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Yu DS, Outram MA, Smith A, McCombe CL, Khambalkar PB, Rima SA, Sun X, Ma L, Ericsson DJ, Jones DA, Williams SJ. The structural repertoire of Fusarium oxysporum f. sp. lycopersici effectors revealed by experimental and computational studies. eLife 2024; 12:RP89280. [PMID: 38411527 PMCID: PMC10942635 DOI: 10.7554/elife.89280] [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: 02/28/2024] Open
Abstract
Plant pathogens secrete proteins, known as effectors, that function in the apoplast or inside plant cells to promote virulence. Effector recognition by cell-surface or cytosolic receptors results in the activation of defence pathways and plant immunity. Despite their importance, our general understanding of fungal effector function and recognition by immunity receptors remains poor. One complication often associated with effectors is their high sequence diversity and lack of identifiable sequence motifs precluding prediction of structure or function. In recent years, several studies have demonstrated that fungal effectors can be grouped into structural classes, despite significant sequence variation and existence across taxonomic groups. Using protein X-ray crystallography, we identify a new structural class of effectors hidden within the secreted in xylem (SIX) effectors from Fusarium oxysporum f. sp. lycopersici (Fol). The recognised effectors Avr1 (SIX4) and Avr3 (SIX1) represent the founding members of the Fol dual-domain (FOLD) effector class, with members containing two distinct domains. Using AlphaFold2, we predicted the full SIX effector repertoire of Fol and show that SIX6 and SIX13 are also FOLD effectors, which we validated experimentally for SIX6. Based on structural prediction and comparisons, we show that FOLD effectors are present within three divisions of fungi and are expanded in pathogens and symbionts. Further structural comparisons demonstrate that Fol secretes effectors that adopt a limited number of structural folds during infection of tomato. This analysis also revealed a structural relationship between transcriptionally co-regulated effector pairs. We make use of the Avr1 structure to understand its recognition by the I receptor, which leads to disease resistance in tomato. This study represents an important advance in our understanding of Fol-tomato, and by extension plant-fungal interactions, which will assist in the development of novel control and engineering strategies to combat plant pathogens.
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Affiliation(s)
- Daniel S Yu
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Megan A Outram
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Ashley Smith
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Carl L McCombe
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Pravin B Khambalkar
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Sharmin A Rima
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Xizhe Sun
- Research School of Biology, The Australian National UniversityCanberraAustralia
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agriculture UniversityBaodingChina
| | - Lisong Ma
- Research School of Biology, The Australian National UniversityCanberraAustralia
- State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural UniversityBaodingChina
| | - Daniel J Ericsson
- Research School of Biology, The Australian National UniversityCanberraAustralia
- The Australian Nuclear Science and Technology Organisation, Australian SynchrotronClaytonAustralia
| | - David A Jones
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Simon J Williams
- Research School of Biology, The Australian National UniversityCanberraAustralia
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Pandey SK, Melichercik M, Řeha D, Ettrich RH, Carey J. Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors. Molecules 2020; 25:molecules25092247. [PMID: 32397647 PMCID: PMC7248756 DOI: 10.3390/molecules25092247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 11/23/2022] Open
Abstract
Hexameric arginine repressor, ArgR, is the feedback regulator of bacterial L-arginine regulons, and sensor of L-arg that controls transcription of genes for its synthesis and catabolism. Although ArgR function, as well as its secondary, tertiary, and quaternary structures, is essentially the same in E. coli and B. subtilis, the two proteins differ significantly in sequence, including residues implicated in the response to L-arg. Molecular dynamics simulations are used here to evaluate the behavior of intact B. subtilis ArgR with and without L-arg, and are compared with prior MD results for a domain fragment of E. coli ArgR. Relative to its crystal structure, B. subtilis ArgR in absence of L-arg undergoes a large-scale rotational shift of its trimeric subassemblies that is very similar to that observed in the E. coli protein, but the residues driving rotation have distinct secondary and tertiary structural locations, and a key residue that drives rotation in E. coli is missing in B. subtilis. The similarity of trimer rotation despite different driving residues suggests that a rotational shift between trimers is integral to ArgR function. This conclusion is supported by phylogenetic analysis of distant ArgR homologs reported here that indicates at least three major groups characterized by distinct sequence motifs but predicted to undergo a common rotational transition. The dynamic consequences of L-arg binding for transcriptional activation of intact ArgR are evaluated here for the first time in two-microsecond simulations of B. subtilis ArgR. L-arg binding to intact B. subtilis ArgR causes a significant further shift in the angle of rotation between trimers that causes the N-terminal DNA-binding domains lose their interactions with the C-terminal domains, and is likely the first step toward adopting DNA-binding-competent conformations. The results aid interpretation of crystal structures of ArgR and ArgR-DNA complexes.
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Affiliation(s)
- Saurabh Kumar Pandey
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, 84248 Bratislava, Slovakia
- Faculty of Sciences, University of South Bohemia, 37005 Ceske Budejovice, Czechia
| | - Milan Melichercik
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, 84248 Bratislava, Slovakia
| | - David Řeha
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Faculty of Sciences, University of South Bohemia, 37005 Ceske Budejovice, Czechia
| | - Rüdiger H. Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- College of Biomedical Sciences, Larkin University, Miami, FL 33169, USA
- Department of Cellular Biology & Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
- Correspondence: (R.H.E.); (J.C.); Tel.: +1-954-682-8347 (R.H.E.); +1-609-258-1631 (J.C.)
| | - Jannette Carey
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Correspondence: (R.H.E.); (J.C.); Tel.: +1-954-682-8347 (R.H.E.); +1-609-258-1631 (J.C.)
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Mariutti RB, Ullah A, Araujo GC, Murakami MT, Arni RK. Tyrosine binding and promiscuity in the arginine repressor from the pathogenic bacterium Corynebacterium pseudotuberculosis. Biochem Biophys Res Commun 2016; 475:350-5. [PMID: 27233609 DOI: 10.1016/j.bbrc.2016.05.091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 05/19/2016] [Indexed: 11/17/2022]
Abstract
The arginine repressor (ArgR) regulates arginine biosynthesis in a number of microorganisms and consists of two domains interlinked by a short peptide; the N-terminal domain is involved in DNA binding and the C-terminal domain binds arginine and forms a hexamer made-up of a dimer of trimers. The crystal structure of the C-terminal domain of ArgR from the pathogenic Corynebacterium pseudotuberculosis determined at 1.9 Å resolution contains a tightly bound tyrosine at the arginine-binding site indicating hitherto unobserved promiscuity. Structural analysis of the binding pocket displays clear molecular adaptations to accommodate tyrosine binding suggesting the possible existence of an alternative regulatory process in this pathogenic bacterium.
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Affiliation(s)
- Ricardo Barros Mariutti
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, 15054-000, Brazil.
| | - Anwar Ullah
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, 15054-000, Brazil; Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Islamabad 45550, Pakistan
| | | | - Mario Tyago Murakami
- Biosciences National Laboratory (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil
| | - Raghuvir Krishnaswamy Arni
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, 15054-000, Brazil; Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP, 15054-000, Brazil.
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Strawn R, Melichercik M, Green M, Stockner T, Carey J, Ettrich R. Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues. PLoS Comput Biol 2010; 6:e1000801. [PMID: 20532206 PMCID: PMC2880562 DOI: 10.1371/journal.pcbi.1000801] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 04/29/2010] [Indexed: 12/20/2022] Open
Abstract
An elegantly simple and probably ancient molecular mechanism of allostery is described for the Escherichia coli arginine repressor ArgR, the master feedback regulator of transcription in L-arginine metabolism. Molecular dynamics simulations with ArgRC, the hexameric domain that binds L-arginine with negative cooperativity, reveal that conserved arginine and aspartate residues in each ligand-binding pocket promote rotational oscillation of apoArgRC trimers by engagement and release of hydrogen-bonded salt bridges. Binding of exogenous L-arginine displaces resident arginine residues and arrests oscillation, shifting the equilibrium quaternary ensemble and promoting motions that maintain the configurational entropy of the system. A single L-arg ligand is necessary and sufficient to arrest oscillation, and enables formation of a cooperative hydrogen-bond network at the subunit interface. The results are used to construct a free-energy reaction coordinate that accounts for the negative cooperativity and distinctive thermodynamic signature of L-arginine binding detected by calorimetry. The symmetry of the hexamer is maintained as each ligand binds, despite the conceptual asymmetry of partially-liganded states. The results thus offer the first opportunity to describe in structural and thermodynamic terms the symmetric relaxed state predicted by the concerted allostery model of Monod, Wyman, and Changeux, revealing that this state is achieved by exploiting the dynamics of the assembly and the distributed nature of its cohesive free energy. The ArgR example reveals that symmetry can be maintained even when binding sites fill sequentially due to negative cooperativity, which was not anticipated by the Monod, Wyman, and Changeux model. The molecular mechanism identified here neither specifies nor requires a pathway for transmission of the allosteric signal through the protein, and it suggests the possibility that binding of free amino acids was an early innovation in the evolution of allostery.
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Affiliation(s)
- Rebecca Strawn
- Chemistry Department, Princeton University, Princeton, New Jersey, United States of America
| | - Milan Melichercik
- Department of Structure and Function of Proteins, Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, and Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
| | - Michael Green
- Biology Department, The College of New Jersey, Ewing, New Jersey, United States of America
| | - Thomas Stockner
- Department of Medical Chemistry, Medical University of Vienna, Vienna, Austria
| | - Jannette Carey
- Chemistry Department, Princeton University, Princeton, New Jersey, United States of America
| | - Rüdiger Ettrich
- Department of Structure and Function of Proteins, Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, and Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
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Crystal structure of the intermediate complex of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator reveals detailed mechanism of arginine repression. J Mol Biol 2010; 399:240-54. [PMID: 20382162 DOI: 10.1016/j.jmb.2010.03.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 03/27/2010] [Accepted: 03/31/2010] [Indexed: 11/24/2022]
Abstract
The concentration of L-arginine in Mycobacterium tuberculosis (Mtb) and in many other bacteria is controlled by a transcriptional factor called the arginine repressor (ArgR). It regulates the transcription of the biosynthetic genes of the arginine operon by interacting with the approximately 16- to 20-bp ARG boxes in the promoter site of the operon. ArgRs in the arginine bound form are hexamers in which each protomer has two separately folded domains. The C-terminal domains form a hexameric core, whereas the N-terminal domains have the winged helix-turn-helix DNA-binding motif. Here, we present the crystal structure of the MtbArgR hexamer bound to three copies of the 16-bp DNA operator in the presence of trace amounts of L-arginine, determined to 2.15 A resolution. In contrast to our previously published structure of the ternary MtbArgR-DNA complex in the presence of 10 mM L-arginine, the DNA operators do not form a double ARG box in the structure reported here. The present structure not only retains the noncrystallographic 32 symmetry of the core (as in the earlier structure), but it also has the 3-fold axis for the whole complex. The core trimers are rotated relative to one another as in the other holo hexamers of MtbArgR, although the L-arginine ligands have only partial density and do not fully occupy the arginine-binding sites. Refinement of the occupancies and B-factors of ligands resulted in a value of approximately 4.4 arginine ligands per hexamer. This has allowed the dissociation constant of arginine from the arginine-binding site to be estimated. The present structure also has two protomer conformations, folded and extended. However, they are different from the conformations in the complex determined at an L-arginine concentration of 10 mM and do not form an interlocking arrangement. The new complex is less stable than the earlier described complex bound with nine arginine residues. Thus, the former can be considered as an intermediate in a pathway to the latter. On the basis of the structure of this intermediate complex, a more detailed mechanism of the arginine biosynthesis regulation in Mtb is proposed.
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Cherney LT, Cherney MM, Garen CR, James MNG. The structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and Co-repressor, L-arginine. J Mol Biol 2009; 388:85-97. [PMID: 19265706 DOI: 10.1016/j.jmb.2009.02.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 02/17/2009] [Accepted: 02/20/2009] [Indexed: 10/21/2022]
Abstract
The biosynthesis of arginine is an essential function for the metabolism of Mycobacterium tuberculosis (Mtb) and for the metabolism of many other microorganisms. The arginine repressor (ArgR) proteins control the transcription of genes encoding the arginine biosynthetic enzymes; they belong to repressors having one of the most intricate oligomerization patterns. Here, we present the crystal structure of the MtbArgR hexamer bound to three copies of the 20 base-pair DNA operator and to the co-repressor, L-arginine, determined to 3.3 A resolution. This is the first ternary structure of an intact hexameric ArgR in complex with its DNA operator. The structure reported here is very different from the suggested models of the ternary ArgR-DNA complexes; it has revealed the sophisticated symmetry of the complex and the presence of two remarkably different protomer conformations, folded and extended. Both features provide flexibility to DNA binding and are important for understanding the detailed function of ArgRs. Two of the 20 base-pair DNA operators align in a unified double-helical structure, suggesting the possible presence of a double ARG box in the promoter region of the Mtb arginine operon. Two pairs of protomers bind to the unified double ARG box so that the two folded protomers bind to the central half-sites of the double ARG box, whereas the two extended protomers bind to the remote half-sites. The protomers of the third pair bound to the single DNA operator also have a folded and an extended conformation. A probable mechanism for arginine repression is suggested on the basis of this structure.
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Affiliation(s)
- Leonid T Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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Cherney LT, Cherney MM, Garen CR, Lu GJ, James MNG. Crystal structure of the arginine repressor protein in complex with the DNA operator from Mycobacterium tuberculosis. J Mol Biol 2008; 384:1330-40. [PMID: 18952097 DOI: 10.1016/j.jmb.2008.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 10/02/2008] [Accepted: 10/03/2008] [Indexed: 11/25/2022]
Abstract
The arginine repressor (ArgR) from Mycobacterium tuberculosis (Mtb) is a gene product encoded by the open reading frame Rv1657. It regulates the L-arginine concentration in cells by interacting with ARG boxes in the promoter regions of the arginine biosynthesis and catabolism operons. Here we present a 2.5-A structure of MtbArgR in complex with a 16-bp DNA operator in the absence of arginine. A biological trimer of the protein-DNA complex is formed via the crystallographic 3-fold symmetry axis. The N-terminal domain of MtbArgR has a winged helix-turn-helix motif that binds to the major groove of the DNA. This structure shows that, in the absence of arginine, the ArgR trimer can bind three ARG box half-sites. It also reveals the structure of the whole MtbArgR molecule itself containing both N-terminal and C-terminal domains.
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Affiliation(s)
- Leonid T Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, 431 Medical Sciences Building, Edmonton, Alberta, Canada T6G 2H7
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