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Cao W, Huang C, Zhou X, Zhou S, Deng Y. Engineering two-component systems for advanced biosensing: From architecture to applications in biotechnology. Biotechnol Adv 2024; 75:108404. [PMID: 39002783 DOI: 10.1016/j.biotechadv.2024.108404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/05/2024] [Accepted: 07/07/2024] [Indexed: 07/15/2024]
Abstract
Two-component systems (TCSs) are prevalent signaling pathways in bacteria. These systems mediate phosphotransfer between histidine kinase and a response regulator, facilitating responses to diverse physical, chemical, and biological stimuli. Advancements in synthetic and structural biology have repurposed TCSs for applications in monitoring heavy metals, disease-associated biomarkers, and the production of bioproducts. However, the utility of many TCS biosensors is hindered by undesired performance due to the lack of effective engineering methods. Here, we briefly discuss the architectures and regulatory mechanisms of TCSs. We also summarize the recent advancements in TCS engineering by experimental or computational-based methods to fine-tune the biosensor functional parameters, such as response curve and specificity. Engineered TCSs have great potential in the medical, environmental, and biorefinery fields, demonstrating a crucial role in a wide area of biotechnology.
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Affiliation(s)
- Wenyan Cao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Chao Huang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xuan Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shenghu Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China.
| | - Yu Deng
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China.
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2
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Zhang R, Wang Y. EvgS/EvgA, the unorthodox two-component system regulating bacterial multiple resistance. Appl Environ Microbiol 2023; 89:e0157723. [PMID: 38019025 PMCID: PMC10734491 DOI: 10.1128/aem.01577-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE EvgS/EvgA, one of the five unorthodox two-component systems in Escherichia coli, plays an essential role in adjusting bacterial behaviors to adapt to the changing environment. Multiple resistance regulated by EvgS/EvgA endows bacteria to survive in adverse conditions such as acidic pH, multidrug, and heat. In this minireview, we summarize the specific structures and regulation mechanisms of EvgS/EvgA and its multiple resistance. By discussing several unresolved issues and proposing our speculations, this review will be helpful and enlightening for future directions about EvgS/EvgA.
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Affiliation(s)
- Ruizhen Zhang
- MoE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yan Wang
- MoE Key Laboratory of Evolution and Marine Biodiversity, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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3
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Schmidl SR, Ekness F, Sofjan K, Daeffler KNM, Brink KR, Landry BP, Gerhardt KP, Dyulgyarov N, Sheth RU, Tabor JJ. Rewiring bacterial two-component systems by modular DNA-binding domain swapping. Nat Chem Biol 2019; 15:690-698. [PMID: 31110305 DOI: 10.1038/s41589-019-0286-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/04/2019] [Indexed: 01/16/2023]
Abstract
Two-component systems (TCSs) are the largest family of multi-step signal transduction pathways and valuable sensors for synthetic biology. However, most TCSs remain uncharacterized or difficult to harness for applications. Major challenges are that many TCS output promoters are unknown, subject to cross-regulation, or silent in heterologous hosts. Here, we demonstrate that the two largest families of response regulator DNA-binding domains can be interchanged with remarkable flexibility, enabling the corresponding TCSs to be rewired to synthetic output promoters. We exploit this plasticity to eliminate cross-regulation, un-silence a gram-negative TCS in a gram-positive host, and engineer a system with over 1,300-fold activation. Finally, we apply DNA-binding domain swapping to screen uncharacterized Shewanella oneidensis TCSs in Escherichia coli, leading to the discovery of a previously uncharacterized pH sensor. This work should accelerate fundamental TCS studies and enable the engineering of a large family of genetically encoded sensors with diverse applications.
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Affiliation(s)
- Sebastian R Schmidl
- Department of Bioengineering, Rice University, Houston, TX, USA.,RELLIS campus, Texas A&M University, Bryan, TX, USA
| | - Felix Ekness
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Katri Sofjan
- Department of Biosciences, Rice University, Houston, TX, USA
| | | | - Kathryn R Brink
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Brian P Landry
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Karl P Gerhardt
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Ravi U Sheth
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, Houston, TX, USA. .,PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA. .,Department of Biosciences, Rice University, Houston, TX, USA.
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Abstract
Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. In the prototypical two-component system, a sensor histidine kinase catalyzes its autophosphorylation and then subsequently transfers the phosphoryl group to a response regulator, which can then effect changes in cellular physiology, often by regulating gene expression. The utility of these signaling systems is underscored by their prevalence throughout the bacterial kingdom and by the fact that many bacteria contain dozens, or sometimes hundreds, of these signaling proteins. The presence of so many highly related signaling proteins in individual cells creates both an opportunity and a challenge. Do cells take advantage of the similarity between signaling proteins to integrate signals or diversify responses, and thereby enhance their ability to process information? Conversely, how do cells prevent unwanted cross-talk and maintain the insulation of distinct pathways? Here we address both questions by reviewing the cellular and molecular mechanisms that dictate the specificity of two-component signaling pathways.
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Affiliation(s)
- Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Substitutions at auxiliary operator O3 enhance repression by nitrate-responsive regulator NarL at synthetic lac control regions in Escherichia coli K-12. J Bacteriol 2007; 190:428-33. [PMID: 17965164 DOI: 10.1128/jb.01431-07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We constructed monocopy lac operon control regions in which the operators O1-lac and O3-lac were replaced by NarL and NarP binding sites from the nirB or napF operon control regions. The results support the hypothesis that DNA-bound dimers of phospho-NarL can participate in higher-order cooperative interactions.
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Horvat A, Gross R. Molecular characterization of the BvgA response regulator of Bordetella holmesii. Microbiol Res 2007; 164:243-52. [PMID: 17400438 DOI: 10.1016/j.micres.2006.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Revised: 10/25/2006] [Accepted: 11/08/2006] [Indexed: 11/28/2022]
Abstract
The BvgAS system controls the expression of most virulence factors in Bordetella pertussis. Recently, we identified an orthologous system in the related human pathogen Bordetella holmesii. However, while we found that the orthologous histidine kinases BvgS could be functionally exchanged between the two species, the B. holmesii response regulator BvgA(BH) could not substitute for its B. pertussis counterpart in vivo and, accordingly, was not able to bind to B. pertussis virulence promoters in vitro. Here we show that a hybrid response regulator consisting of the B. pertussis derived DNA-binding output domain of BvgA(BP) combined with the B. holmesii receiver domain binds to BvgA(BP) regulated virulence promoters of B. pertussis in vitro and is functional in B. pertussis in vivo. This shows that the inability of BvgA(BH) to complement BvgA(BP) in B. pertussis is due to the small number of sequence variations present in its output domain. However, by mutation analysis we show that four amino acid exchanges present in the helix-turn-helix motif of BvgA(BH) as compared to BvgA(BP) are not the only reason for its inability to substitute for BvgA(BP) but additional mutations present in the output domain must play a role.
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Affiliation(s)
- Aleksandra Horvat
- Lehrstuhl für Mikrobiologie, Biozentrum, Universität Würzburg, Am Hubland, Würzburg, Germany
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Middendorf B, Stubs D, Guiso N, Deppisch H, Gross R, Fuchs TM. Phg, a novel member of the autotransporter family present in Bordetella species. Microbiol Res 2005; 160:329-36. [PMID: 16035245 DOI: 10.1016/j.micres.2005.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Several proteins encoded in the genomes of Bordetella species show significant sequence similarity to the autotransporter domains of surface exposed or secreted virulence factors of bordetellae such as pertactin, tracheal colonization factor or Vag8. One of these putative autotransporters, provisionally termed Phg, is encoded by the pertactin homologous gene (phg), which is highly conserved in Bordetella pertussis, B. bronchiseptica and B. parapertussis, but absent in B. avium and B. petrii. In contrast to homologues with documented functions in host interaction and virulence, several key amino acids probably involved in proteolytic processing of the autotransporter domain are not conserved in Phg. The transcription start site of phg was identified by primer extension analysis, but differential transcription of phg could not be detected in B. bronchiseptica strains under conditions that lead to enhanced expression of other known Bordetella autotransporter proteins. A mutant of B. pertussis was constructed in which major parts of phg are substituted by a kanamycin resistance cassette. Virulence testing of this mutant in a mouse respiratory infection model showed the same colonization properties as the wild-type strain.
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Affiliation(s)
- Barbara Middendorf
- Lehrstuhl für Mikrobiologie, Biozentrum, Universität Würzburg, D-97074 Würzburg, Germany
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Gerlach G, Janzen S, Beier D, Gross R. Functional characterization of the BvgAS two-component system of Bordetella holmesii. MICROBIOLOGY-SGM 2005; 150:3715-3729. [PMID: 15528658 DOI: 10.1099/mic.0.27432-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The BvgAS two-component system is the master regulator of virulence gene expression in the mammalian pathogens Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. This paper reports the partial cloning and characterization of the bvgAS loci of the 'new' Bordetella species Bordetella holmesii, Bordetella trematum and Bordetella hinzii, which are increasingly recognized as opportunistic pathogens in humans. It is demonstrated that the cytoplasmic signalling domains of the BvgS histidine kinases of B. pertussis and B. holmesii are functionally interchangeable, while signal perception by the two sensor proteins seems to be different. Furthermore, it is shown that, despite the high similarity of the BvgA proteins of B. pertussis and B. holmesii, promoter recognition by the response regulator proteins differs substantially in these organisms.
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Affiliation(s)
- Gabriele Gerlach
- Theodor-Boveri-Institut für Biowissenschaften, Lehrstuhl für Mikrobiologie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Simone Janzen
- Theodor-Boveri-Institut für Biowissenschaften, Lehrstuhl für Mikrobiologie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Dagmar Beier
- Theodor-Boveri-Institut für Biowissenschaften, Lehrstuhl für Mikrobiologie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Roy Gross
- Theodor-Boveri-Institut für Biowissenschaften, Lehrstuhl für Mikrobiologie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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Birck C, Malfois M, Svergun D, Samama J. Insights into signal transduction revealed by the low resolution structure of the FixJ response regulator. J Mol Biol 2002; 321:447-57. [PMID: 12162958 DOI: 10.1016/s0022-2836(02)00651-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Two-component regulatory systems mediate most of the bacterial cells responses to a variety of signals. In Sinorhizobium meliloti, the FixL-FixJ couple controls the expression of the nitrogen fixation genes through the binding of the two-domains response regulator FixJ to the fixK and nifA promoters. Phosphorylation of the N-terminal regulatory domain activates the protein and releases the inhibition of the C-terminal DNA-binding domain that occurs in the unphosphorylated protein. Insights into the transition from the inactive to the active form are provided by the architecture of the unphosphorylated response regulator reported in this study. The relative position and orientation of the N and C-terminal domains were defined from the molecular envelope restored from small-angle X-ray scattering (SAXS) data. The involvement of the alpha4-beta5-alpha5 surface of the regulatory domain, the linker region and the C-terminal helix of the DNA-binding domain in the interdomain interface of unphosphorylated FixJ was supported by biochemical investigations. These results, together with the previously reported studies on the phosphorylated regulatory domain of FixJ, emphasize the role of the alpha4-beta5-alpha5 surface in mediating a flow of information in this response regulator. This first study by SAXS of proteins from two-component systems suggests that the method could be successfully applied to other members of this family and could be suitable for the study of multidomain proteins and protein-protein complexes regulated through molecular interfaces in the low micromolar range.
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Affiliation(s)
- Catherine Birck
- Groupe de Cristallographie Biologique, CNRS-IPBS, 205 route de Narbonne, 31077- Cedex, Toulouse, France
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Bock A, Gross R. The unorthodox histidine kinases BvgS and EvgS are responsive to the oxidation status of a quinone electron carrier. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:3479-84. [PMID: 12135487 DOI: 10.1046/j.1432-1033.2002.03029.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The purified soluble forms of the histidine kinases BvgS and EvgS of Bordetella pertussis and Escherichia coli, respectively, are shown to be responsive to oxidized ubiquinone-0 (Q-0) in vitro. The oxidized ubiquinone is a strong inhibitor of kinase activity of both enzymes with half maximal inhibition occurring at 11 microm (BvgS) and 4 microm (EvgS). Reduced Q-0 has no effect on the histidine kinases. Kinase activity can reversibly be switched off and on by changing the oxidation status of the quinone. This inhibitory effect is due to a decrease of the kinase activity of BvgS rather than an increase of intrinsic phosphatase activities. Other electron carriers such as menadione (MK-3), NAD or FAD did not have a significant effect on the kinase activities of BvgS and EvgS. Nicotinic acid and sulfate ions, known to inhibit the histidine kinases in vivo, did not affect the purified truncated sensor proteins lacking their periplasmic domains in vitro. Mutations introduced by site-directed mutagenesis into the putative PAS domain of BvgS caused a weak decrease of quinone-dependent inhibition of autophosphorylation. These data suggest that BvgS and EvgS are connected with the oxidation status of the cell via the link to the ubiquinone pool.
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Affiliation(s)
- Andreas Bock
- Lehrstuhl für Mikrobiologie, Biozentrum, Universität Würzburg, Am Hubland, Würzburg, Germany
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