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Swackhammer A, Provencher EAP, Donkor AK, Garofalo J, Dowling S, Garchitorena K, Phyo A, Ramírez Veliz N, Karen M, Kwon A, Diep R, Norris M, Safo MK, Pierce BD. Mechanistic Analysis of the VirA Sensor Kinase in Agrobacterium tumefaciens Using Structural Models. Front Microbiol 2022; 13:898785. [PMID: 35651496 PMCID: PMC9149312 DOI: 10.3389/fmicb.2022.898785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Agrobacterium tumefaciens pathogenesis of plants is initiated with signal reception and culminates with transforming the genomic DNA of its host. The histidine sensor kinase VirA receives and reacts to discrete signaling molecules for the full induction of the genes necessary for this process. Though many of the components of this process have been identified, the precise mechanism of how VirA coordinates the response to host signals, namely phenols and sugars, is unknown. Recent advances of molecular modeling have allowed us to test structure/function predictions and contextualize previous experiments with VirA. In particular, the deep mind software AlphaFold has generated a structural model for the entire protein, allowing us to construct a model that addresses the mechanism of VirA signal reception. Here, we deepen our analysis of the region of VirA that is critical for phenol reception, model and probe potential phenol-binding sites of VirA, and refine its mechanism to strengthen our understanding of A. tumefaciens signal perception.
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Affiliation(s)
| | - Edward A. P. Provencher
- Department of Biology, University of Richmond, Richmond, VA, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA, United States
| | - Akua K. Donkor
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - Jessica Garofalo
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Sinead Dowling
- Department of Biology, University of Richmond, Richmond, VA, United States
| | | | - Ahkar Phyo
- Department of Biology, University of Richmond, Richmond, VA, United States
| | | | - Matthew Karen
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Annie Kwon
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Rich Diep
- Department of Biology, University of Richmond, Richmond, VA, United States
| | - Michael Norris
- Department of Chemistry, University of Richmond, Richmond, VA, United States
| | - Martin K. Safo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - B. Daniel Pierce
- Department of Biology, University of Richmond, Richmond, VA, United States
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2
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The upcycled roles of pseudoenzymes in two-component signal transduction. Curr Opin Microbiol 2021; 61:82-90. [PMID: 33872991 DOI: 10.1016/j.mib.2021.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/23/2022]
Abstract
Upon first glance at a bacterial genome, pseudoenzymes appear unremarkable due to their lack of critical motifs that facilitate catalysis. These pseudoenzymes exist within signal transduction enzymes including histidine kinases, response regulators, diguanylate cyclases, and phosphodiesterases. Here, we summarize recent studies of bacterial pseudo-histidine kinases and pseudo-response regulators that regulate cell division, capsule formation, and the circadian rhythm. These examples illuminate the mechanistic potential of catalytically dead signaling enzymes and their impact upon bacterial signal transduction. Moreover, proteins lacking characteristic catalytic features of two-component systems reveal the sophisticated underlying potential of canonical two-component systems.
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3
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Kowallis KA, Silfani EM, Kasumu AP, Rong G, So V, Childers WS. Synthetic Control of Signal Flow Within a Bacterial Multi-Kinase Network. ACS Synth Biol 2020; 9:1705-1713. [PMID: 32559383 DOI: 10.1021/acssynbio.0c00043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The signal processing capabilities of bacterial signaling networks offer immense potential for advanced phospho-signaling systems for synthetic biology. Emerging models suggest that complex development may require interconnections between what were once thought to be isolated signaling arrays. For example, Caulobacter crescentus achieves the feat of asymmetric division by utilizing a novel pseudokinase DivL, which senses the output of one signaling pathway to modulate a second pathway. It has been proposed that DivL reverses signal flow by exploiting conserved kinase conformational changes and protein-protein interactions. We engineered a series of DivL-based modulators to synthetically stimulate reverse signaling of the network in vivo. Stimulation of conformational changes through the DivL signal transmission helix resulted in changes to hallmark features of the network: C. crescentus motility and DivL accumulation at the cell poles. Additionally, mutations to a conserved PAS sensor transmission motif disrupted reverse signaling flow in vivo. We propose that synthetic stimulation and sensor disruption provide strategies to define signaling circuit organization principles for the rational design and validation of synthetic pathways.
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Affiliation(s)
- Kimberly A. Kowallis
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Elayna M. Silfani
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Amanda P. Kasumu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Grace Rong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Victor So
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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4
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Binns AN, Zhao J. The MexE/MexF/AmeC Efflux Pump of Agrobacterium tumefaciens and Its Role in Ti Plasmid Virulence Gene Expression. J Bacteriol 2020; 202:e00609-19. [PMID: 32015146 PMCID: PMC7099130 DOI: 10.1128/jb.00609-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/25/2020] [Indexed: 12/21/2022] Open
Abstract
Expression of the tumor-inducing (Ti) plasmid virulence genes of Agrobacterium tumefaciens is required for the transfer of DNA from the bacterium into plant cells, ultimately resulting in the initiation of plant tumors. The vir genes are induced as a result of exposure to certain phenol derivatives, monosaccharides, and low pH in the extracellular milieu. The soil, as well as wound sites on a plant-the usual site of the virulence activity of this bacterium-can contain these signals, but vir gene expression in the soil would be a wasteful utilization of energy. This suggests that mechanisms may exist to ensure that vir gene expression occurs only at the higher concentrations of inducers typically found at a plant wound site. In a search for transposon-mediated mutations that affect sensitivity for the virulence gene-inducing activity of the phenol, 3,5-dimethoxy-4-hydroxyacetophenone (acetosyringone [AS]), an RND-type efflux pump homologous to the MexE/MexF/OprN pump of Pseudomonas aeruginosa was identified. Phenotypes of mutants carrying an insertion or deletion of pump components included hypersensitivity to the vir-inducing effects of AS, hypervirulence in the tobacco leaf explant virulence assay, and hypersensitivity to the toxic effects of chloramphenicol. Furthermore, the methoxy substituents on the phenol ring of AS appear to be critical for recognition as a pump substrate. These results support the hypothesis that the regulation of virulence gene expression is integrated with cellular activities that elevate the level of plant-derived inducers required for induction so that this occurs preferentially, if not exclusively, in a plant environment.IMPORTANCE Expression of genes controlling the virulence activities of a bacterial pathogen is expected to occur preferentially at host sites vulnerable to that pathogen. Host-derived molecules that induce such activities in the plant pathogen Agrobacterium tumefaciens are found in the soil, as well as in the plant. Here, we tested the hypothesis that mechanisms exist to suppress the sensitivity of Agrobacterium species to a virulence gene-inducing molecule by selecting for mutant bacteria that are hypersensitive to its inducing activity. The mutant genes identified encode an efflux pump whose proposed activity increases the concentration of the inducer necessary for vir gene expression; this pump is also involved in antibiotic resistance, demonstrating a relationship between cellular defense activities and the control of virulence in Agrobacterium.
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Affiliation(s)
- Andrew N Binns
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jinlei Zhao
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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5
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Kowallis KA, Duvall SW, Zhao W, Childers WS. Manipulation of Bacterial Signaling Using Engineered Histidine Kinases. Methods Mol Biol 2020; 2077:141-163. [PMID: 31707657 DOI: 10.1007/978-1-4939-9884-5_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two-component systems allow bacteria to respond to changes in environmental or cytosolic conditions through autophosphorylation of a histidine kinase (HK) and subsequent transfer of the phosphate group to its downstream cognate response regulator (RR). The RR then elicits a cellular response, commonly through regulation of transcription. Engineering two-component system signaling networks provides a strategy to study bacterial signaling mechanisms related to bacterial cell survival, symbiosis, and virulence, and to develop sensory devices in synthetic biology. Here we focus on the principles for engineering the HK to identify unknown signal inputs, test signal transmission mechanisms, design small molecule sensors, and rewire two-component signaling networks.
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Affiliation(s)
| | - Samuel W Duvall
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Zhao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA. .,Chevron Science Center, University of Pittsburgh, Pittsburgh, PA, USA.
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Mann TH, Seth Childers W, Blair JA, Eckart MR, Shapiro L. A cell cycle kinase with tandem sensory PAS domains integrates cell fate cues. Nat Commun 2016; 7:11454. [PMID: 27117914 PMCID: PMC4853435 DOI: 10.1038/ncomms11454] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 03/22/2016] [Indexed: 11/11/2022] Open
Abstract
All cells must integrate sensory information to coordinate developmental events in space and time. The bacterium Caulobacter crescentus uses two-component phospho-signalling to regulate spatially distinct cell cycle events through the master regulator CtrA. Here, we report that CckA, the histidine kinase upstream of CtrA, employs a tandem-PAS domain sensor to integrate two distinct spatiotemporal signals. Using CckA reconstituted on liposomes, we show that one PAS domain modulates kinase activity in a CckA density-dependent manner, mimicking the stimulation of CckA kinase activity that occurs on its transition from diffuse to densely packed at the cell poles. The second PAS domain interacts with the asymmetrically partitioned second messenger cyclic-di-GMP, inhibiting kinase activity while stimulating phosphatase activity, consistent with the selective inactivation of CtrA in the incipient stalked cell compartment. The integration of these spatially and temporally regulated signalling events within a single signalling receptor enables robust orchestration of cell-type-specific gene regulation. The membrane-bound kinase CckA controls the activity of the Caulobacter crescentus master regulator CtrA, which in turn coordinates asymmetric cell division. Here, the authors show that CckA contains two sensory domains that have distinct sensitivities to fluctuations in cyclic-di-GMP concentration and subcellular niche.
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Affiliation(s)
- Thomas H Mann
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
| | - W Seth Childers
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jimmy A Blair
- Department of Chemistry, Williams College, Williamstown, Massachusetts 01267, USA
| | - Michael R Eckart
- Stanford Protein and Nucleic Acid Facility, Beckman Center, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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7
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Abstract
Agrobacterium tumefaciens is a plant pathogen with the capacity to deliver a segment of oncogenic DNA carried on a large plasmid called the tumor-inducing or Ti plasmid to susceptible plant cells. A. tumefaciens belongs to the class Alphaproteobacteria, whose members include other plant pathogens (Agrobacterium rhizogenes), plant and insect symbionts (Rhizobium spp. and Wolbachia spp., respectively), human pathogens (Brucella spp., Bartonella spp., Rickettsia spp.), and nonpathogens (Caulobacter crescentus, Rhodobacter sphaeroides). Many species of Alphaproteobacteria carry large plasmids ranging in size from ∼100 kb to nearly 2 Mb. These large replicons typically code for functions essential for cell physiology, pathogenesis, or symbiosis. Most of these elements rely on a conserved gene cassette termed repABC for replication and partitioning, and maintenance at only one or a few copies per cell. The subject of this review is the ∼200-kb Ti plasmids carried by infectious strains of A. tumefaciens. We will summarize the features of this plasmid as a representative of the repABC family of megaplasmids. We will also describe novel features of this plasmid that enable A. tumefaciens cells to incite tumor formation in plants, sense and respond to an array of plant host and bacterial signal molecules, and maintain and disseminate the plasmid among populations of agrobacteria. At the end of this review, we will describe how this natural genetic engineer has been adapted to spawn an entire industry of plant biotechnology and review its potential for use in future therapeutic applications of plant and nonplant species.
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Wise AA, Binns AN. The Receiver of the Agrobacterium tumefaciens VirA Histidine Kinase Forms a Stable Interaction with VirG to Activate Virulence Gene Expression. Front Microbiol 2016; 6:1546. [PMID: 26779177 PMCID: PMC4705274 DOI: 10.3389/fmicb.2015.01546] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/21/2015] [Indexed: 01/20/2023] Open
Abstract
The plant pathogen Agrobacterium tumefaciens carries a virulence gene system that is required for the initiation of crown gall tumors on susceptible plants. Expression of the vir genes is activated by the VirA/VirG two component regulatory system. VirA is a histidine kinase which signals the presence of certain chemicals found at the site of a plant wound. The receiver domain located at its carboxyl terminus defines VirA as a hybrid histidine kinase. Here, we show that the VirA receiver interacts with the DNA-binding domain of VirG. This finding supports the hypothesis that the receiver acts as a recruiting factor for VirG. In addition, we show that removal of the VirA receiver allowed vir gene expression in response to glucose in a dose dependent manner, indicating that the receiver controls VirG activation and suggesting that the supplementary ChvE-sugar signal increases this activity.
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Affiliation(s)
- Arlene A Wise
- Binns Lab, Department of Biology, University of Pennsylvania, Philadelphia PA, USA
| | - Andrew N Binns
- Binns Lab, Department of Biology, University of Pennsylvania, Philadelphia PA, USA
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9
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Fang F, Lin YH, Pierce BD, Lynn DG. A Rhizobium radiobacter Histidine Kinase Can Employ Both Boolean AND and OR Logic Gates to Initiate Pathogenesis. Chembiochem 2015; 16:2183-90. [PMID: 26310519 DOI: 10.1002/cbic.201500334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Indexed: 11/12/2022]
Abstract
The molecular logic gates that regulate gene circuits are necessarily intricate and highly regulated, particularly in the critical commitments necessary for pathogenesis. We now report simple AND and OR logic gates to be accessible within a single protein receptor. Pathogenesis by the bacterium Rhizobium radiobacter is mediated by a single histidine kinase, VirA, which processes multiple small molecule host signals (phenol and sugar). Mutagenesis analyses converged on a single signal integration node, and finer functional analyses revealed that a single residue could switch VirA from a functional AND logic gate to an OR gate where each of two signals activate independently. Host range preferences among natural strains of R. radiobacter correlate with these gate logic strategies. Although the precise mechanism for the signal integration node requires further analyses, long-range signal transmission through this histidine kinase can now be exploited for synthetic signaling circuits.
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Affiliation(s)
- Fang Fang
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, 30322, USA
| | - Yi-Han Lin
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, 30322, USA
| | - B Daniel Pierce
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, 30322, USA
| | - David G Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, 30322, USA.
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10
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Chen JC, Liu JH, Hsu DW, Shu JC, Chen CY, Chen CC. Methylatable Signaling Helix Coordinated Inhibitory Receiver Domain in Sensor Kinase Modulates Environmental Stress Response in Bacillus Cereus. PLoS One 2015; 10:e0137952. [PMID: 26379238 PMCID: PMC4574943 DOI: 10.1371/journal.pone.0137952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/25/2015] [Indexed: 02/08/2023] Open
Abstract
σB, an alternative transcription factor, controls the response of the cell to a variety of environmental stresses in Bacillus cereus. Previously, we reported that RsbM negatively regulates σB through the methylation of RsbK, a hybrid sensor kinase, on a signaling helix (S-helix). However, RsbK comprises a C-terminal receiver (REC) domain whose function remains unclear. In this study, deletion of the C-terminal REC domain of RsbK resulted in high constitutive σB expression independent of environmental stimuli. Thus, the REC domain may serve as an inhibitory element. Mutagenic substitution was employed to modify the putative phospho-acceptor residue D827 in the REC domain of RsbK. The expression of RsbKD827N and RsbKD827E exhibited high constitutive σB, indicating that D827, if phosphorylatable, possibly participates in σB regulation. Bacterial two-hybrid analyses demonstrated that RsbK forms a homodimer and the REC domain interacts mainly with the histidine kinase (HK) domain and partly with the S-helix. In particular, co-expression of RsbM strengthens the interaction between the REC domain and the S-helix. Consistently, our structural model predicts a significant interaction between the HK and REC domains of the RsbK intradimer. Here, we demonstrated that coordinated the methylatable S-helix and the REC domain of RsbK is functionally required to modulate σB-mediated stress response in B. cereus and maybe ubiquitous in microorganisms encoded RsbK-type sensor kinases.
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Affiliation(s)
- Jung-Chi Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Jyung-Hurng Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center (ABC), National Chung Hsing University, Taichung, Taiwan
| | - Duen-Wei Hsu
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Jwu-Ching Shu
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
| | - Chien-Yen Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
- * E-mail:
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11
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Dupré E, Herrou J, Lensink MF, Wintjens R, Vagin A, Lebedev A, Crosson S, Villeret V, Locht C, Antoine R, Jacob-Dubuisson F. Virulence regulation with Venus flytrap domains: structure and function of the periplasmic moiety of the sensor-kinase BvgS. PLoS Pathog 2015; 11:e1004700. [PMID: 25738876 PMCID: PMC4352136 DOI: 10.1371/journal.ppat.1004700] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/14/2015] [Indexed: 11/23/2022] Open
Abstract
Two-component systems (TCS) represent major signal-transduction pathways for adaptation to environmental conditions, and regulate many aspects of bacterial physiology. In the whooping cough agent Bordetella pertussis, the TCS BvgAS controls the virulence regulon, and is therefore critical for pathogenicity. BvgS is a prototypical TCS sensor-kinase with tandem periplasmic Venus flytrap (VFT) domains. VFT are bi-lobed domains that typically close around specific ligands using clamshell motions. We report the X-ray structure of the periplasmic moiety of BvgS, an intricate homodimer with a novel architecture. By combining site-directed mutagenesis, functional analyses and molecular modeling, we show that the conformation of the periplasmic moiety determines the state of BvgS activity. The intertwined structure of the periplasmic portion and the different conformation and dynamics of its mobile, membrane-distal VFT1 domains, and closed, membrane-proximal VFT2 domains, exert a conformational strain onto the transmembrane helices, which sets the cytoplasmic moiety in a kinase-on state by default corresponding to the virulent phase of the bacterium. Signaling the presence of negative signals perceived by the periplasmic domains implies a shift of BvgS to a distinct state of conformation and activity, corresponding to the avirulent phase. The response to negative modulation depends on the integrity of the periplasmic dimer, indicating that the shift to the kinase-off state implies a concerted conformational transition. This work lays the bases to understand virulence regulation in Bordetella. As homologous sensor-kinases control virulence features of diverse bacterial pathogens, the BvgS structure and mechanism may pave the way for new modes of targeted therapeutic interventions.
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Affiliation(s)
- Elian Dupré
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Julien Herrou
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Marc F. Lensink
- Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, University Lille North of France, Villeneuve d’Ascq, France
| | - René Wintjens
- Laboratory of Biopolymers and Supramolecular Nanomaterials, Université Libre de Bruxelles, Brussels, Belgium
| | - Alexey Vagin
- Structural Biology Laboratory, University of York, York, England, United Kingdom
| | - Andrey Lebedev
- Research Complex at Harwell, Science and Technology Facilities Council Rutherford Appleton Laboratory, Didcot, England, United Kingdom
| | - Sean Crosson
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Vincent Villeret
- Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, University Lille North of France, Villeneuve d’Ascq, France
| | - Camille Locht
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Rudy Antoine
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
| | - Françoise Jacob-Dubuisson
- Center for Infection and Immunity (CIIL), Institut Pasteur de Lille, Lille, France
- Center for Infection and Immunity (CIIL), University Lille North of France, Lille, France
- UMR 8204, Centre National de la Recherche Scientifique (CNRS), Lille, France
- U1019, Institut National de la Santé et de la Recherche Médicale (INSERM), Lille, France
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12
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Shalaby S, Horwitz BA. Plant phenolic compounds and oxidative stress: integrated signals in fungal-plant interactions. Curr Genet 2014; 61:347-57. [PMID: 25407462 DOI: 10.1007/s00294-014-0458-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/17/2014] [Accepted: 10/21/2014] [Indexed: 01/09/2023]
Abstract
Upon invasion of a host, fungal pathogens are exposed to a variety of stresses. Plants release reactive oxygen species, and mount a variety of preformed and induced chemical defenses. Phenolic compounds are one example: they are ubiquitous in plants, and an invading pathogen encounters them already at the leaf surface, or for soil-borne pathogens, in the rhizosphere. Phenolic and related aromatic compounds show varying degrees of toxicity to cells. Some compounds are quite readily metabolized, and others less so. It was known already from classical studies that phenolic substrates induce the expression of the enzymes for their degradation. Recently, the ability to degrade phenolics was shown to be a virulence factor. Conversely, phenolic compounds can increase the effectiveness of antifungals. Phenolics are known antioxidants, yet they have been shown to elicit cellular responses that would usually be triggered to counter oxidant stress. Here, we review the evidence for a connection between the fungal response to phenolics as small-molecule signals, and the response to oxidants. The connections proposed here should enable genetic screens to identify specific fungal receptors for plant phenolics. Furthermore, understanding how the pathogen detects plant phenolic compounds as a stress signal may facilitate new antifungal strategies.
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Affiliation(s)
- Samer Shalaby
- Department of Biology, Technion, Israel Institute of Technology, 3200000, Haifa, Israel
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13
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Cell fate regulation governed by a repurposed bacterial histidine kinase. PLoS Biol 2014; 12:e1001979. [PMID: 25349992 PMCID: PMC4211667 DOI: 10.1371/journal.pbio.1001979] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/17/2014] [Indexed: 11/19/2022] Open
Abstract
The pathway that regulates asymmetric cell division in Caulobacter involves a signaling kinase whose catalytic output domain has been repurposed as an input sensor of the phosphorylation state of the response regulator – a reversal of the conventional direction of information flow; this allows wiring of simple linear signaling pathways into complex eukaryote-like networks. One of the simplest organisms to divide asymmetrically is the bacterium Caulobacter crescentus. The DivL pseudo-histidine kinase, positioned at one cell pole, regulates cell-fate by controlling the activation of the global transcription factor CtrA via an interaction with the response regulator (RR) DivK. DivL uniquely contains a tyrosine at the histidine phosphorylation site, and can achieve these regulatory functions in vivo without kinase activity. Determination of the DivL crystal structure and biochemical analysis of wild-type and site-specific DivL mutants revealed that the DivL PAS domains regulate binding specificity for DivK∼P over DivK, which is modulated by an allosteric intramolecular interaction between adjacent domains. We discovered that DivL's catalytic domains have been repurposed as a phosphospecific RR input sensor, thereby reversing the flow of information observed in conventional histidine kinase (HK)-RR systems and coupling a complex network of signaling proteins for cell-fate regulation. Across all kingdoms of life the generation of cell-type diversity is the consequence of asymmetry at the point of cell division. The bacterium Caulobacter crescentus divides asymmetrically to produce daughter cells that have distinct morphology and behavior. As in eukaryotes, an unequal distribution of signaling proteins in daughter Caulobacter cells triggers the differential read-out of identical genomes. A critical interaction between two protein molecules – a protein kinase (DivL) and a response regulator (DivK) – is known to occur exclusively in one daughter cell and to thereby regulate differentiation. However, mapping the observed signaling interconnections that drive asymmetric division has been difficult to reconcile with traditional models of bacterial signaling. Here we determine how DivL detects and processes this DivK signal. Although DivL has an architecture that is typical of histidine kinases, which normally act by regulating the phosphorylation state of the appropriate response regulator, DivL's essential functions do not require kinase activity and DivL does not add or remove phosphate from DivK. Instead we find that DivL has converted its output kinase domain into an input sensor domain that specifically detects phosphorylated DivK, and we identify key features of DivL that underlie this specificity. This novel reassignment of sensory functions reverses the conventional kinase-to-response-regulator signaling flow and logically couples linear signaling pathways into complex eukaryote-like networks to regulate cell development.
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14
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Affiliation(s)
- Diego de Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000-Rosario, Argentina;
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15
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Lin YH, Pierce BD, Fang F, Wise A, Binns AN, Lynn DG. Role of the VirA histidine autokinase of Agrobacterium tumefaciens in the initial steps of pathogenesis. FRONTIERS IN PLANT SCIENCE 2014; 5:195. [PMID: 24860585 PMCID: PMC4030172 DOI: 10.3389/fpls.2014.00195] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/23/2014] [Indexed: 05/27/2023]
Abstract
Histidine kinases serve as critical environmental sensing modules, and despite their designation as simple two-component modules, their functional roles are remarkably diverse. In Agrobacterium tumefaciens pathogenesis, VirA serves with VirG as the initiating sensor/transcriptional activator for inter-kingdom gene transfer and transformation of higher plants. Through responses to three separate signal inputs, low pH, sugars, and phenols, A. tumefaciens commits to pathogenesis in virtually all flowering plants. However, how these three signals are integrated to regulate the response and why these signals might be diagnostic for susceptible cells across such a broad host-range remains poorly understood. Using a homology model of the VirA linker region, we provide evidence for coordinated long-range transmission of inputs perceived both outside and inside the cell through the creation of targeted VirA truncations. Further, our evidence is consistent with signal inputs weakening associations between VirA domains to position the active site histidine for phosphate transfer. This mechanism requires long-range regulation of inter-domain stability and the transmission of input signals through a common integrating domain for VirA signal transduction.
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Affiliation(s)
- Yi-Han Lin
- Lynn Lab, Department of Chemistry and Biology, Emory UniversityAtlanta, GA, USA
| | - B. Daniel Pierce
- Lynn Lab, Department of Chemistry and Biology, Emory UniversityAtlanta, GA, USA
| | - Fang Fang
- Lynn Lab, Department of Chemistry and Biology, Emory UniversityAtlanta, GA, USA
| | - Arlene Wise
- Binns Lab, Department of Biology, Plant Sciences Institute, University of PennsylvaniaPhiladelphia, PA, USA
| | - Andrew N. Binns
- Binns Lab, Department of Biology, Plant Sciences Institute, University of PennsylvaniaPhiladelphia, PA, USA
| | - David G. Lynn
- Lynn Lab, Department of Chemistry and Biology, Emory UniversityAtlanta, GA, USA
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16
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Venturi V, Fuqua C. Chemical signaling between plants and plant-pathogenic bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:17-37. [PMID: 23915131 DOI: 10.1146/annurev-phyto-082712-102239] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Studies of chemical signaling between plants and bacteria in the past have been largely confined to two models: the rhizobial-legume symbiotic association and pathogenesis between agrobacteria and their host plants. Recent studies are beginning to provide evidence that many plant-associated bacteria undergo chemical signaling with the plant host via low-molecular-weight compounds. Plant-produced compounds interact with bacterial regulatory proteins that then affect gene expression. Similarly, bacterial quorum-sensing signals result in a range of functional responses in plants. This review attempts to highlight current knowledge in chemical signaling that takes place between pathogenic bacteria and plants. This chemical communication between plant and bacteria, also referred to as interkingdom signaling, will likely become a major research field in the future, as it allows the design of specific strategies to create plants that are resistant to plant pathogens.
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Affiliation(s)
- Vittorio Venturi
- International Center for Genetic Engineering and Biotechnology, 34149 Trieste, Italy.
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17
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The integrity of the periplasmic domain of the VirA sensor kinase is critical for optimal coordination of the virulence signal response in Agrobacterium tumefaciens. J Bacteriol 2011; 193:1436-48. [PMID: 21216996 DOI: 10.1128/jb.01227-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The plant pathogen Agrobacterium tumefaciens responds to three main signals at the plant-bacterium interface: phenolics, such as acetosyringone (AS), monosaccharides, and acidic pH (∼5.5). These signals are transduced via the chromosomally encoded sugar binding protein ChvE and the Ti plasmid-encoded VirA/VirG two-component regulatory system, resulting in the transcriptional activation of the Ti plasmid virulence genes. Here, we present genetic and physical evidence that the periplasmic domain of VirA dimerizes independently of other parts of the protein, and we examine the effects of several engineered mutations in the periplasmic and transmembrane regions of VirA on vir-inducing capacity as indicated by AS sensitivity and maximal level of vir-inducing activity at saturating AS levels. The data indicate that helix-breaking mutations throughout the periplasmic domain of VirA or mutations that reposition the second transmembrane domain (TM2) of VirA relieve the periplasmic domain's repressive effects on the maximal activity of this kinase in response to phenolics, effects normally relieved only when ChvE, sugars, and low pH are also present. Such relief, however, does not sensitize VirA to low concentrations of phenolics, the other major effect of the ChvE-sugar and low pH signals. We further demonstrate that amino acid residues in a small Trg-like motif in the periplasmic domain of VirA are crucial for transmission of the ChvE-sugar signal to the cytoplasmic domain. These experiments provide evidence that small perturbations in the periplasmic domain of VirA can uncouple sugar-mediated changes in AS sensitivity from the sugar-mediated effects on maximal activity.
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18
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Structural plasticity and catalysis regulation of a thermosensor histidine kinase. Proc Natl Acad Sci U S A 2009; 106:16185-90. [PMID: 19805278 DOI: 10.1073/pnas.0906699106] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Temperature sensing is essential for the survival of living cells. A major challenge is to understand how a biological thermometer processes thermal information to optimize cellular functions. Using structural and biochemical approaches, we show that the thermosensitive histidine kinase, DesK, from Bacillus subtilis is cold-activated through specific interhelical rearrangements in its central four-helix bundle domain. As revealed by the crystal structures of DesK in different functional states, the plasticity of this helical domain influences the catalytic activities of the protein, either by modifying the mobility of the ATP-binding domains for autokinase activity or by modulating binding of the cognate response regulator to sustain the phosphotransferase and phosphatase activities. The structural and biochemical data suggest a model in which the transmembrane sensor domain of DesK promotes these structural changes through conformational signals transmitted by the membrane-connecting two-helical coiled-coil, ultimately controlling the alternation between output autokinase and phosphatase activities. The structural comparison of the different DesK variants indicates that incoming signals can take the form of helix rotations and asymmetric helical bends similar to those reported for other sensing systems, suggesting that a similar switching mechanism could be operational in a wide range of sensor histidine kinases.
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19
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George Cisar EA, Geisinger E, Muir TW, Novick RP. Symmetric signalling within asymmetric dimers of the Staphylococcus aureus receptor histidine kinase AgrC. Mol Microbiol 2009; 74:44-57. [PMID: 19708918 DOI: 10.1111/j.1365-2958.2009.06849.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Virulence in Staphylococcus aureus is largely under control of the accessory gene regulator (agr) quorum-sensing system. The AgrC receptor histidine kinase detects its autoinducing peptide (AIP) ligand and generates an intracellular signal resulting in secretion of virulence factors. Although agr is a well-studied quorum-sensing system, little is known about the mechanism of AgrC activation. By co-immunoprecipitation analysis and intermolecular complementation of receptor mutants, we showed that AgrC forms ligand-independent dimers that undergo trans-autophosphorylation upon interaction with AIP. Remarkably, addition of specific AIPs to AgrC mutant dimers with only one functional sensor domain caused symmetric activation of either kinase domain despite the sensor asymmetry. Furthermore, mutant dimers involving one constitutive protomer demonstrated ligand-independent activity, irrespective of which protomer was kinase deficient. These results demonstrate that signalling through either individual AgrC protomer causes symmetric activation of both kinase domains. We suggest that such signalling across the dimer interface may be an important mechanism for dimeric quorum-sensing receptors to rapidly elicit a response upon signal detection.
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Affiliation(s)
- Elizabeth A George Cisar
- Laboratory of Synthetic Protein Chemistry, Training Program in Chemical Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.Molecular Pathogenesis Program and Departments of Microbiology and Medicine, the Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Edward Geisinger
- Laboratory of Synthetic Protein Chemistry, Training Program in Chemical Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.Molecular Pathogenesis Program and Departments of Microbiology and Medicine, the Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Tom W Muir
- Laboratory of Synthetic Protein Chemistry, Training Program in Chemical Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.Molecular Pathogenesis Program and Departments of Microbiology and Medicine, the Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Richard P Novick
- Laboratory of Synthetic Protein Chemistry, Training Program in Chemical Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.Molecular Pathogenesis Program and Departments of Microbiology and Medicine, the Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
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20
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Lin YH, Gao R, Binns AN, Lynn DG. Capturing the VirA/VirG TCS of Agrobacterium tumefaciens. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 631:161-77. [PMID: 18792688 DOI: 10.1007/978-0-387-78885-2_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two-component systems (TCS) regulate pathogenic commitment in many interactions and provide an opportunity for unique therapeutic intervention. The VirA/VirG TCS of Agrobacterium tumefaciens mediates inter-kingdom gene transfer in the development of host tumors and sets in motion the events that underlie the great success of this multi-host plant pathogen. Significant proof for the feasibility of interventions has now emerged with the discovery of a natural product that effectively "blinds" the pathogen to the host via inhibition of VirA/VirG signal transduction. Moreover, the emerging studies on the mechanism of signal perception have revealed general sites suitable for intervention of TCS signaling. Given the extensive functional homology, it should now be possible to transfer the models discovered for VirA/VirG broadly to other pathogenic interactions.
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Affiliation(s)
- Yi-Han Lin
- Center for Fundamental and Applied Molecular Evolution, Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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21
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Ponts N, Yang J, Chung DWD, Prudhomme J, Girke T, Horrocks P, Le Roch KG. Deciphering the ubiquitin-mediated pathway in apicomplexan parasites: a potential strategy to interfere with parasite virulence. PLoS One 2008; 3:e2386. [PMID: 18545708 PMCID: PMC2408969 DOI: 10.1371/journal.pone.0002386] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 04/24/2008] [Indexed: 11/19/2022] Open
Abstract
Background Reversible modification of proteins through the attachment of ubiquitin or ubiquitin-like modifiers is an essential post-translational regulatory mechanism in eukaryotes. The conjugation of ubiquitin or ubiquitin-like proteins has been demonstrated to play roles in growth, adaptation and homeostasis in all eukaryotes, with perturbation of ubiquitin-mediated systems associated with the pathogenesis of many human diseases, including cancer and neurodegenerative disorders. Methodology/Principal Findings Here we describe the use of an HMM search of functional Pfam domains found in the key components of the ubiquitin-mediated pathway necessary to activate and reversibly modify target proteins in eight apicomplexan parasitic protozoa for which complete or late-stage genome projects exist. In parallel, the same search was conducted on five model organisms, single-celled and metazoans, to generate data to validate both the search parameters employed and aid paralog classification in Apicomplexa. For each of the 13 species investigated, a set of proteins predicted to be involved in the ubiquitylation pathway has been identified and demonstrates increasing component members of the ubiquitylation pathway correlating with organism and genome complexity. Sequence homology and domain architecture analyses facilitated prediction of apicomplexan-specific protein function, particularly those involved in regulating cell division during these parasite's complex life cycles. Conclusions/Significance This study provides a comprehensive analysis of proteins predicted to be involved in the apicomplexan ubiquitin-mediated pathway. Given the importance of such pathway in a wide variety of cellular processes, our data is a key step in elucidating the biological networks that, in part, direct the pathogenicity of these parasites resulting in a massive impact on global health. Moreover, apicomplexan-specific adaptations of the ubiquitylation pathway may represent new therapeutic targets for much needed drugs against apicomplexan parasites.
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Affiliation(s)
- Nadia Ponts
- Department of Cell Biology and Neurosciences, University of California at Riverside, Riverside, California, United States of America
| | - Jianfeng Yang
- Department of Cell Biology and Neurosciences, University of California at Riverside, Riverside, California, United States of America
| | - Duk-Won Doug Chung
- Department of Cell Biology and Neurosciences, University of California at Riverside, Riverside, California, United States of America
| | - Jacques Prudhomme
- Department of Cell Biology and Neurosciences, University of California at Riverside, Riverside, California, United States of America
| | - Thomas Girke
- Center for Plant Cell Biology (CEPCEB), University of California at Riverside, Riverside, California, United States of America
| | - Paul Horrocks
- Department of Medicine, Institute for Science and Technology in Medicine, Keele University, Keele, United Kingdom
| | - Karine G. Le Roch
- Department of Cell Biology and Neurosciences, University of California at Riverside, Riverside, California, United States of America
- * E-mail:
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