sensing in Bacteria in Regulating Metabolism and Motility. Front Microbiol 2020; 10:3055. [PMID: 32010106 PMCID: PMC6978683 DOI: 10.3389/fmicb.2019.03055] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/18/2019] [Indexed: 01/24/2023] Open
Abstract
Bacteria have evolved complex sensing and signaling systems to react to their changing environments, most of which are present in all domains of life. Canonical bacterial sensing and signaling modules, such as membrane-bound ligand-binding receptors and kinases, are very well described. However, there are distinct sensing mechanisms in bacteria that are less studied. For instance, the sensing of internal or external cues can also be mediated by changes in protein conformation, which can either be implicated in enzymatic reactions, transport channel formation or other important cellular functions. These activities can then feed into pathways of characterized kinases, which translocate the information to the DNA or other response units. This type of bacterial sensory activity has previously been termed protein activity sensing. In this review, we highlight the recent findings about this non-canonical sensory mechanism, as well as its involvement in metabolic functions and bacterial motility. Additionally, we explore some of the specific proteins and protein-protein interactions that mediate protein activity sensing and their downstream effects. The complex sensory activities covered in this review are important for bacterial navigation and gene regulation in their dynamic environment, be it host-associated, in microbial communities or free-living.
Collapse
Affiliation(s)
- Alejandra Alvarado
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany
| | - Wiebke Behrens
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
| | - Christine Josenhans
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
| |
Collapse
|
10
|
Bañares AB, Valdehuesa KNG, Ramos KRM, Nisola GM, Lee WK, Chung WJ. A pH-responsive genetic sensor for the dynamic regulation of D-xylonic acid accumulation in Escherichia coli. Appl Microbiol Biotechnol 2020; 104:2097-2108. [PMID: 31900554 DOI: 10.1007/s00253-019-10297-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/28/2019] [Accepted: 12/03/2019] [Indexed: 11/25/2022]
Abstract
The xylose oxidative pathway (XOP) is continuously gaining prominence as an alternative for the traditional pentose assimilative pathways in prokaryotes. It begins with the oxidation of D-xylose to D-xylonic acid, which is further converted to α-ketoglutarate or pyruvate + glycolaldehyde through a series of enzyme reactions. The persistent drawback of XOP is the accumulation of D-xylonic acid intermediate that causes culture media acidification. This study addresses this issue through the development of a novel pH-responsive synthetic genetic controller that uses a modified transmembrane transcription factor called CadCΔ. This genetic circuit was tested for its ability to detect extracellular pH and to control the buildup of D-xylonic acid in the culture media. Results showed that the pH-responsive genetic sensor confers dynamic regulation of D-xylonic acid accumulation, which adjusts with the perturbation of culture media pH. This is the first report demonstrating the use of a pH-responsive transmembrane transcription factor as a transducer in a synthetic genetic circuit that was designed for XOP. This may serve as a benchmark for the development of other genetic controllers for similar pathways that involve acidic intermediates.
Collapse
Affiliation(s)
- Angelo B Bañares
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea
| | - Kris Niño G Valdehuesa
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea
| | - Kristine Rose M Ramos
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea
| | - Grace M Nisola
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea.
| | - Wook-Jin Chung
- Department of Energy Science and Technology (DEST), Energy and Environment Fusion Technology Center (E2FTC), Myongji University, Myongji-ro 116, Cheoin-gu, Yongin, 17058, Gyeonggi-do, Republic of Korea.
| |
Collapse
|
11
|
Dropping Out and Other Fates of Transmembrane Segments Inserted by the SecA ATPase. J Mol Biol 2019; 431:2006-2019. [PMID: 30914293 DOI: 10.1016/j.jmb.2019.03.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 11/22/2022]
Abstract
Type II single-span membrane proteins, such as CadC or RodZ, lacking a signal sequence and having a far-downstream hydrophobic segment, require the SecA secretion motor for insertion into the inner membrane of Escherichia coli. Using two chimeric single-span proteins containing a designed hydrophobic segment H, we have determined the requirements for SecA-mediated secretion, the molecular distinction between TM domains and signal peptides, and the propensity for hydrophobic H-segments to remain embedded within the bilayer after targeting. By means of engineered H-segments and a strategically placed SPase I cleavage site, we determined how targeting and stability of the chimeric proteins are affected by the length and hydrophobicity of the H-segment. Very hydrophobic segments (e.g., 16 Leu) are stably incorporated into the inner membrane, resulting in a C-terminal anchored membrane protein, while a 24L construct was not targeted to the membrane by SecA and remained in the cytoplasm. However, a construct carrying preMalE at the N-terminus led to SecA targeting to SecYEG via the native signal sequence and stable insertion of the downstream 24L H-segment. We show that the RseP intramembrane protease degrades weakly stable H-segments and is a useful tool for investigating the borderline between stable and unstable TM segments. Using RseP- cells, we find that moderately hydrophobic sequences (e.g., 5Leu + 11Ala) are targeted to SecYEG by SecA and inserted, but subsequently drop out of the membrane into the cytoplasm. Therefore, the free energy of transfer from translocon to bilayer is different from the transfer free energy from membrane to water.
Collapse
|
12
|
Jung K, Fabiani F, Hoyer E, Lassak J. Bacterial transmembrane signalling systems and their engineering for biosensing. Open Biol 2019; 8:rsob.180023. [PMID: 29695618 PMCID: PMC5936718 DOI: 10.1098/rsob.180023] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/03/2018] [Indexed: 12/27/2022] Open
Abstract
Every living cell possesses numerous transmembrane signalling systems that receive chemical and physical stimuli from the environment and transduce this information into an intracellular signal that triggers some form of cellular response. As unicellular organisms, bacteria require these systems for survival in rapidly changing environments. The receptors themselves act as ‘sensory organs’, while subsequent signalling circuits can be regarded as forming a ‘neural network’ that is involved in decision making, adaptation and ultimately in ensuring survival. Bacteria serve as useful biosensors in industry and clinical diagnostics, in addition to producing drugs for therapeutic purposes. Therefore, there is a great demand for engineered bacterial strains that contain transmembrane signalling systems with high molecular specificity, sensitivity and dose dependency. In this review, we address the complexity of transmembrane signalling systems and discuss principles to rewire receptors and their signalling outputs.
Collapse
Affiliation(s)
- Kirsten Jung
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Florian Fabiani
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Elisabeth Hoyer
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Jürgen Lassak
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| |
Collapse
|
13
|
Brameyer S, Rösch TC, El Andari J, Hoyer E, Schwarz J, Graumann PL, Jung K. DNA-binding directs the localization of a membrane-integrated receptor of the ToxR family. Commun Biol 2019; 2:4. [PMID: 30740540 PMCID: PMC6320335 DOI: 10.1038/s42003-018-0248-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/30/2018] [Indexed: 11/28/2022] Open
Abstract
All living cells have a large number of proteins that are anchored with one transmembrane helix in the cytoplasmic membrane. Almost nothing is known about their spatiotemporal organization in whole cells. Here we report on the localization and dynamics of one representative, the pH sensor and transcriptional regulator CadC in Escherichia coli. Fluorophore-tagged CadC was detectable as distinct cluster only when the receptor was activated by external stress, which results in DNA-binding. Clusters immediately disappeared under non-stress conditions. CadC variants that mimic the active state of CadC independent of environmental stimuli corroborated the correlation between CadC clustering and binding to the DNA, as did altering the number or location of the DNA-binding site(s) in whole cells. These studies reveal a novel diffusion-and-capture mechanism to organize a membrane-integrated receptor dependent on the DNA in a rod-shaped bacterium.
Collapse
Affiliation(s)
- Sophie Brameyer
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Thomas C. Rösch
- LOEWE SYNMIKRO, LOEWE Center for Synthetic Microbiology and Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Strasse, Marburg, Germany
| | - Jihad El Andari
- LOEWE SYNMIKRO, LOEWE Center for Synthetic Microbiology and Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Strasse, Marburg, Germany
| | - Elisabeth Hoyer
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Julia Schwarz
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Peter L. Graumann
- LOEWE SYNMIKRO, LOEWE Center for Synthetic Microbiology and Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein Strasse, Marburg, Germany
| | - Kirsten Jung
- Munich Center for Integrated Protein Science (CiPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| |
Collapse
|
14
|
Chang HJ, Mayonove P, Zavala A, De Visch A, Minard P, Cohen-Gonsaud M, Bonnet J. A Modular Receptor Platform To Expand the Sensing Repertoire of Bacteria. ACS Synth Biol 2018; 7:166-175. [PMID: 28946740 PMCID: PMC5880506 DOI: 10.1021/acssynbio.7b00266] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Engineered
bacteria promise to revolutionize diagnostics and therapeutics,
yet many applications are precluded by the limited number of detectable
signals. Here we present a general framework to engineer synthetic
receptors enabling bacterial cells to respond to novel ligands. These
receptors are activated via ligand-induced dimerization
of a single-domain antibody fused to monomeric DNA-binding domains
(split-DBDs). Using E. coli as a model system,
we engineer both transmembrane and cytosolic receptors using a VHH
for ligand detection and demonstrate the scalability of our platform
by using the DBDs of two different transcriptional regulators. We
provide a method to optimize receptor behavior by finely tuning protein
expression levels and optimizing interdomain linker regions. Finally,
we show that these receptors can be connected to downstream synthetic
gene circuits for further signal processing. The general nature of
the split-DBD principle and the versatility of antibody-based detection
should support the deployment of these receptors into various hosts
to detect ligands for which no receptor is found in nature.
Collapse
Affiliation(s)
- Hung-Ju Chang
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Pauline Mayonove
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Agustin Zavala
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Angelique De Visch
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Philippe Minard
- Institute
for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Martin Cohen-Gonsaud
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre
de Biochimie Structurale, INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| |
Collapse
|
15
|
Okada R, Matsuda S, Iida T. Vibrio parahaemolyticus VtrA is a membrane-bound regulator and is activated via oligomerization. PLoS One 2017; 12:e0187846. [PMID: 29149170 PMCID: PMC5693285 DOI: 10.1371/journal.pone.0187846] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/29/2017] [Indexed: 12/31/2022] Open
Abstract
Vibrio parahaemolyticus is a Gram-negative pathogen that causes food-borne gastroenteritis. A major virulence determinant of the organism is a type III secretion system (T3SS2) encoded on a pathogenicity island, Vp-PAI. Vp-PAI gene expression is regulated by two transcriptional regulators, VtrA and VtrB, whose N-terminal regions share homology with an OmpR-family DNA-binding domain. VtrA activates the gene expression of VtrB, which in turn activates Vp-PAI gene expression; however, the mechanism of this transcriptional activation by VtrA is not well understood. In this study, we determined that VtrA is a membrane protein with a transmembrane (TM) domain, which was required for its transcriptional regulatory activity. Although the N-terminal region of VtrA alone is insufficient for its transcriptional regulatory activity, forced oligomerization using the leucine-zipper dimerization domain of yeast GCN4 conferred transcriptional regulatory activity and a greater affinity for the promoter region of vtrB. A ToxR-based assay demonstrated that VtrA oligomerizes in vivo. We also showed that bile, a host-derived activator of VtrA, induces the oligomerization of VtrA, which requires the C-terminal domain. The promoter region of vtrB contained repetitive T-rich DNA elements, which are important for vtrB transcriptional activation and are conserved among T3SS2-possessing Vibrio species. These findings propose that VtrA is active as oligomers, which may facilitate its N-terminus binding the target DNA, thus enhancing its transcriptional regulatory activity.
Collapse
Affiliation(s)
- Ryu Okada
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shigeaki Matsuda
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- * E-mail:
| | - Tetsuya Iida
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| |
Collapse
|
16
|
Wang S, Yang CI, Shan SO. SecA mediates cotranslational targeting and translocation of an inner membrane protein. J Cell Biol 2017; 216:3639-3653. [PMID: 28928132 PMCID: PMC5674894 DOI: 10.1083/jcb.201704036] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/17/2017] [Accepted: 08/02/2017] [Indexed: 12/02/2022] Open
Abstract
Protein targeting to the bacterial plasma membrane was generally thought to occur via two major pathways: cotranslational targeting by signal recognition particle (SRP) and posttranslational targeting by SecA and SecB. Recently, SecA was found to also bind ribosomes near the nascent polypeptide exit tunnel, but the function of this SecA-ribosome contact remains unclear. In this study, we show that SecA cotranslationally recognizes the nascent chain of an inner membrane protein, RodZ, with high affinity and specificity. In vitro reconstitution and in vivo targeting assays show that SecA is necessary and sufficient to direct the targeting and translocation of RodZ to the bacterial plasma membrane in an obligatorily cotranslational mechanism. Sequence elements upstream and downstream of the RodZ transmembrane domain dictate nascent polypeptide selection by SecA instead of the SRP machinery. These findings identify a new route for the targeting of inner membrane proteins in bacteria and highlight the diversity of targeting pathways that enables an organism to accommodate diverse nascent proteins.
Collapse
Affiliation(s)
- Shuai Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
| | - Chien-I Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA
| |
Collapse
|
17
|
Structure-function analysis of the DNA-binding domain of a transmembrane transcriptional activator. Sci Rep 2017; 7:1051. [PMID: 28432336 PMCID: PMC5430869 DOI: 10.1038/s41598-017-01031-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/23/2017] [Indexed: 11/08/2022] Open
Abstract
The transmembrane DNA-binding protein CadC of E. coli, a representative of the ToxR-like receptor family, combines input and effector domains for signal sensing and transcriptional activation, respectively, in a single protein, thus representing one of the simplest signalling systems. At acidic pH in a lysine-rich environment, CadC activates the transcription of the cadBA operon through recruitment of the RNA polymerase (RNAP) to the two cadBA promoter sites, Cad1 and Cad2, which are directly bound by CadC. However, the molecular details for its interaction with DNA have remained elusive. Here, we present the crystal structure of the CadC DNA-binding domain (DBD) and show that it adopts a winged helix-turn-helix fold. The interaction with the cadBA promoter site Cad1 is studied by using nuclear magnetic resonance (NMR) spectroscopy, biophysical methods and functional assays and reveals a preference for AT-rich regions. By mutational analysis we identify amino acids within the CadC DBD that are crucial for DNA-binding and functional activity. Experimentally derived structural models of the CadC-DNA complex indicate that the CadC DBD employs mainly non-sequence-specific over a few specific contacts. Our data provide molecular insights into the CadC-DNA interaction and suggest how CadC dimerization may provide high-affinity binding to the Cad1 promoter.
Collapse
|
18
|
Buchner S, Schlundt A, Lassak J, Sattler M, Jung K. Structural and Functional Analysis of the Signal-Transducing Linker in the pH-Responsive One-Component System CadC of Escherichia coli. J Mol Biol 2015; 427:2548-2561. [DOI: 10.1016/j.jmb.2015.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/13/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
|