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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] [MESH Headings] [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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Dietler N, Abbara A, Choudhury S, Bitbol AF. Impact of phylogeny on the inference of functional sectors from protein sequence data. PLoS Comput Biol 2024; 20:e1012091. [PMID: 39312591 DOI: 10.1371/journal.pcbi.1012091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024] Open
Abstract
Statistical analysis of multiple sequence alignments of homologous proteins has revealed groups of coevolving amino acids called sectors. These groups of amino-acid sites feature collective correlations in their amino-acid usage, and they are associated to functional properties. Modeling showed that nonlinear selection on an additive functional trait of a protein is generically expected to give rise to a functional sector. These modeling results motivated a principled method, called ICOD, which is designed to identify functional sectors, as well as mutational effects, from sequence data. However, a challenge for all methods aiming to identify sectors from multiple sequence alignments is that correlations in amino-acid usage can also arise from the mere fact that homologous sequences share common ancestry, i.e. from phylogeny. Here, we generate controlled synthetic data from a minimal model comprising both phylogeny and functional sectors. We use this data to dissect the impact of phylogeny on sector identification and on mutational effect inference by different methods. We find that ICOD is most robust to phylogeny, but that conservation is also quite robust. Next, we consider natural multiple sequence alignments of protein families for which deep mutational scan experimental data is available. We show that in this natural data, conservation and ICOD best identify sites with strong functional roles, in agreement with our results on synthetic data. Importantly, these two methods have different premises, since they respectively focus on conservation and on correlations. Thus, their joint use can reveal complementary information.
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Affiliation(s)
- Nicola Dietler
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alia Abbara
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Subham Choudhury
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Anne-Florence Bitbol
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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3
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Westrip CAE, Smerdon SJ, Coleman ML. Rewiring protein binding specificity in paralogous DRG/DFRP complexes. Structure 2024:S0969-2126(24)00329-0. [PMID: 39276770 DOI: 10.1016/j.str.2024.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 05/02/2024] [Accepted: 08/20/2024] [Indexed: 09/17/2024]
Abstract
Eukaryotes have two paralogous developmentally regulated GTP-binding (DRG) proteins: DRG1 and DRG2, both of which have a conserved binding partner called DRG family regulatory protein 1 and 2 (DFRP1 and DFRP2), respectively. DFRPs are important for the function of DRGs and interact with their respective DRG via a conserved region called the DFRP domain. Despite being highly similar, DRG1 and DRG2 have strict binding specificity for their respective DFRP. Using AlphaFold generated structure models of the human DRG/DFRP complexes, we have biochemically characterized their interactions and identified interface residues involved in determining specificity. This analysis revealed that as few as five mutations in DRG1 can switch binding from DFRP1 to DFRP2. Moreover, while DFRP1 binding confers increased stability and GTPase activity to DRG1, DFRP2 binding only supports increased stability. Overall, this work provides new insight into the structural determinants responsible for the binding specificities of the DRG/DFRP complexes.
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Affiliation(s)
- Christian A E Westrip
- Institute of Cancer and Genomics Sciences, University of Birmingham, B15 2TT Birmingham, UK.
| | - Stephen J Smerdon
- Institute of Cancer and Genomics Sciences, University of Birmingham, B15 2TT Birmingham, UK
| | - Mathew L Coleman
- Institute of Cancer and Genomics Sciences, University of Birmingham, B15 2TT Birmingham, UK.
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4
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Sasazawa M, Tomares DT, Childers WS, Saurabh S. Biomolecular condensates as stress sensors and modulators of bacterial signaling. PLoS Pathog 2024; 20:e1012413. [PMID: 39146259 PMCID: PMC11326607 DOI: 10.1371/journal.ppat.1012413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024] Open
Abstract
Microbes exhibit remarkable adaptability to environmental fluctuations. Signaling mechanisms, such as two-component systems and secondary messengers, have long been recognized as critical for sensing and responding to environmental cues. However, recent research has illuminated the potential of a physical adaptation mechanism in signaling-phase separation, which may represent a ubiquitous mechanism for compartmentalizing biochemistry within the cytoplasm in the context of bacteria that frequently lack membrane-bound organelles. This review considers the broader prospect that phase separation may play critical roles as rapid stress sensing and response mechanisms within pathogens. It is well established that weak multivalent interactions between disordered regions, coiled-coils, and other structured domains can form condensates via phase separation and be regulated by specific environmental parameters in some cases. The process of phase separation itself acts as a responsive sensor, influenced by changes in protein concentration, posttranslational modifications, temperature, salts, pH, and oxidative stresses. This environmentally triggered phase separation can, in turn, regulate the functions of recruited biomolecules, providing a rapid response to stressful conditions. As examples, we describe biochemical pathways organized by condensates that are essential for cell physiology and exhibit signaling features. These include proteins that organize and modify the chromosome (Dps, Hu, SSB), regulate the decay, and modification of RNA (RNase E, Hfq, Rho, RNA polymerase), those involved in signal transduction (PopZ, PodJ, and SpmX) and stress response (aggresomes and polyphosphate granules). We also summarize the potential of proteins within pathogens to function as condensates and the potential and challenges in targeting biomolecular condensates for next-generation antimicrobial therapeutics. Together, this review illuminates the emerging significance of biomolecular condensates in microbial signaling, stress responses, and regulation of cell physiology and provides a framework for microbiologists to consider the function of biomolecular condensates in microbial adaptation and response to diverse environmental conditions.
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Affiliation(s)
- Moeka Sasazawa
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Dylan T Tomares
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Saumya Saurabh
- Department of Chemistry, New York University, New York, New York, United States of America
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5
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Xu G, Yang S. Evolution of orphan and atypical histidine kinases and response regulators for microbial signaling diversity. Int J Biol Macromol 2024; 275:133635. [PMID: 38964677 DOI: 10.1016/j.ijbiomac.2024.133635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 06/22/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Two-component signaling systems (TCS) are the predominant means of microbes for sensing and responding to environmental stimuli. Typically, TCS is comprised of a sensor histidine kinase (HK) and a cognate response regulator (RR), which might have coevolved together. They usually involve the phosphoryl transfer signaling mechanism. However, there are also some orphan and atypical HK and RR homologs, and their evolutionary origins are still not very clear. They are not associated with cognate pairs or lack the conserved residues for phosphoryl transfer, but they could receive or respond to signals from other regulators. The objective of this study is to reveal the evolutionary history of these orphan and atypical HK and RR homologs. Structural, domain, sequence, and phylogenetic analyses indicated that their evolution process might undergo gene duplication, divergence, and domain shuffling. Meanwhile, lateral gene transfer might also be involved for their gene distribution. Evolution of orphan and atypical HK and RR homologs have increased their signaling diversity, which could be helpful for microbial adaption in complex environments.
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Affiliation(s)
- Gangming Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Suiqun Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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Gerken H, Shetty D, Kern B, Kenney LJ, Misra R. Effects of pleiotropic ompR and envZ alleles of Escherichia coli on envelope stress and antibiotic sensitivity. J Bacteriol 2024; 206:e0017224. [PMID: 38809006 PMCID: PMC11332150 DOI: 10.1128/jb.00172-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024] Open
Abstract
The EnvZ-OmpR two-component system of Escherichia coli regulates the expression of the ompF and ompC porin genes in response to medium osmolarity. However, certain mutations in envZ confer pleiotropy by affecting the expression of genes of the iron and maltose regulons not normally controlled by EnvZ-OmpR. In this study, we obtained two novel envZ and ompR pleiotropic alleles, envZT15P and ompRL19Q, among revertants of a mutant with heightened envelope stress and an outer membrane (OM) permeability defect. Unlike envZ, pleiotropic mutations in ompR have not been described previously. The mutant alleles reduced the expression of several outer membrane proteins (OMPs), overcame the temperature-sensitive growth defect of a protease-deficient (ΔdegP) strain, and lowered envelope stress and OM permeability defects in a background lacking the BamB protein of an essential β-barrel assembly machinery complex. Biochemical analysis showed OmpRL19Q, like wild-type OmpR, is readily phosphorylated by EnvZ, but the EnvZ-dependent dephosphorylation of OmpRL19Q~P was drastically impaired compared to wild-type OmpR. This defect would lead to a prolonged half-life for OmpRL19Q~P, an outcome remarkably similar to what we had previously described for EnvZR397L, resulting in pleiotropy. By employing null alleles of the OMP genes, it was determined that the three pleiotropic alleles lowered envelope stress by reducing OmpF and LamB levels. The absence of LamB was principally responsible for lowering the OM permeability defect, as assessed by the reduced sensitivity of a ΔbamB mutant to vancomycin and rifampin. Possible mechanisms by which novel EnvZ and OmpR mutants influence EnvZ-OmpR interactions and activities are discussed.IMPORTANCEMaintenance of the outer membrane (OM) integrity is critical for the survival of Gram-negative bacteria. Several envelope homeostasis systems are activated when OM integrity is perturbed. Through the isolation and characterization of novel pleiotropic ompR/envZ alleles, this study highlights the involvement of the EnvZ-OmpR two-component system in lowering envelope stress and the OM permeability defect caused by the loss of proteins that are involved in OM biogenesis, envelope homeostasis, and structural integrity.
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Affiliation(s)
- Henri Gerken
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Dasvit Shetty
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Brea Kern
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Linda J. Kenney
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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7
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Ali L, Abdel Aziz MH. Crosstalk involving two-component systems in Staphylococcus aureus signaling networks. J Bacteriol 2024; 206:e0041823. [PMID: 38456702 PMCID: PMC11025333 DOI: 10.1128/jb.00418-23] [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: 03/09/2024] Open
Abstract
Staphylococcus aureus poses a serious global threat to human health due to its pathogenic nature, adaptation to environmental stress, high virulence, and the prevalence of antimicrobial resistance. The signaling network in S. aureus coordinates and integrates various internal and external inputs and stimuli to adapt and formulate a response to the environment. Two-component systems (TCSs) of S. aureus play a central role in this network where surface-expressed histidine kinases (HKs) receive and relay external signals to their cognate response regulators (RRs). Despite the purported high fidelity of signaling, crosstalk within TCSs, between HK and non-cognate RR, and between TCSs and other systems has been detected widely in bacteria. The examples of crosstalk in S. aureus are very limited, and there needs to be more understanding of its molecular recognition mechanisms, although some crosstalk can be inferred from similar bacterial systems that share structural similarities. Understanding the cellular processes mediated by this crosstalk and how it alters signaling, especially under stress conditions, may help decipher the emergence of antibiotic resistance. This review highlights examples of signaling crosstalk in bacteria in general and S. aureus in particular, as well as the effect of TCS mutations on signaling and crosstalk.
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Affiliation(s)
- Liaqat Ali
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - May H. Abdel Aziz
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
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8
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Ahator SD, Wenzl K, Hegstad K, Lentz CS, Johannessen M. Comprehensive virulence profiling and evolutionary analysis of specificity determinants in Staphylococcus aureus two-component systems. mSystems 2024; 9:e0013024. [PMID: 38470253 PMCID: PMC11019936 DOI: 10.1128/msystems.00130-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
In the Staphylococcus aureus genome, a set of highly conserved two-component systems (TCSs) composed of histidine kinases (HKs) and their cognate response regulators (RRs) sense and respond to environmental stimuli, which drive the adaptation of the bacteria. This study investigates the complex interplay between TCSs in S. aureus USA300, a predominant methicillin-resistant S. aureus strain, revealing shared and unique virulence regulatory pathways and genetic variations mediating signal specificity within TCSs. Using TCS-related mutants from the Nebraska Transposon Mutant Library, we analyzed the effects of inactivated TCS HKs and RRs on the production of various virulence factors, in vitro infection abilities, and adhesion assays. We found that the TCSs' influence on virulence determinants was not associated with their phylogenetic relationship, indicating divergent functional evolution. Using the co-crystallized structure of the DesK-DesR from Bacillus subtilis and the modeled structures of the four NarL TCSs in S. aureus, we identified interacting residues, revealing specificity determinants and conservation within the same TCS, even from different strain backgrounds. The interacting residues were highly conserved within strains but varied between species due to selection pressures and the coevolution of cognate pairs. This study unveils the complex interplay and divergent functional evolution of TCSs, highlighting their potential for future experimental exploration of phosphotransfer between cognate and non-cognate recombinant HK and RRs.IMPORTANCEGiven the widespread conservation of two-component systems (TCSs) in bacteria and their pivotal role in regulating metabolic and virulence pathways, they present a compelling target for anti-microbial agents, especially in the face of rising multi-drug-resistant infections. Harnessing TCSs therapeutically necessitates a profound understanding of their evolutionary trajectory in signal transduction, as this underlies their unique or shared virulence regulatory pathways. Such insights are critical for effectively targeting TCS components, ensuring an optimized impact on bacterial virulence, and mitigating the risk of resistance emergence via the evolution of alternative pathways. Our research offers an in-depth exploration of virulence determinants controlled by TCSs in S. aureus, shedding light on the evolving specificity determinants that orchestrate interactions between their cognate pairs.
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Affiliation(s)
- Stephen Dela Ahator
- Research Group for Host-Microbe Interactions, Centre for New Antibacterial Strategies (CANS), Department of Medical Biology, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Karoline Wenzl
- Research Group for Host-Microbe Interactions, Centre for New Antibacterial Strategies (CANS), Department of Medical Biology, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Research Group for Host-Microbe Interactions, Centre for New Antibacterial Strategies (CANS), Department of Medical Biology, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Christian S. Lentz
- Research Group for Host-Microbe Interactions, Centre for New Antibacterial Strategies (CANS), Department of Medical Biology, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Mona Johannessen
- Research Group for Host-Microbe Interactions, Centre for New Antibacterial Strategies (CANS), Department of Medical Biology, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
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9
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Yan Z, Wang J. Evolution shapes interaction patterns for epistasis and specific protein binding in a two-component signaling system. Commun Chem 2024; 7:13. [PMID: 38233668 PMCID: PMC10794238 DOI: 10.1038/s42004-024-01098-2] [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: 06/27/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
The elegant design of protein sequence/structure/function relationships arises from the interaction patterns between amino acid positions. A central question is how evolutionary forces shape the interaction patterns that encode long-range epistasis and binding specificity. Here, we combined family-wide evolutionary analysis of natural homologous sequences and structure-oriented evolution simulation for two-component signaling (TCS) system. The magnitude-frequency relationship of coupling conservation between positions manifests a power-law-like distribution and the positions with highly coupling conservation are sparse but distributed intensely on the binding surfaces and hydrophobic core. The structure-specific interaction pattern involves further optimization of local frustrations at or near the binding surface to adapt the binding partner. The construction of family-wide conserved interaction patterns and structure-specific ones demonstrates that binding specificity is modulated by both direct intermolecular interactions and long-range epistasis across the binding complex. Evolution sculpts the interaction patterns via sequence variations at both family-wide and structure-specific levels for TCS system.
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Affiliation(s)
- Zhiqiang Yan
- Center for Theoretical Interdisciplinary Sciences, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, PR China
| | - Jin Wang
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY, 11790, USA.
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10
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Giulini M, Honorato RV, Rivera JL, Bonvin AMJJ. ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information. Commun Biol 2024; 7:49. [PMID: 38184711 PMCID: PMC10771469 DOI: 10.1038/s42003-023-05718-w] [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] [Received: 07/25/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024] Open
Abstract
The formation of a stable complex between proteins lies at the core of a wide variety of biological processes and has been the focus of countless experiments. The huge amount of information contained in the protein structural interactome in the Protein Data Bank can now be used to characterise and classify the existing biological interfaces. We here introduce ARCTIC-3D, a fast and user-friendly data mining and clustering software to retrieve data and rationalise the interface information associated with the protein input data. We demonstrate its use by various examples ranging from showing the increased interaction complexity of eukaryotic proteins, 20% of which on average have more than 3 different interfaces compared to only 10% for prokaryotes, to associating different functions to different interfaces. In the context of modelling biomolecular assemblies, we introduce the concept of "recognition entropy", related to the number of possible interfaces of the components of a protein-protein complex, which we demonstrate to correlate with the modelling difficulty in classical docking approaches. The identified interface clusters can also be used to generate various combinations of interface-specific restraints for integrative modelling. The ARCTIC-3D software is freely available at github.com/haddocking/arctic3d and can be accessed as a web-service at wenmr.science.uu.nl/arctic3d.
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Affiliation(s)
- Marco Giulini
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584, Utrecht, CH, The Netherlands
| | - Rodrigo V Honorato
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584, Utrecht, CH, The Netherlands
| | - Jesús L Rivera
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584, Utrecht, CH, The Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584, Utrecht, CH, The Netherlands.
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11
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Xi C, Diao J, Moon TS. Advances in ligand-specific biosensing for structurally similar molecules. Cell Syst 2023; 14:1024-1043. [PMID: 38128482 PMCID: PMC10751988 DOI: 10.1016/j.cels.2023.10.009] [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] [Received: 05/21/2023] [Revised: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023]
Abstract
The specificity of biological systems makes it possible to develop biosensors targeting specific metabolites, toxins, and pollutants in complex medical or environmental samples without interference from structurally similar compounds. For the last two decades, great efforts have been devoted to creating proteins or nucleic acids with novel properties through synthetic biology strategies. Beyond augmenting biocatalytic activity, expanding target substrate scopes, and enhancing enzymes' enantioselectivity and stability, an increasing research area is the enhancement of molecular specificity for genetically encoded biosensors. Here, we summarize recent advances in the development of highly specific biosensor systems and their essential applications. First, we describe the rational design principles required to create libraries containing potential mutants with less promiscuity or better specificity. Next, we review the emerging high-throughput screening techniques to engineer biosensing specificity for the desired target. Finally, we examine the computer-aided evaluation and prediction methods to facilitate the construction of ligand-specific biosensors.
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Affiliation(s)
- Chenggang Xi
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jinjin Diao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA.
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12
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Yang X, Rocks JW, Jiang K, Walters AJ, Rai K, Liu J, Nguyen J, Olson SD, Mehta P, Collins JJ, Daringer NM, Bashor CJ. Engineering synthetic phosphorylation signaling networks in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557100. [PMID: 37745327 PMCID: PMC10515791 DOI: 10.1101/2023.09.11.557100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Protein phosphorylation signaling networks play a central role in how cells sense and respond to their environment. Here, we describe the engineering of artificial phosphorylation networks in which "push-pull" motifs-reversible enzymatic phosphorylation cycles consisting of opposing kinase and phosphatase activities-are assembled from modular protein domain parts and then wired together to create synthetic phosphorylation circuits in human cells. We demonstrate that the composability of our design scheme enables model-guided tuning of circuit function and the ability to make diverse network connections; synthetic phosphorylation circuits can be coupled to upstream cell surface receptors to enable fast-timescale sensing of extracellular ligands, while downstream connections can regulate gene expression. We leverage these capabilities to engineer cell-based cytokine controllers that dynamically sense and suppress activated T cells. Our work introduces a generalizable approach for designing and building phosphorylation signaling circuits that enable user-defined sense-and-respond function for diverse biosensing and therapeutic applications.
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Affiliation(s)
- Xiaoyu Yang
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
- Graduate Program in Systems, Synthetic and Physical Biology, Rice University; Houston, TX 77030, USA
| | - Jason W. Rocks
- Department of Physics, Boston University; Boston, MA 02215, USA
| | - Kaiyi Jiang
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
| | - Andrew J. Walters
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
- Graduate Program in Bioengineering, Rice University; Houston, TX 77030, USA
- Department of Pediatric Surgery, McGovern Medical School, University of Texas Health Science Center at Houston; Houston, TX 77030, USA
| | - Kshitij Rai
- Graduate Program in Systems, Synthetic and Physical Biology, Rice University; Houston, TX 77030, USA
| | - Jing Liu
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
| | - Jason Nguyen
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
| | - Scott D. Olson
- Department of Pediatric Surgery, McGovern Medical School, University of Texas Health Science Center at Houston; Houston, TX 77030, USA
| | - Pankaj Mehta
- Department of Physics, Boston University; Boston, MA 02215, USA
- Biological Design Center, Boston University; Boston, MA 02215, USA
- Faculty of Computing and Data Science, Boston University; Boston, MA 02215, USA
| | - James J. Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University; Boston, MA 02115, USA
| | - Nichole M Daringer
- Department of Biomedical Engineering, Rowan University; Glassboro, NJ 08028, USA
| | - Caleb J. Bashor
- Department of Bioengineering, Rice University; Houston, TX 77030, USA
- Department of Biosciences, Rice University; Houston, TX 77030, USA
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13
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Mao Y, Huang C, Zhou X, Han R, Deng Y, Zhou S. Genetically Encoded Biosensor Engineering for Application in Directed Evolution. J Microbiol Biotechnol 2023; 33:1257-1267. [PMID: 37449325 PMCID: PMC10619561 DOI: 10.4014/jmb.2304.04031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023]
Abstract
Although rational genetic engineering is nowadays the favored method for microbial strain improvement, building up mutant libraries based on directed evolution for improvement is still in many cases the better option. In this regard, the demand for precise and efficient screening methods for mutants with high performance has stimulated the development of biosensor-based high-throughput screening strategies. Genetically encoded biosensors provide powerful tools to couple the desired phenotype to a detectable signal, such as fluorescence and growth rate. Herein, we review recent advances in engineering several classes of biosensors and their applications in directed evolution. Furthermore, we compare and discuss the screening advantages and limitations of two-component biosensors, transcription-factor-based biosensors, and RNA-based biosensors. Engineering these biosensors has focused mainly on modifying the expression level or structure of the biosensor components to optimize the dynamic range, specificity, and detection range. Finally, the applications of biosensors in the evolution of proteins, metabolic pathways, and genome-scale metabolic networks are described. This review provides potential guidance in the design of biosensors and their applications in improving the bioproduction of microbial cell factories through directed evolution.
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Affiliation(s)
- Yin Mao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Chao Huang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Xuan Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yu Deng
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Shenghu Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
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14
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Bhattarai S, Marsh L, Knight K, Ali L, Gomez A, Sunderhaus A, Abdel Aziz MH. NH125 Sensitizes Staphylococcus aureus to Cell Wall-Targeting Antibiotics through the Inhibition of the VraS Sensor Histidine Kinase. Microbiol Spectr 2023; 11:e0486122. [PMID: 37227302 PMCID: PMC10269531 DOI: 10.1128/spectrum.04861-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Staphylococcus aureus utilizes the two-component regulatory system VraSR to receive and relay environmental stress signals, and it is implicated in the development of bacterial resistance to several antibiotics through the upregulation of cell wall synthesis. VraS inhibition was shown to extend or restore the efficacy of several clinically used antibiotics. In this work, we study the enzymatic activity of the VraS intracellular domain (GST-VraS) to determine the kinetic parameters of the ATPase reaction and characterize the inhibition of NH125 under in vitro and microbiological settings. The rate of the autophosphorylation reaction was determined at different GST-VraS concentrations (0.95 to 9.49 μM) and temperatures (22 to 40°C) as well as in the presence of different divalent cations. The activity and inhibition by NH125, which is a known kinase inhibitor, were assessed in the presence and absence of the binding partner, VraR. The effects of inhibition on the bacterial growth kinetics and gene expression levels were determined. The GST-VraS rate of autophosphorylation increases with temperature and with the addition of VraR, with magnesium being the preferred divalent cation for the metal-ATP substrate complex. The mechanism of inhibition of NH125 was noncompetitive in nature and was attenuated in the presence of VraR. The addition of NH125 in the presence of sublethal doses of the cell wall-targeting antibiotics carbenicillin and vancomycin led to the complete abrogation of Staphylococcus aureus Newman strain growth and significantly decreased the gene expression levels of pbpB, blaZ, and vraSR in the presence of the antibiotics. IMPORTANCE This work characterizes the activity and inhibition of VraS, which is a key histidine kinase in a bacterial two-component system that is involved in Staphylococcus aureus antibiotic resistance. The results show the effect of temperature, divalent ions, and VraR on the activity and the kinetic parameters of ATP binding. The value of the KM of ATP is vital in designing screening assays to discover potent and effective VraS inhibitors with high translational potential. We report the ability of NH125 to inhibit VraS in vitro in a noncompetitive manner and investigate its effect on gene expression and bacterial growth kinetics in the presence and absence of cell wall-targeting antibiotics. NH125 effectively potentiated the effects of the antibiotics on bacterial growth and altered the expression of the genes that are regulated by VraS and are involved in mounting a resistance to antibiotics.
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Affiliation(s)
- Shrijan Bhattarai
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Lane Marsh
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Kelsey Knight
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Liaqat Ali
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Antonio Gomez
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Allison Sunderhaus
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - May H. Abdel Aziz
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
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15
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Peruzzi JA, Galvez NR, Kamat NP. Engineering transmembrane signal transduction in synthetic membranes using two-component systems. Proc Natl Acad Sci U S A 2023; 120:e2218610120. [PMID: 37126679 PMCID: PMC10175788 DOI: 10.1073/pnas.2218610120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023] Open
Abstract
Cells use signal transduction across their membranes to sense and respond to a wide array of chemical and physical signals. Creating synthetic systems which can harness cellular signaling modalities promises to provide a powerful platform for biosensing and therapeutic applications. As a first step toward this goal, we investigated how bacterial two-component systems (TCSs) can be leveraged to enable transmembrane-signaling with synthetic membranes. Specifically, we demonstrate that a bacterial two-component nitrate-sensing system (NarX-NarL) can be reproduced outside of a cell using synthetic membranes and cell-free protein expression systems. We find that performance and sensitivity of the TCS can be tuned by altering the biophysical properties of the membrane in which the histidine kinase (NarX) is integrated. Through protein engineering efforts, we modify the sensing domain of NarX to generate sensors capable of detecting an array of ligands. Finally, we demonstrate that these systems can sense ligands in relevant sample environments. By leveraging membrane and protein design, this work helps reveal how transmembrane sensing can be recapitulated outside of the cell, adding to the arsenal of deployable cell-free systems primed for real world biosensing.
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Affiliation(s)
- Justin A. Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL60208
- Center for Synthetic Biology, Northwestern University, Evanston, IL60208
| | - Nina R. Galvez
- Center for Synthetic Biology, Northwestern University, Evanston, IL60208
- Department of Biomedical Engineering, Northwestern University, Evanston, IL60208
| | - Neha P. Kamat
- Center for Synthetic Biology, Northwestern University, Evanston, IL60208
- Department of Biomedical Engineering, Northwestern University, Evanston, IL60208
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL60208
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16
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Ghose DA, Przydzial KE, Mahoney EM, Keating AE, Laub MT. Marginal specificity in protein interactions constrains evolution of a paralogous family. Proc Natl Acad Sci U S A 2023; 120:e2221163120. [PMID: 37098061 PMCID: PMC10160972 DOI: 10.1073/pnas.2221163120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/24/2023] [Indexed: 04/26/2023] Open
Abstract
The evolution of novel functions in biology relies heavily on gene duplication and divergence, creating large paralogous protein families. Selective pressure to avoid detrimental cross-talk often results in paralogs that exhibit exquisite specificity for their interaction partners. But how robust or sensitive is this specificity to mutation? Here, using deep mutational scanning, we demonstrate that a paralogous family of bacterial signaling proteins exhibits marginal specificity, such that many individual substitutions give rise to substantial cross-talk between normally insulated pathways. Our results indicate that sequence space is locally crowded despite overall sparseness, and we provide evidence that this crowding has constrained the evolution of bacterial signaling proteins. These findings underscore how evolution selects for "good enough" rather than optimized phenotypes, leading to restrictions on the subsequent evolution of paralogs.
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Affiliation(s)
- Dia A. Ghose
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Kaitlyn E. Przydzial
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Emily M. Mahoney
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Koch Center for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Massachusetts Institute of Technology, Cambridge, MA02139
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17
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Structural features discriminating hybrid histidine kinase Rec domains from response regulator homologs. Nat Commun 2023; 14:1002. [PMID: 36864019 PMCID: PMC9981736 DOI: 10.1038/s41467-023-36597-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/07/2023] [Indexed: 03/04/2023] Open
Abstract
In two-component systems, the information gathered by histidine kinases (HKs) are relayed to cognate response regulators (RRs). Thereby, the phosphoryl group of the auto-phosphorylated HK is transferred to the receiver (Rec) domain of the RR to allosterically activate its effector domain. In contrast, multi-step phosphorelays comprise at least one additional Rec (Recinter) domain that is typically part of the HK and acts as an intermediary for phosphoryl-shuttling. While RR Rec domains have been studied extensively, little is known about discriminating features of Recinter domains. Here we study the Recinter domain of the hybrid HK CckA by X-ray crystallography and NMR spectroscopy. Strikingly, all active site residues of the canonical Rec-fold are pre-arranged for phosphoryl-binding and BeF3- binding does not alter secondary or quaternary structure, indicating the absence of allosteric changes, the hallmark of RRs. Based on sequence-covariation and modeling, we analyze the intra-molecular DHp/Rec association in hybrid HKs.
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18
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Control of Cell Size by c-di-GMP Requires a Two-Component Signaling System in the Cyanobacterium Anabaena sp. Strain PCC 7120. Microbiol Spectr 2023; 11:e0422822. [PMID: 36625639 PMCID: PMC9927289 DOI: 10.1128/spectrum.04228-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Each bacterial species possesses a specific cell size and morphology, which constitute important and recognizable physical traits. How bacteria maintain their particular cell size and morphology remains an essential question in microbiology. Cyanobacteria are oxygen-evolving photosynthetic prokaryotes. Although monophyletic, these organisms are highly diverse in their cell morphology and cell size. How these physical traits of cyanobacteria are controlled is poorly understood. Here, we report the identification of a two-component signaling system, composed of a histidine kinase CdgK and a response regulator CdgS, involved in cell size regulation in the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Inactivation of cdgK or cdgS led to reduction of cell length and width with little effect on cell growth capacity. CdgS has a GGDEF domain responsible for the synthesis of the second messenger c-di-GMP. Based on genetic and biochemical studies, we proposed a signaling pathway initiated by CdgK, leading to the phosphorylation of CdgS, and thereby an enhanced enzymatic activity for c-di-GMP synthesis of the latter. The GGDEF domain of CdgS was essential in cell size control, and the reduction of cell size observed in various mutants could be rescued by the expression of a c-di-GMP synthetase from E. coli. These results provided evidence that a minimal threshold of c-di-GMP level was required for maintaining cell size in Anabaena. IMPORTANCE Cyanobacteria are considered the first organisms to produce oxygen on Earth, and their activities shaped the evolution of our ecosystems. Cell size is an important trait fixed early in evolution, with the diversification of micro- and macrocyanobacterial species during the Great Oxidation Event. However, the genetic basis underlying cell size control in cyanobacteria was not understood. Our studies demonstrated that the CdgK-CdgS signaling pathway participates in the control of cell size, and their absence did not affect cell growth. CdgK has multiple domains susceptible to signal input, which are necessary for cell size regulation. This observation suggests that cell size in Anabaena could respond to environmental signals. These studies paved the way for genetic dissection of cell size regulation in cyanobacteria.
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19
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Nieves M, Buschiazzo A, Trajtenberg F. Structural features of sensory two component systems: a synthetic biology perspective. Biochem J 2023; 480:127-140. [PMID: 36688908 DOI: 10.1042/bcj20210798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/24/2023]
Abstract
All living organisms include a set of signaling devices that confer the ability to dynamically perceive and adapt to the fluctuating environment. Two-component systems are part of this sensory machinery that regulates the execution of different genetic and/or biochemical programs in response to specific physical or chemical signals. In the last two decades, there has been tremendous progress in our molecular understanding on how signals are detected, the allosteric mechanisms that control intramolecular information transmission and the specificity determinants that guarantee correct wiring. All this information is starting to be exploited in the development of new synthetic networks. Connecting multiple molecular players, analogous to programming lines of code, can provide the resources to build new sophisticated biocomputing systems. The Synthetic Biology field is starting to revolutionize several scientific fields, such as biomedicine and agriculture, propelling the development of new solutions. Expanding the spectrum of available nanodevices in the toolbox is key to unleash its full potential. This review aims to discuss, from a structural perspective, how to take advantage of the vast array of sensor and effector protein modules involved in two-component systems for the construction of new synthetic circuits.
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Affiliation(s)
- Marcos Nieves
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Département de Microbiologie, Institut Pasteur, Paris, France
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
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20
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Lima S, Blanco J, Olivieri F, Imelio JA, Nieves M, Carrión F, Alvarez B, Buschiazzo A, Marti MA, Trajtenberg F. An allosteric switch ensures efficient unidirectional information transmission by the histidine kinase DesK from Bacillus subtilis. Sci Signal 2023; 16:eabo7588. [PMID: 36693130 DOI: 10.1126/scisignal.abo7588] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Phosphorylation carries chemical information in biological systems. In two-component systems (TCSs), the sensor histidine kinase and the response regulator are connected through phosphoryl transfer reactions that may be uni- or bidirectional. Directionality enables the construction of complex regulatory networks that optimize signal propagation and ensure the forward flow of information. We combined x-ray crystallography, hybrid quantum mechanics/molecular mechanics (QM/MM) simulations, and systems-integrative kinetic modeling approaches to study phosphoryl flow through the Bacillus subtilis thermosensing TCS DesK-DesR. The allosteric regulation of the histidine kinase DesK was critical to avoid back transfer of phosphoryl groups and futile phosphorylation-dephosphorylation cycles by isolating phosphatase, autokinase, and phosphotransferase activities. Interactions between the kinase's ATP-binding domain and the regulator's receiver domain placed the regulator in two distinct positions in the phosphotransferase and phosphatase complexes, thereby determining whether a key glutamine residue in DesK was properly situated to assist in the dephosphorylation reaction. Moreover, an energetically unfavorable phosphotransferase conformation when DesK was not phosphorylated minimized reverse phosphoryl transfer. DesR dimerization and a dissociative phosphoryl transfer reaction also enforced the direction of phosphoryl flow. Shorter or longer distances between the phosphoryl acceptor and donor residues shifted the phosphoryl transfer equilibrium by modulating the stabilizing effect of the Mg2+ cofactor. These mechanisms control the directionality of signal transmission and show how structure-encoded allostery stores and transmits information in signaling systems.
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Affiliation(s)
- Sofía Lima
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Juan Blanco
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico Olivieri
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Juan A Imelio
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcos Nieves
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Federico Carrión
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Centro de Investigaciones Biomédicas, Universidad de la República, Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Département de Microbiologie, Institut Pasteur, Paris, France
| | - Marcelo A Marti
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
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21
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Mansour M, Abou-Aisha K. regO: a novel locus in the regulation of tetrapyrrole biosynthesis in Rhodospirillum rubrum. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-022-01709-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Abstract
Purpose
A new locus, regO, involved in the regulation of photosynthesis gene expression in response to oxygen and light, has been studied in Rhodosprillum rubrum ATCC1117 (Rsp. rubrum) for identification of its function.
Methods
Inactivation of regO by interposon mutagenesis resulted in the inability of cells to grow photosynthetically, (i.e. become PS–). Protein domain analysis of RegO using the BLAST engine was also performed.
Results
The mutant strain was able to grow only anaerobically in the dark in the presence of DMSO as an external electron acceptor. Under these conditions, the mutant strain produced substantially lower amounts of photosynthetic membranes, indicating that regO is involved in the regulation of photosynthetic gene expression in response to anaerobiosis. The Rsp. rubrum REGO–disrupted mutant recovered the synthesis of photosynthetic membranes and retained regulation by light and/or oxygen tension when wild-type regO was provided in-trans.
Protein domain analysis of RegO revealed that it encodes a multi-domain sensor histidine kinase (HK). The signal-input domains, or PAS domains, bear strong similarities to putative heme-bound sensors involved in sensing light, redox potential, and/or oxygen. The output HK domain exhibits strong homology to sensor domains from bacterial two-component systems involved in signal transduction in response to the same environmental signals.
Conclusion
regO is coding for a sensor histidine kinase that belongs to bacterial two-component systems responsible for signal transduction in response to light and oxygen, particularly in the absence of oxygen. It is believed to be involved in the regulation of tetrapyrrole biosynthesis, which was shown as a lack of photosynthetic membranes in the mutant strain REGO– .Unlike other sensor kinase homologues from related anoxygenic phototrophic bacterial species, although functionally similar to RegB and PrrB, RegO is predicted to lack transmembrane domains and is thus expected to be a cytosolic member of a two-component signal transduction system. RegO also differs from its functional homologues, Reg B/PrrB sensor protein kinases, of the two component systems in that it lacks the second component of this two-component signal transduction system found in the neighboring genes. That encouraged us to give it the name RegO, indicating the lack of a cognate response regulator similar to Reg A/PrrA on other closely related anoxygenic Rhodobacter species.
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22
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Kennedy EN, Foster CA, Barr SA, Bourret RB. General strategies for using amino acid sequence data to guide biochemical investigation of protein function. Biochem Soc Trans 2022; 50:1847-1858. [PMID: 36416676 PMCID: PMC10257402 DOI: 10.1042/bst20220849] [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] [Received: 08/18/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022]
Abstract
The rapid increase of '-omics' data warrants the reconsideration of experimental strategies to investigate general protein function. Studying individual members of a protein family is likely insufficient to provide a complete mechanistic understanding of family functions, especially for diverse families with thousands of known members. Strategies that exploit large amounts of available amino acid sequence data can inspire and guide biochemical experiments, generating broadly applicable insights into a given family. Here we review several methods that utilize abundant sequence data to focus experimental efforts and identify features truly representative of a protein family or domain. First, coevolutionary relationships between residues within primary sequences can be successfully exploited to identify structurally and/or functionally important positions for experimental investigation. Second, functionally important variable residue positions typically occupy a limited sequence space, a property useful for guiding biochemical characterization of the effects of the most physiologically and evolutionarily relevant amino acids. Third, amino acid sequence variation within domains shared between different protein families can be used to sort a particular domain into multiple subtypes, inspiring further experimental designs. Although generally applicable to any kind of protein domain because they depend solely on amino acid sequences, the second and third approaches are reviewed in detail because they appear to have been used infrequently and offer immediate opportunities for new advances. Finally, we speculate that future technologies capable of analyzing and manipulating conserved and variable aspects of the three-dimensional structures of a protein family could lead to broad insights not attainable by current methods.
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Affiliation(s)
- Emily N. Kennedy
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Clay A. Foster
- Department of Pediatrics, Section Hematology/Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Sarah A. Barr
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Robert B. Bourret
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States of America
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23
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Kim JS, Born A, Till JKA, Liu L, Kant S, Henen MA, Vögeli B, Vázquez-Torres A. Promiscuity of response regulators for thioredoxin steers bacterial virulence. Nat Commun 2022; 13:6210. [PMID: 36266276 PMCID: PMC9584953 DOI: 10.1038/s41467-022-33983-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
The exquisite specificity between a sensor kinase and its cognate response regulator ensures faithful partner selectivity within two-component pairs concurrently firing in a single bacterium, minimizing crosstalk with other members of this conserved family of paralogous proteins. We show that conserved hydrophobic and charged residues on the surface of thioredoxin serve as a docking station for structurally diverse response regulators. Using the OmpR protein, we identify residues in the flexible linker and the C-terminal β-hairpin that enable associations of this archetypical response regulator with thioredoxin, but are dispensable for interactions of this transcription factor to its cognate sensor kinase EnvZ, DNA or RNA polymerase. Here we show that the promiscuous interactions of response regulators with thioredoxin foster the flow of information through otherwise highly dedicated two-component signaling systems, thereby enabling both the transcription of Salmonella pathogenicity island-2 genes as well as growth of this intracellular bacterium in macrophages and mice.
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Affiliation(s)
- Ju-Sim Kim
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado USA
| | - Alexandra Born
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Biochemistry & Molecular Genetics, Aurora, Colorado USA
| | - James Karl A. Till
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado USA
| | - Lin Liu
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado USA
| | - Sashi Kant
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado USA
| | - Morkos A. Henen
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Biochemistry & Molecular Genetics, Aurora, Colorado USA ,grid.10251.370000000103426662Faculty of Pharmacy, Mansoura University, Mansoura, 35516 Egypt
| | - Beat Vögeli
- grid.430503.10000 0001 0703 675XUniversity of Colorado School of Medicine, Department of Biochemistry & Molecular Genetics, Aurora, Colorado USA
| | - Andrés Vázquez-Torres
- University of Colorado School of Medicine, Department of Immunology & Microbiology, Aurora, Colorado, USA. .,Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado, USA.
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24
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Ohlendorf R, Möglich A. Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives. Front Bioeng Biotechnol 2022; 10:1029403. [PMID: 36312534 PMCID: PMC9614035 DOI: 10.3389/fbioe.2022.1029403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.
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Affiliation(s)
- Robert Ohlendorf
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
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25
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Nocedal I, Laub MT. Ancestral reconstruction of duplicated signaling proteins reveals the evolution of signaling specificity. eLife 2022; 11:e77346. [PMID: 35686729 PMCID: PMC9208753 DOI: 10.7554/elife.77346] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/27/2022] [Indexed: 01/30/2023] Open
Abstract
Gene duplication is crucial to generating novel signaling pathways during evolution. However, it remains unclear how the redundant proteins produced by gene duplication ultimately acquire new interaction specificities to establish insulated paralogous signaling pathways. Here, we used ancestral sequence reconstruction to resurrect and characterize a bacterial two-component signaling system that duplicated in α-proteobacteria. We determined the interaction specificities of the signaling proteins that existed before and immediately after this duplication event and then identified key mutations responsible for establishing specificity in the two systems. Just three mutations, in only two of the four interacting proteins, were sufficient to establish specificity of the extant systems. Some of these mutations weakened interactions between paralogous systems to limit crosstalk. However, others strengthened interactions within a system, indicating that the ancestral interaction, although functional, had the potential to be strengthened. Our work suggests that protein-protein interactions with such latent potential may be highly amenable to duplication and divergence.
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Affiliation(s)
- Isabel Nocedal
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
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26
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Gentili PL, Stano P. Chemical Neural Networks Inside Synthetic Cells? A Proposal for Their Realization and Modeling. Front Bioeng Biotechnol 2022; 10:927110. [PMID: 35733531 PMCID: PMC9208290 DOI: 10.3389/fbioe.2022.927110] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology and Biotechnology, Università Degli Studi di Perugia, Perugia, Italy
- *Correspondence: Pier Luigi Gentili, ; Pasquale Stano,
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
- *Correspondence: Pier Luigi Gentili, ; Pasquale Stano,
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27
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Kong L, Su M, Sang J, Huang S, Wang M, Cai Y, Xie M, Wu J, Wang S, Foster SJ, Zhang J, Han A. The W-Acidic Motif of Histidine Kinase WalK Is Required for Signaling and Transcriptional Regulation in Streptococcus mutans. Front Microbiol 2022; 13:820089. [PMID: 35558126 PMCID: PMC9087282 DOI: 10.3389/fmicb.2022.820089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
In Streptococcus mutans, we find that the histidine kinase WalK possesses the longest C-terminal tail (CTT) among all 14 TCSs, and this tail plays a key role in the interaction of WalK with its response regulator WalR. We demonstrate that the intrinsically disordered CTT is characterized by a conserved tryptophan residue surrounded by acidic amino acids. Mutation in the tryptophan not only disrupts the stable interaction, but also impairs the efficient phosphotransferase and phosphatase activities of WalRK. In addition, the tryptophan is important for WalK to compete with DNA containing a WalR binding motif for the WalR interaction. We further show that the tryptophan is important for in vivo transcriptional regulation and bacterial biofilm formation by S. mutans. Moreover, Staphylococcus aureus WalK also has a characteristic CTT, albeit relatively shorter, with a conserved W-acidic motif, that is required for the WalRK interaction in vitro. Together, these data reveal that the W-acidic motif of WalK is indispensable for its interaction with WalR, thereby playing a key role in the WalRK-dependent signal transduction, transcriptional regulation and biofilm formation.
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Affiliation(s)
- Lingyuan Kong
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingyang Su
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiayan Sang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shanshan Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Min Wang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingquan Xie
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jun Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shida Wang
- State Key Laboratory for Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Simon J Foster
- Department of Molecular Biology and Biotechnology, The Florey Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Jiaqin Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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28
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Mahilkar A, Venkataraman P, Mall A, Saini S. Experimental Evolution of Anticipatory Regulation in Escherichia coli. Front Microbiol 2022; 12:796228. [PMID: 35087497 PMCID: PMC8787300 DOI: 10.3389/fmicb.2021.796228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Environmental cues in an ecological niche are often temporal in nature. For instance, in temperate climates, temperature is higher in daytime compared to during night. In response to these temporal cues, bacteria have been known to exhibit anticipatory regulation, whereby triggering response to a yet to appear cue. Such an anticipatory response in known to enhance Darwinian fitness, and hence, is likely an important feature of regulatory networks in microorganisms. However, the conditions under which an anticipatory response evolves as an adaptive response are not known. In this work, we develop a quantitative model to study response of a population to two temporal environmental cues, and predict variables which are likely important for evolution of anticipatory regulatory response. We follow this with experimental evolution of Escherichia coli in alternating environments of rhamnose and paraquat for ∼850 generations. We demonstrate that growth in this cyclical environment leads to evolution of anticipatory regulation. As a result, pre-exposure to rhamnose leads to a greater fitness in paraquat environment. Genome sequencing reveals that this anticipatory regulation is encoded via mutations in global regulators. Overall, our study contributes to understanding of how environment shapes the topology of regulatory networks in an organism.
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Affiliation(s)
- Anjali Mahilkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pavithra Venkataraman
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Akshat Mall
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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29
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Miller CA, Ho JML, Bennett MR. Strategies for Improving Small-Molecule Biosensors in Bacteria. BIOSENSORS 2022; 12:bios12020064. [PMID: 35200325 PMCID: PMC8869690 DOI: 10.3390/bios12020064] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 05/03/2023]
Abstract
In recent years, small-molecule biosensors have become increasingly important in synthetic biology and biochemistry, with numerous new applications continuing to be developed throughout the field. For many biosensors, however, their utility is hindered by poor functionality. Here, we review the known types of mechanisms of biosensors within bacterial cells, and the types of approaches for optimizing different biosensor functional parameters. Discussed approaches for improving biosensor functionality include methods of directly engineering biosensor genes, considerations for choosing genetic reporters, approaches for tuning gene expression, and strategies for incorporating additional genetic modules.
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Affiliation(s)
- Corwin A. Miller
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
| | - Joanne M. L. Ho
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
| | - Matthew R. Bennett
- Department of Biosciences, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA; (C.A.M.); (J.M.L.H.)
- Department of Bioengineering, Rice University MS-140, 6100 Main St., Houston, TX 77005, USA
- Correspondence:
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30
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Extracting phylogenetic dimensions of coevolution reveals hidden functional signals. Sci Rep 2022; 12:820. [PMID: 35039514 PMCID: PMC8764114 DOI: 10.1038/s41598-021-04260-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/17/2021] [Indexed: 11/08/2022] Open
Abstract
Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's phylogenetic history and gives rise to concurrent variation between protein sequences that is not driven by selection for function. Here, we introduce a background model for phylogenetic contributions of statistical coupling that separates the coevolution signal due to inter-clade and intra-clade sequence comparisons and demonstrate that coevolution can be measured on multiple phylogenetic timescales within a single protein. Our method, nested coevolution (NC), can be applied as an extension to any coevolution metric. We use NC to demonstrate that poorly conserved residues can nonetheless have important roles in protein function. Moreover, NC improved the structural-contact predictions of several coevolution-based methods, particularly in subsampled alignments with fewer sequences. NC also lowered the noise in detecting functional sectors of collectively coevolving residues. Sectors of coevolving residues identified after application of NC were more spatially compact and phylogenetically distinct from the rest of the protein, and strongly enriched for mutations that disrupt protein activity. Thus, our conceptualization of the phylogenetic separation of coevolution provides the potential to further elucidate relationships among protein evolution, function, and genetic diseases.
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31
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Miyazawa S. Boltzmann Machine Learning and Regularization Methods for Inferring Evolutionary Fields and Couplings From a Multiple Sequence Alignment. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:328-342. [PMID: 32396099 DOI: 10.1109/tcbb.2020.2993232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The inverse Potts problem to infer a Boltzmann distribution for homologous protein sequences from their single-site and pairwise amino acid frequencies recently attracts a great deal of attention in the studies of protein structure and evolution. We study regularization and learning methods and how to tune regularization parameters to correctly infer interactions in Boltzmann machine learning. Using L2 regularization for fields, group L1 for couplings is shown to be very effective for sparse couplings in comparison with L2 and L1. Two regularization parameters are tuned to yield equal values for both the sample and ensemble averages of evolutionary energy. Both averages smoothly change and converge, but their learning profiles are very different between learning methods. The Adam method is modified to make stepsize proportional to the gradient for sparse couplings and to use a soft-thresholding function for group L1. It is shown by first inferring interactions from protein sequences and then from Monte Carlo samples that the fields and couplings can be well recovered, but that recovering the pairwise correlations in the resolution of a total energy is harder for the natural proteins than for the protein-like sequences. Selective temperature for folding/structural constrains in protein evolution is also estimated.
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32
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Mensa B, Polizzi NF, Molnar KS, Natale AM, Lemmin T, DeGrado WF. Allosteric mechanism of signal transduction in the two-component system histidine kinase PhoQ. eLife 2021; 10:73336. [PMID: 34904568 PMCID: PMC8719878 DOI: 10.7554/elife.73336] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/13/2021] [Indexed: 12/05/2022] Open
Abstract
Transmembrane signaling proteins couple extracytosolic sensors to cytosolic effectors. Here, we examine how binding of Mg2+ to the sensor domain of an E. coli two component histidine kinase (HK), PhoQ, modulates its cytoplasmic kinase domain. We use cysteine-crosslinking and reporter-gene assays to simultaneously and independently probe the signaling state of PhoQ’s sensor and autokinase domains in a set of over 30 mutants. Strikingly, conservative single-site mutations distant from the sensor or catalytic site strongly influence PhoQ’s ligand-sensitivity as well as the magnitude and direction of the signal. Data from 35 mutants are explained by a semi-empirical three-domain model in which the sensor, intervening HAMP, and catalytic domains can adopt kinase-promoting or inhibiting conformations that are in allosteric communication. The catalytic and sensor domains intrinsically favor a constitutively ‘kinase-on’ conformation, while the HAMP domain favors the ‘off’ state; when coupled, they create a bistable system responsive to physiological concentrations of Mg2+. Mutations alter signaling by locally modulating domain intrinsic equilibrium constants and interdomain couplings. Our model suggests signals transmit via interdomain allostery rather than propagation of a single concerted conformational change, explaining the diversity of signaling structural transitions observed in individual HK domains.
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Affiliation(s)
- Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Chemistry and Chemical Biology PhD program, University of California, San Francisco, San Francisco, United States
| | - Nicholas F Polizzi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | | | - Andrew M Natale
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Biophysics PhD program, University of California, San Francisco, San Francisco, United States
| | - Thomas Lemmin
- Euler Institute, Università della Svizzera Italiana, Lugano, Switzerland
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
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33
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Chu WT, Yan Z, Chu X, Zheng X, Liu Z, Xu L, Zhang K, Wang J. Physics of biomolecular recognition and conformational dynamics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:126601. [PMID: 34753115 DOI: 10.1088/1361-6633/ac3800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Biomolecular recognition usually leads to the formation of binding complexes, often accompanied by large-scale conformational changes. This process is fundamental to biological functions at the molecular and cellular levels. Uncovering the physical mechanisms of biomolecular recognition and quantifying the key biomolecular interactions are vital to understand these functions. The recently developed energy landscape theory has been successful in quantifying recognition processes and revealing the underlying mechanisms. Recent studies have shown that in addition to affinity, specificity is also crucial for biomolecular recognition. The proposed physical concept of intrinsic specificity based on the underlying energy landscape theory provides a practical way to quantify the specificity. Optimization of affinity and specificity can be adopted as a principle to guide the evolution and design of molecular recognition. This approach can also be used in practice for drug discovery using multidimensional screening to identify lead compounds. The energy landscape topography of molecular recognition is important for revealing the underlying flexible binding or binding-folding mechanisms. In this review, we first introduce the energy landscape theory for molecular recognition and then address four critical issues related to biomolecular recognition and conformational dynamics: (1) specificity quantification of molecular recognition; (2) evolution and design in molecular recognition; (3) flexible molecular recognition; (4) chromosome structural dynamics. The results described here and the discussions of the insights gained from the energy landscape topography can provide valuable guidance for further computational and experimental investigations of biomolecular recognition and conformational dynamics.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Xiakun Chu
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
| | - Xiliang Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Li Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Kun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Jin Wang
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
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34
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Hwang T, Parker SS, Hill SM, Ilunga MW, Grant RA, Mouneimne G, Keating AE. A distributed residue network permits conformational binding specificity in a conserved family of actin remodelers. eLife 2021; 10:e70601. [PMID: 34854809 PMCID: PMC8639148 DOI: 10.7554/elife.70601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Metazoan proteomes contain many paralogous proteins that have evolved distinct functions. The Ena/VASP family of actin regulators consists of three members that share an EVH1 interaction domain with a 100 % conserved binding site. A proteome-wide screen revealed photoreceptor cilium actin regulator (PCARE) as a high-affinity ligand for ENAH EVH1. Here, we report the surprising observation that PCARE is ~100-fold specific for ENAH over paralogs VASP and EVL and can selectively bind ENAH and inhibit ENAH-dependent adhesion in cells. Specificity arises from a mechanism whereby PCARE stabilizes a conformation of the ENAH EVH1 domain that is inaccessible to family members VASP and EVL. Structure-based modeling rapidly identified seven residues distributed throughout EVL that are sufficient to differentiate binding by ENAH vs. EVL. By exploiting the ENAH-specific conformation, we rationally designed the tightest and most selective ENAH binder to date. Our work uncovers a conformational mechanism of interaction specificity that distinguishes highly similar paralogs and establishes tools for dissecting specific Ena/VASP functions in processes including cancer cell invasion.
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Affiliation(s)
- Theresa Hwang
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Sara S Parker
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of ArizonaTucsonUnited States
| | - Samantha M Hill
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of ArizonaTucsonUnited States
| | - Meucci W Ilunga
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ghassan Mouneimne
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of ArizonaTucsonUnited States
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering and Koch Institue for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
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35
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Lazar JT, Tabor JJ. Bacterial two-component systems as sensors for synthetic biology applications. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100398. [PMID: 34917859 PMCID: PMC8670732 DOI: 10.1016/j.coisb.2021.100398] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Two-component systems (TCSs) are a ubiquitous family of signal transduction pathways that enable bacteria to sense and respond to diverse physical, chemical, and biological stimuli outside and inside the cell. Synthetic biologists have begun to repurpose TCSs for applications in optogenetics, materials science, gut microbiome engineering, and soil nutrient biosensing, among others. New engineering methods including genetic refactoring, DNA-binding domain swapping, detection threshold tuning, and phosphorylation cross-talk insulation are being used to increase the reliability of TCS sensor performance and tailor TCS signaling properties to the requirements of specific applications. There is now potential to combine these methods with large-scale gene synthesis and laboratory screening to discover the inputs sensed by many uncharacterized TCSs and develop a large new family of genetically-encoded sensors that respond to an unrivaled breadth of stimuli.
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Affiliation(s)
- John T Lazar
- Department of Chemical and Biomolecular Engineering, 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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36
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Párraga Solórzano PK, Shupe AC, Kehl-Fie TE. The Sensor Histidine Kinase ArlS Is Necessary for Staphylococcus aureus To Activate ArlR in Response to Nutrient Availability. J Bacteriol 2021; 203:e0042221. [PMID: 34606376 PMCID: PMC8604075 DOI: 10.1128/jb.00422-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/25/2021] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus is a versatile opportunistic pathogen whose success is driven by its ability to adapt to diverse environments and host-imposed stresses. Two-component signal transduction systems, such as ArlRS, often mediate these adaptations. Loss of ArlRS or the response regulator ArlR alone impairs the ability of S. aureus to respond to host-imposed manganese starvation and glucose limitation. As sensor histidine kinases and response regulators frequently work as pairs, it has been assumed that ArlS senses and activates ArlR in response to these stimuli. However, recent work suggests that the sensor histidine kinase GraS can also activate ArlR, calling the contribution of ArlS in responding to manganese and glucose availability into question. The results of current studies reveal that ArlS is necessary to activate ArlR in response to manganese sequestration by the host immune effector calprotectin and glucose limitation. Although the loss of ArlS does not completely eliminate ArlR activity, this response regulator is no longer responsive to manganese or glucose availability in the absence of its cognate histidine kinase. Despite the residual activity of ArlR in the absence of ArlS, ArlR phosphorylation by ArlS is required for S. aureus to resist calprotectin-imposed metal starvation. Cumulatively, these findings contribute to the understanding of S. aureus signal transduction in response to nutritional immunity and support the previous observation indicating that ArlRS is activated by a common signal derived from host-imposed manganese and glucose limitation. IMPORTANCE The ability of pathogens, including Staphylococcus aureus, to sense and adapt to diverse environments partially relies on two-component systems, such as ArlRS. Recent work revealed that the response regulator ArlR can be cross-activated by the sensor histidine kinase GraS, rendering the role of its cognate partner, ArlS, in response to manganese and glucose limitation uncertain. The results of this study reveal that ArlS is necessary for the activation of ArlR in response to calprotectin and glucose limitation. Although a low level of ArlR activity remains in the absence of ArlS, ArlS phosphotransfer to ArlR is required for S. aureus to overcome calprotectin-induced nutritional stress. Collectively, this study provides fundamental information to understand how ArlRS mediates staphylococcal adaptation during infection.
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Affiliation(s)
| | - Angela C. Shupe
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Thomas E. Kehl-Fie
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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37
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Epistasis shapes the fitness landscape of an allosteric specificity switch. Nat Commun 2021; 12:5562. [PMID: 34548494 PMCID: PMC8455584 DOI: 10.1038/s41467-021-25826-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 09/03/2021] [Indexed: 11/08/2022] Open
Abstract
Epistasis is a major determinant in the emergence of novel protein function. In allosteric proteins, direct interactions between inducer-binding mutations propagate through the allosteric network, manifesting as epistasis at the level of biological function. Elucidating this relationship between local interactions and their global effects is essential to understanding evolution of allosteric proteins. We integrate computational design, structural and biophysical analysis to characterize the emergence of novel inducer specificity in an allosteric transcription factor. Adaptive landscapes of different inducers of the designed mutant show that a few strong epistatic interactions constrain the number of viable sequence pathways, revealing ridges in the fitness landscape leading to new specificity. The structure of the designed mutant shows that a striking change in inducer orientation still retains allosteric function. Comparing biophysical and functional properties suggests a nonlinear relationship between inducer binding affinity and allostery. Our results highlight the functional and evolutionary complexity of allosteric proteins. Epistasis plays an important role in the evolution of novel protein functions because it determines the mutational path a protein takes. Here, the authors combine functional, structural and biophysical analyses to characterize epistasis in a computationally redesigned ligand-inducible allosteric transcription factor and found that epistasis creates distinct biophysical and biological functional landscapes.
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38
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Abstract
Duplication and divergence is a major mechanism by which new proteins and functions emerge in biology. Consequently, most organisms, in all domains of life, have genomes that encode large paralogous families of proteins. For recently duplicated pathways to acquire different, independent functions, the two paralogs must acquire mutations that effectively insulate them from one another. For instance, paralogous signaling proteins must acquire mutations that endow them with different interaction specificities such that they can participate in different signaling pathways without disruptive cross-talk. Although duplicated genes undoubtedly shape each other's evolution as they diverge and attain new functions, it is less clear how other paralogs impact or constrain gene duplication. Does the establishment of a new pathway by duplication and divergence require the system-wide optimization of all paralogs? The answer has profound implications for molecular evolution and our ability to engineer biological systems. Here, we discuss models, experiments, and approaches for tackling this question, and for understanding how new proteins and pathways are born.
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Affiliation(s)
- Conor J McClune
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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39
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Lindorff-Larsen K, Kragelund BB. On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins. J Mol Biol 2021; 433:167196. [PMID: 34390736 DOI: 10.1016/j.jmb.2021.167196] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as having no persistent tertiary structure; instead they interconvert between a large number of different and often expanded structures. IDPs and IDRs are involved in an enormously wide range of biological functions and reveal novel mechanisms of interactions, and while they defy the common structure-function paradigm of folded proteins, their structural preferences and dynamics are important for their function. We here discuss open questions in the field of IDPs and IDRs, focusing on areas where machine learning and other computational methods play a role. We discuss computational methods aimed to predict transiently formed local and long-range structure, including methods for integrative structural biology. We discuss the many different ways in which IDPs and IDRs can bind to other molecules, both via short linear motifs, as well as in the formation of larger dynamic complexes such as biomolecular condensates. We discuss how experiments are providing insight into such complexes and may enable more accurate predictions. Finally, we discuss the role of IDPs in disease and how new methods are needed to interpret the mechanistic effects of genomic variants in IDPs.
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Affiliation(s)
- Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen. Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen. Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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40
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The ChvG-ChvI and NtrY-NtrX Two-Component Systems Coordinately Regulate Growth of Caulobacter crescentus. J Bacteriol 2021; 203:e0019921. [PMID: 34124942 DOI: 10.1128/jb.00199-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Two-component signaling systems (TCSs) are comprised of a sensory histidine kinase and a response regulator protein. In response to environmental changes, sensor kinases directly phosphorylate their cognate response regulator to affect gene expression. Bacteria typically express multiple TCSs that are insulated from one another and regulate distinct physiological processes. There are examples of cross-regulation between TCSs, but this phenomenon remains relatively unexplored. We have identified regulatory links between the ChvG-ChvI (ChvGI) and NtrY-NtrX (NtrYX) TCSs, which control important and often overlapping processes in alphaproteobacteria, including maintenance of the cell envelope. Deletion of chvG and chvI in Caulobacter crescentus limited growth in defined medium, and a selection for genetic suppressors of this growth phenotype uncovered interactions among chvGI, ntrYX, and ntrZ, which encodes a previously uncharacterized periplasmic protein. Significant overlap in the experimentally defined ChvI and NtrX transcriptional regulons provided support for the observed genetic connections between ntrYX and chvGI. Moreover, we present evidence that the growth defect of strains lacking chvGI is influenced by the phosphorylation state of NtrX and, to some extent, by levels of the TonB-dependent receptor ChvT. Measurements of NtrX phosphorylation in vivo indicated that NtrZ is an upstream regulator of NtrY and that NtrY primarily functions as an NtrX phosphatase. We propose a model in which NtrZ functions in the periplasm to inhibit NtrY phosphatase activity; regulation of phosphorylated NtrX levels by NtrZ and NtrY provides a mechanism to modulate and balance expression of the NtrX and ChvI regulons under different growth conditions. IMPORTANCE TCSs enable bacteria to regulate gene expression in response to physiochemical changes in their environment. The ChvGI and NtrYX TCSs regulate diverse pathways associated with pathogenesis, growth, and cell envelope function in many alphaproteobacteria. We used Caulobacter crescentus as a model to investigate regulatory connections between ChvGI and NtrYX. Our work defined the ChvI transcriptional regulon in C. crescentus and revealed a genetic interaction between ChvGI and NtrYX, whereby modulation of NtrYX signaling affects the survival of cells lacking ChvGI. In addition, we identified NtrZ as a periplasmic inhibitor of NtrY phosphatase activity in vivo. Our work establishes C. crescentus as an excellent model to investigate multilevel regulatory connections between ChvGI and NtrYX in alphaproteobacteria.
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Abstract
Measurement of biological systems containing biomolecules and bioparticles is a key task in the fields of analytical chemistry, biology, and medicine. Driven by the complex nature of biological systems and unprecedented amounts of measurement data, artificial intelligence (AI) in measurement science has rapidly advanced from the use of silicon-based machine learning (ML) for data mining to the development of molecular computing with improved sensitivity and accuracy. This review presents an overview of fundamental ML methodologies and discusses their applications in disease diagnostics, biomarker discovery, and imaging analysis. We next provide the working principles of molecular computing using logic gates and arithmetical devices, which can be employed for in situ detection, computation, and signal transduction for biological systems. This review concludes by summarizing the strengths and limitations of AI-involved biological measurement in fundamental and applied research.
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Affiliation(s)
- Chao Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
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42
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Multamäki E, Nanekar R, Morozov D, Lievonen T, Golonka D, Wahlgren WY, Stucki-Buchli B, Rossi J, Hytönen VP, Westenhoff S, Ihalainen JA, Möglich A, Takala H. Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling. Nat Commun 2021; 12:4394. [PMID: 34285211 PMCID: PMC8292422 DOI: 10.1038/s41467-021-24676-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (Agp1). Whereas Agp1 acts as a conventional histidine kinase, we identify DrBphP as a light-sensitive phosphatase. While Agp1 binds its cognate response regulator only transiently, DrBphP does so strongly, which is rationalized at the structural level. Our data pinpoint two key residues affecting the balance between kinase and phosphatase activities, which immediately bears on photoreception and two-component signaling. The opposing output activities in two highly similar bacteriophytochromes suggest the use of light-controllable histidine kinases and phosphatases for optogenetics.
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Affiliation(s)
- Elina Multamäki
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland
| | - Rahul Nanekar
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Dmitry Morozov
- grid.9681.60000 0001 1013 7965Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Topias Lievonen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - David Golonka
- grid.7384.80000 0004 0467 6972Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Weixiao Yuan Wahlgren
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Brigitte Stucki-Buchli
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Jari Rossi
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland
| | - Vesa P. Hytönen
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, BioMediTech, Tampere University, Tampere, Finland ,grid.511163.10000 0004 0518 4910Fimlab Laboratories, Tampere, Finland
| | - Sebastian Westenhoff
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Janne A. Ihalainen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Andreas Möglich
- grid.7384.80000 0004 0467 6972Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Heikki Takala
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland ,grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
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43
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Wellington Miranda S, Cong Q, Schaefer AL, MacLeod EK, Zimenko A, Baker D, Greenberg EP. A covariation analysis reveals elements of selectivity in quorum sensing systems. eLife 2021; 10:69169. [PMID: 34180398 PMCID: PMC8328516 DOI: 10.7554/elife.69169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022] Open
Abstract
Many bacteria communicate with kin and coordinate group behaviors through a form of cell-cell signaling called acyl-homoserine lactone (AHL) quorum sensing (QS). In these systems, a signal synthase produces an AHL to which its paired receptor selectively responds. Selectivity is fundamental to cell signaling. Despite its importance, it has been challenging to determine how this selectivity is achieved and how AHL QS systems evolve and diversify. We hypothesized that we could use covariation within the protein sequences of AHL synthases and receptors to identify selectivity residues. We began by identifying about 6000 unique synthase-receptor pairs. We then used the protein sequences of these pairs to identify covariation patterns and mapped the patterns onto the LasI/R system from Pseudomonas aeruginosa PAO1. The covarying residues in both proteins cluster around the ligand-binding sites. We demonstrate that these residues are involved in system selectivity toward the cognate signal and go on to engineer the Las system to both produce and respond to an alternate AHL signal. We have thus demonstrated that covariation methods provide a powerful approach for investigating selectivity in protein-small molecule interactions and have deepened our understanding of how communication systems evolve and diversify.
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Affiliation(s)
| | - Qian Cong
- Department of Biochemistry, University of Washington, Seattle, United States.,Institute for Protein Design, University of Washington, Seattle, United States.,Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Amy L Schaefer
- Department of Microbiology, University of Washington, Seattle, United States
| | - Emily Kenna MacLeod
- Department of Microbiology, University of Washington, Seattle, United States
| | - Angelina Zimenko
- Department of Microbiology, University of Washington, Seattle, United States
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, United States.,Institute for Protein Design, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - E Peter Greenberg
- Department of Microbiology, University of Washington, Seattle, United States
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44
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Ortet P, Fochesato S, Bitbol AF, Whitworth DE, Lalaouna D, Santaella C, Heulin T, Achouak W, Barakat M. Evolutionary history expands the range of signaling interactions in hybrid multikinase networks. Sci Rep 2021; 11:11763. [PMID: 34083699 PMCID: PMC8175716 DOI: 10.1038/s41598-021-91260-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein communicating via intramolecular phosphotransfer. Here, we report how evolutionary relationships between hybrid HKs can be used as predictors of potential intermolecular and intramolecular interactions (‘phylogenetic promiscuity’). We used domain-swap genes chimeras to investigate the specificity of phosphotransfer within hybrid HKs of the GacS–GacA multikinase network of Pseudomonas brassicacearum. The receiver domain of GacS was replaced with those from nine donor hybrid HKs. Three chimeras with receivers from other hybrid HKs demonstrated correct functioning through complementation of a gacS mutant, which was dependent on strains having a functional gacA. Formation of functional chimeras was predictable on the basis of evolutionary heritage, and raises the possibility that HKs sharing a common ancestor with GacS might remain components of the contemporary GacS network. The results also demonstrate that understanding the evolutionary heritage of signaling domains in sophisticated networks allows their rational rewiring by simple domain transplantation, with implications for the creation of designer networks and inference of functional interactions.
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Affiliation(s)
- Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Sylvain Fochesato
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Anne-Florence Bitbol
- CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR8237), Sorbonne Université, 75005, Paris, France.,Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK
| | - David Lalaouna
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.,CNRS, ARN UPR 9002, Université de Strasbourg, 67000, Strasbourg, France
| | - Catherine Santaella
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.
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45
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Chen Z, Elowitz MB. Programmable protein circuit design. Cell 2021; 184:2284-2301. [PMID: 33848464 PMCID: PMC8087657 DOI: 10.1016/j.cell.2021.03.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022]
Abstract
A fundamental challenge in synthetic biology is to create molecular circuits that can program complex cellular functions. Because proteins can bind, cleave, and chemically modify one another and interface directly and rapidly with endogenous pathways, they could extend the capabilities of synthetic circuits beyond what is possible with gene regulation alone. However, the very diversity that makes proteins so powerful also complicates efforts to harness them as well-controlled synthetic circuit components. Recent work has begun to address this challenge, focusing on principles such as orthogonality and composability that permit construction of diverse circuit-level functions from a limited set of engineered protein components. These approaches are now enabling the engineering of circuits that can sense, transmit, and process information; dynamically control cellular behaviors; and enable new therapeutic strategies, establishing a powerful paradigm for programming biology.
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Affiliation(s)
- Zibo Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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46
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Albicoro FJ, Draghi WO, Martini MC, Salas ME, Torres Tejerizo GA, Lozano MJ, López JL, Vacca C, Cafiero JH, Pistorio M, Bednarz H, Meier D, Lagares A, Niehaus K, Becker A, Del Papa MF. The two-component system ActJK is involved in acid stress tolerance and symbiosis in Sinorhizobium meliloti. J Biotechnol 2021; 329:80-91. [PMID: 33539896 DOI: 10.1016/j.jbiotec.2021.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 01/25/2023]
Abstract
The nitrogen-fixing α-proteobacterium Sinorhizobium meliloti genome codifies at least 50 response regulator (RR) proteins mediating different and, in many cases, unknown processes. RR-mutant library screening allowed us to identify genes potentially implicated in survival to acid conditions. actJ mutation resulted in a strain with reduced growth rate under mildly acidic conditions as well as a lower capacity to tolerate a sudden shift to lethal acidic conditions compared with the parental strain. Mutation of the downstream gene actK, which encodes for a histidine kinase, showed a similar phenotype in acidic environments suggesting a functional two-component system. Interestingly, even though nodulation kinetics, quantity, and macroscopic morphology of Medicago sativa nodules were not affected in actJ and actK mutants, ActK was required to express the wild-type nitrogen fixation phenotype and ActJK was necessary for full bacteroid development and nodule occupancy. The actJK regulatory system presented here provides insights into an evolutionary process in rhizobium adaptation to acidic environments and suggests that actJK-controlled functions are crucial for optimal symbiosis development.
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Affiliation(s)
- Francisco J Albicoro
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Walter O Draghi
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María C Martini
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María E Salas
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - G A Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mauricio J Lozano
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - José L López
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Carolina Vacca
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juan H Cafiero
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Hanna Bednarz
- CeBiTec, Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany
| | - Doreen Meier
- CeBiTec, Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Karsten Niehaus
- CeBiTec, Centrum für Biotechnologie, Universität Bielefeld, Bielefeld, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany; Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - M F Del Papa
- Instituto de Biotecnología y Biología Molecular -CONICET CCT La Plata Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
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Singh D, Gupta P, Singla-Pareek SL, Siddique KH, Pareek A. The Journey from Two-Step to Multi-Step Phosphorelay Signaling Systems. Curr Genomics 2021; 22:59-74. [PMID: 34045924 PMCID: PMC8142344 DOI: 10.2174/1389202921666210105154808] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/21/2020] [Accepted: 12/18/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The two-component signaling (TCS) system is an important signal transduction machinery in prokaryotes and eukaryotes, excluding animals, that uses a protein phosphorylation mechanism for signal transmission. CONCLUSION Prokaryotes have a primitive type of TCS machinery, which mainly comprises a membrane-bound sensory histidine kinase (HK) and its cognate cytoplasmic response regulator (RR). Hence, it is sometimes referred to as two-step phosphorelay (TSP). Eukaryotes have more sophisticated signaling machinery, with an extra component - a histidine-containing phosphotransfer (HPT) protein that shuttles between HK and RR to communicate signal baggage. As a result, the TSP has evolved from a two-step phosphorelay (His-Asp) in simple prokaryotes to a multi-step phosphorelay (MSP) cascade (His-Asp-His-Asp) in complex eukaryotic organisms, such as plants, to mediate the signaling network. This molecular evolution is also reflected in the form of considerable structural modifications in the domain architecture of the individual components of the TCS system. In this review, we present TCS system's evolutionary journey from the primitive TSP to advanced MSP type across the genera. This information will be highly useful in designing the future strategies of crop improvement based on the individual members of the TCS machinery.
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Affiliation(s)
| | | | | | | | - Ashwani Pareek
- Address correspondence to this author at the Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Tel/Fax: 91-11-26704504 / 26742558; E-mail:
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48
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Fernández P, Díaz AR, Ré MF, Porrini L, de Mendoza D, Albanesi D, Mansilla MC. Identification of Novel Thermosensors in Gram-Positive Pathogens. Front Mol Biosci 2020; 7:592747. [PMID: 33324680 PMCID: PMC7726353 DOI: 10.3389/fmolb.2020.592747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 10/28/2020] [Indexed: 11/13/2022] Open
Abstract
Temperature is a crucial variable that every living organism, from bacteria to humans, need to sense and respond to in order to adapt and survive. In particular, pathogenic bacteria exploit host-temperature sensing as a cue for triggering virulence gene expression. Here, we have identified and characterized two integral membrane thermosensor histidine kinases (HKs) from Gram-positive pathogens that exhibit high similarity to DesK, the extensively characterized cold sensor histidine kinase from Bacillus subtilis. Through in vivo experiments, we demonstrate that SA1313 from Staphylococcus aureus and BA5598 from Bacillus anthracis, which likely control the expression of putative ATP binding cassette (ABC) transporters, are regulated by environmental temperature. We show here that these HKs can phosphorylate the non-cognate response regulator DesR, partner of DesK, both in vitro and in vivo, inducing in B. subtilis the expression of the des gene upon a cold shock. In addition, we report the characterization of another DesK homolog from B. subtilis, YvfT, also closely associated to an ABC transporter. Although YvfT phosphorylates DesR in vitro, this sensor kinase can only induce des expression in B. subtilis when overexpressed together with its cognate response regulator YvfU. This finding evidences a physiological mechanism to avoid cross talk with DesK after a temperature downshift. Finally, we present data suggesting that the HKs studied in this work appear to monitor different ranges of membrane lipid properties variations to mount adaptive responses upon cooling. Overall, our findings point out that bacteria have evolved sophisticated mechanisms to assure specificity in the response to environmental stimuli. These findings pave the way to understand thermosensing mediated by membrane proteins that could have important roles upon host invasion by bacterial pathogens.
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Affiliation(s)
- Pilar Fernández
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Alejandra Raquel Díaz
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur, Centro de Recursos Naturales Renovables de la Zona Semi-árida (CERZOS-CONICET), Bahía Blanca, Argentina
| | - María Florencia Ré
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Lucía Porrini
- Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Diego de Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina.,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Daniela Albanesi
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina.,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Cecilia Mansilla
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina.,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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Cao Q, Yang N, Wang Y, Xu C, Zhang X, Fan K, Chen F, Liang H, Zhang Y, Deng X, Feng Y, Yang CG, Wu M, Bae T, Lan L. Mutation-induced remodeling of the BfmRS two-component system in Pseudomonas aeruginosa clinical isolates. Sci Signal 2020; 13:13/656/eaaz1529. [PMID: 33144518 DOI: 10.1126/scisignal.aaz1529] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Genetic mutations are a primary driving force behind the adaptive evolution of bacterial pathogens. Multiple clinical isolates of Pseudomonas aeruginosa, an important human pathogen, have naturally evolved one or more missense mutations in bfmS, which encodes the sensor histidine kinase of the BfmRS two-component system (TCS). A mutant BfmS protein containing both the L181P and E376Q substitutions increased the phosphorylation and thus the transcriptional regulatory activity of its cognate downstream response regulator, BfmR. This reduced acute virulence and enhanced biofilm formation, both of which are phenotypic changes associated with a chronic infection state. The increased phosphorylation of BfmR was due, at least in part, to the cross-phosphorylation of BfmR by GtrS, a noncognate sensor kinase. Other spontaneous missense mutations in bfmS, such as A42E/G347D, T242R, and R393H, also caused a similar remodeling of the BfmRS TCS in P. aeruginosa This study highlights the plasticity of TCSs mediated by spontaneous mutations and suggests that mutation-induced activation of BfmRS may contribute to host adaptation by P. aeruginosa during chronic infections.
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Affiliation(s)
- Qiao Cao
- College of Life Science, Northwest University, Xi'an 710127, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Nana Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanhui Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chenchen Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xue Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ke Fan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Feifei Chen
- College of Life Science, Northwest University, Xi'an 710127, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Haihua Liang
- College of Life Science, Northwest University, Xi'an 710127, China
| | - Yingchao Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong 999077, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong 999077, China
| | - Youjun Feng
- School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58203-9037, USA
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN 46408, USA
| | - Lefu Lan
- College of Life Science, Northwest University, Xi'an 710127, China. .,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.,NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
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50
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Lite TLV, Grant RA, Nocedal I, Littlehale ML, Guo MS, Laub MT. Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library. eLife 2020; 9:e60924. [PMID: 33107822 PMCID: PMC7669267 DOI: 10.7554/elife.60924] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/26/2020] [Indexed: 12/27/2022] Open
Abstract
Protein-protein interaction specificity is often encoded at the primary sequence level. However, the contributions of individual residues to specificity are usually poorly understood and often obscured by mutational robustness, sequence degeneracy, and epistasis. Using bacterial toxin-antitoxin systems as a model, we screened a combinatorially complete library of antitoxin variants at three key positions against two toxins. This library enabled us to measure the effect of individual substitutions on specificity in hundreds of genetic backgrounds. These distributions allow inferences about the general nature of interface residues in promoting specificity. We find that positive and negative contributions to specificity are neither inherently coupled nor mutually exclusive. Further, a wild-type antitoxin appears optimized for specificity as no substitutions improve discrimination between cognate and non-cognate partners. By comparing crystal structures of paralogous complexes, we provide a rationale for our observations. Collectively, this work provides a generalizable approach to understanding the logic of molecular recognition.
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Affiliation(s)
- Thuy-Lan V Lite
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
| | - Robert A Grant
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
| | - Isabel Nocedal
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
| | - Megan L Littlehale
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
| | - Monica S Guo
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
| | - Michael T Laub
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute Massachusetts Institute of TechnologyCambridgeUnited States
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