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Carpenter SCD, Bogdanove AJ, Abbot B, Stajich JE, Uehling JK, Lovett B, Kasson MT, Carter ME. Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp. Microb Genom 2024; 10:001261. [PMID: 38860878 PMCID: PMC11261895 DOI: 10.1099/mgen.0.001261] [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: 03/23/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
Endofungal Mycetohabitans (formerly Burkholderia) spp. rely on a type III secretion system to deliver mostly unidentified effector proteins when colonizing their host fungus, Rhizopus microsporus. The one known secreted effector family from Mycetohabitans consists of homologues of transcription activator-like (TAL) effectors, which are used by plant pathogenic Xanthomonas and Ralstonia spp. to activate host genes that promote disease. These 'Burkholderia TAL-like (Btl)' proteins bind corresponding specific DNA sequences in a predictable manner, but their genomic target(s) and impact on transcription in the fungus are unknown. Recent phenotyping of Btl mutants of two Mycetohabitans strains revealed that the single Btl in one Mycetohabitans endofungorum strain enhances fungal membrane stress tolerance, while others in a Mycetohabitans rhizoxinica strain promote bacterial colonization of the fungus. The phenotypic diversity underscores the need to assess the sequence diversity and, given that sequence diversity translates to DNA targeting specificity, the functional diversity of Btl proteins. Using a dual approach to maximize capture of Btl protein sequences for our analysis, we sequenced and assembled nine Mycetohabitans spp. genomes using long-read PacBio technology and also mined available short-read Illumina fungal-bacterial metagenomes. We show that btl genes are present across diverse Mycetohabitans strains from Mucoromycota fungal hosts yet vary in sequences and predicted DNA binding specificity. Phylogenetic analysis revealed distinct clades of Btl proteins and suggested that Mycetohabitans might contain more species than previously recognized. Within our data set, Btl proteins were more conserved across M. rhizoxinica strains than across M. endofungorum, but there was also evidence of greater overall strain diversity within the latter clade. Overall, the results suggest that Btl proteins contribute to bacterial-fungal symbioses in myriad ways.
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Affiliation(s)
- Sara C. D. Carpenter
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
| | - Adam J. Bogdanove
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
| | - Bhuwan Abbot
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - Jessie K. Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARS, Ithaca, NY 14850, USA
| | - Matt T. Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Morgan E. Carter
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- CIPHER Center, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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2
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Ventura C, Banerjee A, Zacharopoulou M, Itzhaki LS, Bahar I. Tandem-repeat proteins conformational mechanics are optimized to facilitate functional interactions and complexations. Curr Opin Struct Biol 2024; 84:102744. [PMID: 38134536 DOI: 10.1016/j.sbi.2023.102744] [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: 09/03/2023] [Revised: 10/30/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023]
Abstract
The architectures of tandem-repeat proteins are distinct from those of globular proteins. Individual modules, each comprising small structural motifs of 20-40 residues, are arrayed in a quasi one-dimensional fashion to form striking, elongated, horseshoe-like, and superhelical architectures, stabilized solely by short-range interaction. The spring-like shapes of repeat arrays point to elastic modes of action, and these proteins function as adapter molecules or 'hubs,' propagating signals within multi-subunit assemblies in diverse biological contexts. This flexibility is apparent in the dramatic variability observed in the structures of tandem-repeat proteins in different complexes. Here, using computational analysis, we demonstrate the striking ability of just one or a few global motions to recapitulate these structures. These findings show how the mechanics of repeat arrays are robustly enabled by their unique architecture. Thus, the repeating architecture has been optimized by evolution to favor functional modes of motions. The global motions enabling functional transitions can be fully visualized at http://bahargroup.org/tr_web.
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Affiliation(s)
- Carlos Ventura
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Anupam Banerjee
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Maria Zacharopoulou
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK. https://twitter.com/maria_zach_
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK.
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, 11794, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA.
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Richter I, Uzum Z, Wein P, Molloy EM, Moebius N, Stinear TP, Pidot SJ, Hertweck C. Transcription activator-like effectors from endosymbiotic bacteria control the reproduction of their fungal host. mBio 2023; 14:e0182423. [PMID: 37971247 PMCID: PMC10746252 DOI: 10.1128/mbio.01824-23] [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] [Received: 07/13/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Interactions between fungi and bacteria are critically important in ecology, medicine, and biotechnology. In this study, we shed light on factors that promote the persistence of a toxin-producing, phytopathogenic Rhizopus-Mycetohabitans symbiosis that causes severe crop losses in Asia. We present an unprecedented case where bacterially produced transcription activator-like (TAL) effectors are key to maintaining a stable endosymbiosis. In their absence, fungal sporulation is abrogated, leading to collapse of the phytopathogenic alliance. The Mycetohabitans TAL (MTAL)-mediated mechanism of host control illustrates a unique role of bacterial effector molecules that has broader implications, potentially serving as a model to understand how prokaryotic symbionts interact with their eukaryotic hosts.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Evelyn M. Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Nadine Moebius
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute, Melbourne, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute, Melbourne, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
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4
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Schornack S, Kamoun S. EVO-MPMI: From fundamental science to practical applications. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102469. [PMID: 37783039 DOI: 10.1016/j.pbi.2023.102469] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
In the unending coevolutionary dance between plants and microbes, each player impacts the evolution of the other. Here, we provide an overview of the burgeoning field of evolutionary molecular plant-microbe interactions (EVO-MPMI)-the study of mechanisms of plant-microbe interactions in the context of their evolutionary history-tracing its progression from foundational science to practical implementation. We present a snapshot of current research and delve into central concepts, such as conserved features and convergent evolution, as well as methodologies such as ancestral reconstruction. Moreover, we shed light on the practical applications of EVO-MPMI, particularly within the realm of disease control. Looking ahead, we discuss potential future trajectories for EVO-MPMI research, spotlighting the innovative tools and technologies propelling the discipline forward.
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Affiliation(s)
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
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5
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Richter I, Wein P, Uzum Z, Stanley CE, Krabbe J, Molloy EM, Moebius N, Ferling I, Hillmann F, Hertweck C. Transcription activator-like effector protects bacterial endosymbionts from entrapment within fungal hyphae. Curr Biol 2023:S0960-9822(23)00623-1. [PMID: 37301202 DOI: 10.1016/j.cub.2023.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/30/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
As an endosymbiont of the ecologically and medically relevant fungus Rhizopus microsporus, the toxin-producing bacterium Mycetohabitans rhizoxinica faces myriad challenges, such as evading the host's defense mechanisms. However, the bacterial effector(s) that facilitate the remarkable ability of M. rhizoxinica to freely migrate within fungal hyphae have thus far remained unknown. Here, we show that a transcription activator-like (TAL) effector released by endobacteria is an essential symbiosis factor. By combining microfluidics with fluorescence microscopy, we observed enrichment of TAL-deficient M. rhizoxinica in side hyphae. High-resolution live imaging showed the formation of septa at the base of infected hyphae, leading to the entrapment of endobacteria. Using a LIVE/DEAD stain, we demonstrate that the intracellular survival of trapped TAL-deficient bacteria is significantly reduced compared with wild-type M. rhizoxinica, indicative of a protective host response in the absence of TAL proteins. Subversion of host defense in TAL-competent endobacteria represents an unprecedented function of TAL effectors. Our data illustrate an unusual survival strategy of endosymbionts in the host and provide deeper insights into the dynamic interactions between bacteria and eukaryotes.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Claire E Stanley
- Department of Bioengineering, Imperial College, South Kensington, London SW7 2AZ, UK
| | - Jana Krabbe
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Evelyn M Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Nadine Moebius
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Iuliia Ferling
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany.
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Sekhon H, Ha JH, Loh SN. Engineering protein and DNA tools for creating DNA-dependent protein switches. Methods Enzymol 2022; 675:1-32. [PMID: 36220266 PMCID: PMC10314797 DOI: 10.1016/bs.mie.2022.07.002] [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: 10/15/2022]
Abstract
Switchable proteins are capable of changing conformations from inactive (OFF) to active (ON) forms in response to inputs such as ligand binding, pH or temperature change, or light absorption. A particularly powerful class of protein switches, exemplified by the Cas nucleases of CRISPR systems, are activated by binding of specific DNA or RNA sequences. The mechanism by which oligonucleotide binding regulates biological activity is complex and highly specialized in the case of Cas enzymes, but recent advancements in protein and DNA engineering have made it possible to introduce this mode of control into other enzymes. This chapter highlights recent examples of protein switches that combine these two fields of engineering for the purpose of creating biosensors that detect pathogen and other genomic sequences. One protein engineering method-alternate frame folding-has the potential to convert many proteins into ligand-activated switches by inserting a binding protein (input domain) into an enzyme (output domain). The steps for doing so are illustrated using GCN4 as a DNA recognition domain and nanoluciferase as a luminescent reporter that changes color as a result of DNA binding. DNA engineering protocols are included for creating DNA tools (de novo designed hairpins and modified aptamers), that enable the biosensor to be activated by arbitrary DNA/RNA sequences and small molecules/proteins, respectively. These methodologies can be applied to other proteins to gain control of their functions by DNA binding.
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Affiliation(s)
- Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States.
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7
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Nowack MK, Holmes DR, Lahaye T. TALE-induced cell death executors: an origin outside immunity? TRENDS IN PLANT SCIENCE 2022; 27:536-548. [PMID: 34924289 PMCID: PMC7612725 DOI: 10.1016/j.tplants.2021.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/21/2021] [Accepted: 11/01/2021] [Indexed: 05/19/2023]
Abstract
Phytopathogenic bacteria inject effector proteins into plant host cells to promote disease. Plant resistance (R) genes encoding nucleotide-binding leucine-rich repeat (NLR) proteins mediate the recognition of functionally and structurally diverse microbial effectors, including transcription-activator like effectors (TALEs) from the bacterial genus Xanthomonas. TALEs bind to plant promoters and transcriptionally activate either disease-promoting host susceptibility (S) genes or cell death-inducing executor-type R genes. It is perplexing that plants contain TALE-perceiving executor-type R genes in addition to NLRs that also mediate the recognition of TALE-containing xanthomonads. We present recent findings on the evolvability of TALEs, which suggest that the native function of executors is not in plant immunity, but possibly in the regulation of developmentally controlled programmed cell death (PCD) processes.
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Affiliation(s)
- Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center of Plant Systems Biology, 9052 Ghent, Belgium.
| | - Danalyn R Holmes
- University of Tübingen, ZMBP - General Genetics, Auf der Morgenstelle 32, 72076 Tuebingen, Germany
| | - Thomas Lahaye
- University of Tübingen, ZMBP - General Genetics, Auf der Morgenstelle 32, 72076 Tuebingen, Germany.
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8
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Zhang B, Han X, Yuan W, Zhang H. TALEs as double-edged swords in plant-pathogen interactions: Progress, challenges, and perspectives. PLANT COMMUNICATIONS 2022; 3:100318. [PMID: 35576155 PMCID: PMC9251431 DOI: 10.1016/j.xplc.2022.100318] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/08/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Xanthomonas species colonize many host plants and cause huge losses worldwide. Transcription activator-like effectors (TALEs) are secreted by Xanthomonas and translocated into host cells to manipulate the expression of target genes, especially by Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, which cause bacterial blight and bacterial leaf streak, respectively, in rice. In this review, we summarize the progress of studies on the interaction between Xanthomonas and hosts, covering both rice and other plants. TALEs are not only key factors that make plants susceptible but are also essential components of plant resistance. Characterization of TALEs and TALE-like proteins has improved our understanding of TALE evolution and promoted the development of gene editing tools. In addition, the interactions between TALEs and hosts have also provided strategies and possibilities for genetic engineering in crop improvement.
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Affiliation(s)
- Biaoming Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaoyuan Han
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wenya Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Haitao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
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9
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Arnesen JA, Hoof JB, Kildegaard HF, Borodina I. Genome Editing of Eukarya. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Malghani Z, Khan AU, Faheem M, Danish MZ, Nadeem H, Ansari SF, Maqbool M. Molecular Docking, Antioxidant, Anticancer and Antileishmanial Effects of Newly Synthesized Quinoline Derivatives. Anticancer Agents Med Chem 2020; 20:1516-1529. [DOI: 10.2174/1871520620666200516145117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 01/27/2023]
Abstract
Background:
Due to the pressing need and adverse effects associated with the available anti-cancer
agents, an attempt was made to develop the new anti-cancer agents with better activity and lesser adverse
effects.
Objective:
Synthetic approaches based on chemical modification of quinoline derivatives have been undertaken
with the aim of improving anti-cancer agents’ safety profile.
Methods:
In the present study, quinoline derivatives 6-hydroxy-2-(4-methoxyphenyl) quinoline-4-carboxylic
acid (M1) and 2-(4-chlorophenyl)-6-hydroxyquinoline-4-carboxylic acid (M3) were synthesized by the reaction
of aldehyde and pyruvic acid. The complete reaction was indicated by thin-layer chromatography. Newly synthesized
M1and M3were tested for in silico and in vitro studies.
Results:
M1 and M3 were docked against selected targets. Both the test compounds showed good affinity against
all targets except the p300\CBP-associated factor target as there was no H-bond formed by M1. IC50 values of
M1 and M3 against 1, 1-diphenyl-picrylhydrazyl free radical scavenging activity were 562 and 136.56ng/mL,
respectively. In brine shrimp lethality assay, M1 and M3 showed IC50 value of 81.98 and 139.2ng/mL, respectively.
IC50 values recorded for M1 and M3 in tumor inhibition activity were 129 and 219μg/mL, respectively.
M1 and M3 exhibited concentration-dependent anti-cancer effects against human cell lines of hepatocellular
carcinoma (HepG2) and colon cancer (HCT-116). Against HepG2 cells, M1 and M3 exhibited IC50 of 88.6 and
43.62μg/mL, respectively. M1 and M3 utilized against HCT-116 cell lines possessed IC50 values of 62.5 and
15.3μg/mL. M1 and M3 also showed an anti-leishmanial effect with IC50 values of 336.64 and 530.142μg/mL,
respectively.
Conclusion:
From the results of pharmacological studies, we conclude that the newly synthesized compound
showed enhanced anti-oxidant, anti-cancer and anti-leishmanial profile with good yield.
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Affiliation(s)
- Zoonish Malghani
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Arif-Ullah Khan
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Muhammad Faheem
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Muhammad Z. Danish
- University College of Pharmacy, University of the Punjab, Lahore, Pakistan
| | - Humaira Nadeem
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Sameen F. Ansari
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Madeeha Maqbool
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
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Lastovetsky OA, Krasnovsky LD, Qin X, Gaspar ML, Gryganskyi AP, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Pawlowska TE. Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism. mBio 2020; 11:e02088-20. [PMID: 32900811 PMCID: PMC7482071 DOI: 10.1128/mbio.02088-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 01/06/2023] Open
Abstract
Fungal-bacterial symbioses range from antagonisms to mutualisms and remain one of the least understood interdomain interactions despite their ubiquity as well as ecological and medical importance. To build a predictive conceptual framework for understanding interactions between fungi and bacteria in different types of symbioses, we surveyed fungal and bacterial transcriptional responses in the mutualism between Rhizopus microsporus (Rm) (ATCC 52813, host) and its Mycetohabitans (formerly Burkholderia) endobacteria versus the antagonism between a nonhost Rm (ATCC 11559) and Mycetohabitans isolated from the host, at two time points, before and after partner physical contact. We found that bacteria and fungi sensed each other before contact and altered gene expression patterns accordingly. Mycetohabitans did not discriminate between the host and nonhost and engaged a common set of genes encoding known as well as novel symbiosis factors. In contrast, responses of the host versus nonhost to endobacteria were dramatically different, converging on the altered expression of genes involved in cell wall biosynthesis and reactive oxygen species (ROS) metabolism. On the basis of the observed patterns, we formulated a set of hypotheses describing fungal-bacterial interactions and tested some of them. By conducting ROS measurements, we confirmed that nonhost fungi increased production of ROS in response to endobacteria, whereas host fungi quenched their ROS output, suggesting that ROS metabolism contributes to the nonhost resistance to bacterial infection and the host ability to form a mutualism. Overall, our study offers a testable framework of predictions describing interactions of early divergent Mucoromycotina fungi with bacteria.IMPORTANCE Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter.
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Affiliation(s)
- Olga A Lastovetsky
- Graduate Field of Microbiology, Cornell University, Ithaca, New York, USA
| | - Lev D Krasnovsky
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - Xiaotian Qin
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | - Maria L Gaspar
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
| | | | - Marcel Huntemann
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Alicia Clum
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Manoj Pillay
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | | | - Neha Varghese
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Mikhailova
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Dimitrios Stamatis
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - T B K Reddy
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nicole Shapiro
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Natalia Ivanova
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Nikos Kyrpides
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Tanja Woyke
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Teresa E Pawlowska
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, New York, USA
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12
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Xue J, Lu Z, Liu W, Wang S, Lu D, Wang X, He X. The genetic arms race between plant and Xanthomonas: lessons learned from TALE biology. SCIENCE CHINA-LIFE SCIENCES 2020; 64:51-65. [PMID: 32661897 DOI: 10.1007/s11427-020-1699-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/29/2020] [Indexed: 10/23/2022]
Abstract
The pathogenic bacterial genus Xanthomonas infects a wide variety of host plants and causes devastating diseases in many crops. Transcription activator-like effectors (TALEs) are important virulence factors secreted by Xanthomonas with the ability to directly bind to the promoters of target genes in plant hosts and activate their expression, which often facilitates the proliferation of pathogens. Understanding how plants cope with TALEs will provide mechanistic insights into crop breeding for Xanthomonas defense. Over the past 30 years, numerous studies have revealed the modes of action of TALEs in plant cells and plant defense strategies to overcome TALE attack. Based on these findings, new technologies were adopted for disease management to optimize crop production. In this article, we will review the most recent advances in the evolutionary arms race between plant resistance and TALEs from Xanthomonas, with a specific focus on TALE applications in the development of novel breeding strategies for durable and broad-spectrum resistance.
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Affiliation(s)
- Jiao Xue
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Zhanhua Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Shiguang Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Dongbai Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Xiaofei Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Xiuying He
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China.
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A TAL effector-like protein of an endofungal bacterium increases the stress tolerance and alters the transcriptome of the host. Proc Natl Acad Sci U S A 2020; 117:17122-17129. [PMID: 32632014 PMCID: PMC7382252 DOI: 10.1073/pnas.2003857117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Endosymbiotic bacteria are found in diverse fungi, but little is known about how they communicate with their hosts. Some plant pathogenic bacteria use type III-translocated TAL effectors to control host transcription, and TAL-like proteins are encoded in genomes of the fungal endosymbiotic bacterium Mycetohabitans rhizoxinica. In this paper, we present evidence that these proteins are, like TAL effectors, type III-secreted, nuclear-localizing effectors that perturb host transcription and show that one enhances tolerance of the fungal host to cell membrane stress. Our characterization of an effector in a bacterial–fungal symbiosis opens a new door to molecular understanding of these interkingdom partnerships. Our findings also provide insight into the functional diversity and evolution of the TAL effector protein family. Symbioses of bacteria with fungi have only recently been described and are poorly understood. In the symbiosis of Mycetohabitans (formerly Burkholderia) rhizoxinica with the fungus Rhizopus microsporus, bacterial type III (T3) secretion is known to be essential. Proteins resembling T3-secreted transcription activator-like (TAL) effectors of plant pathogenic bacteria are encoded in the three sequenced Mycetohabitans spp. genomes. TAL effectors nuclear-localize in plants, where they bind and activate genes important in disease. The Burkholderia TAL-like (Btl) proteins bind DNA but lack the N- and C-terminal regions, in which TAL effectors harbor their T3 and nuclear localization signals, and activation domain. We characterized a Btl protein, Btl19-13, and found that, despite the structural differences, it can be T3-secreted and can nuclear-localize. A btl19-13 gene knockout did not prevent the bacterium from infecting the fungus, but the fungus became less tolerant to cell membrane stress. Btl19-13 did not alter transcription in a plant-based reporter assay, but 15 R. microsporus genes were differentially expressed in comparisons both of the fungus infected with the wild-type bacterium vs. the mutant and with the mutant vs. a complemented strain. Southern blotting revealed btl genes in 14 diverse Mycetohabitans isolates. However, banding patterns and available sequences suggest variation, and the btl19-13 phenotype could not be rescued by a btl gene from a different strain. Our findings support the conclusion that Btl proteins are effectors that act on host DNA and play important but varied or possibly host genotype-specific roles in the M. rhizoxinica–R. microsporus symbiosis.
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Chimerization Enables Gene Synthesis and Lentiviral Delivery of Customizable TALE-Based Effectors. Int J Mol Sci 2020; 21:ijms21030795. [PMID: 31991825 PMCID: PMC7038218 DOI: 10.3390/ijms21030795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/21/2022] Open
Abstract
Designer effectors based on the DNA binding domain (DBD) of Xanthomonas transcription activator-like effectors (TALEs) are powerful sequence-specific tools with an excellent reputation for their specificity in editing the genome, transcriptome, and more recently the epigenome in multiple cellular systems. However, the repetitive structure of the TALE arrays composing the DBD impedes their generation as gene synthesis product and prevents the delivery of TALE-based genes using lentiviral vectors (LVs), a widely used system for human gene therapy. To overcome these limitations, we aimed at chimerizing the DNA sequence encoding for the TALE-DBDs by introducing sufficient diversity to facilitate both their gene synthesis and enable their lentiviral delivery. To this end, we replaced three out of 17 Xanthomonas TALE repeats with TALE-like units from the bacterium Burkholderia rhizoxinica. This was combined with extensive codon variation and specific amino acid substitutions throughout the DBD in order to maximize intra- and inter-repeat sequence variability. We demonstrate that chimerized TALEs can be easily generated using conventional Golden Gate cloning strategy or gene synthesis. Moreover, chimerization enabled the delivery of TALE-based designer nucleases, transcriptome and epigenome editors using lentiviral vectors. When delivered as plasmid DNA, chimerized TALEs targeting the CCR5 and CXCR4 loci showed comparable activities in human cells. However, lentiviral delivery of TALE-based transcriptional activators was only successful in the chimerized form. Similarly, delivery of a chimerized CXCR4-specific epigenome editor resulted in rapid silencing of endogenous CXCR4 expression. In conclusion, extensive codon variation and chimerization of TALE-based DBDs enables both the simplified generation and the lentiviral delivery of designer TALEs, and therefore facilitates the clinical application of these tools to precisely edit the genome, transcriptome and epigenome.
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Liu Y, Li M, Zhang Y, Wu C, Yang K, Gao S, Zheng M, Li X, Li H, Chen L. Structure based discovery of novel hexokinase 2 inhibitors. Bioorg Chem 2020; 96:103609. [PMID: 32007722 DOI: 10.1016/j.bioorg.2020.103609] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 12/11/2022]
Abstract
Hexokinase 2 (HK2) is over-expressed in most of human cancers and has been proved to be a promising target for cancer therapy. In this study, based on the structure of HK2, we screened over 6 millions of compounds to obtain the lead. A total of 26 (E)-N'-(2,3,4-trihydroxybenzylidene) arylhydrazide derivatives were then designed, synthesized, and evaluated for their HK2 enzyme activity and IC50 values against two cancer cell lines. Most of the 26 target compounds showed excellently in vitro activity. Among them, compound 3j showed the strongest inhibitory effects on HK2 enzyme activity with an IC50 of 0.53 ± 0.13 μM and exhibited the most potent growth inhibition against SW480 cells with an IC50 of 7.13 ± 1.12 μM, which deserves further studies.
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Affiliation(s)
- Yang Liu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mingxue Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yujie Zhang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Canrong Wu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kaiyin Yang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Suyu Gao
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mengzhu Zheng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xingzhou Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
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Perez-Quintero AL, Szurek B. A Decade Decoded: Spies and Hackers in the History of TAL Effectors Research. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:459-481. [PMID: 31387457 DOI: 10.1146/annurev-phyto-082718-100026] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transcription activator-like effectors (TALEs) from the genus Xanthomonas are proteins with the remarkable ability to directly bind the promoters of genes in the plant host to induce their expression, which often helps bacterial colonization. Metaphorically, TALEs act as spies that infiltrate the plant disguised as high-ranking civilians (transcription factors) to trick the plant into activating weak points that allow an invasion. Current knowledge of how TALEs operate allows researchers to predict their activity (counterespionage) and exploit their function, engineering them to do our bidding (a Manchurian agent). This has been possible thanks particularly to the discovery of their DNA binding mechanism, which obeys specific amino acid-DNA correspondences (the TALE code). Here, we review the history of how researchers discovered the way these proteins work and what has changed in the ten years since the discovery of the code. Recommended music for reading this review can be found in the Supplemental Material.
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Affiliation(s)
- Alvaro L Perez-Quintero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523-1177, USA;
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
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Bastedo DP, Lo T, Laflamme B, Desveaux D, Guttman DS. Diversity and Evolution of Type III Secreted Effectors: A Case Study of Three Families. Curr Top Microbiol Immunol 2019; 427:201-230. [DOI: 10.1007/82_2019_165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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18
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Ma W, Zou L, Zhiyuan JI, Xiameng XU, Zhengyin XU, Yang Y, Alfano JR, Chen G. Xanthomonas oryzae pv. oryzae TALE proteins recruit OsTFIIAγ1 to compensate for the absence of OsTFIIAγ5 in bacterial blight in rice. MOLECULAR PLANT PATHOLOGY 2018; 19:2248-2262. [PMID: 29704467 PMCID: PMC6638009 DOI: 10.1111/mpp.12696] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 05/12/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight (BB) of rice, uses transcription activator-like effectors (TALEs) to interact with the basal transcription factor gamma subunit OsTFIIAγ5 (Xa5) and activates the transcription of host genes. However, how OsTFIIAγ1, the other OsTFIIAγ protein, functions in the presence of TALEs remains unclear. In this study, we show that OsTFIIAγ1 plays a compensatory role in the absence of Xa5. The expression of OsTFIIAγ1, which is activated by TALE PthXo7, increases the expression of host genes targeted by avirulent and virulent TALEs. Defective OsTFIIAγ1 rice lines show reduced expression of the TALE-targeted susceptibility (S) genes, OsSWEET11 and OsSWEET14, which results in increased BB resistance. Selected TALEs (PthXo1, AvrXa7 and AvrXa27) were evaluated for interactions with OsTFIIAγ1, Xa5 and xa5 (naturally occurring mutant form of Xa5) using biomolecular fluorescence complementation (BiFC) and microscale thermophoresis (MST). BiFC and MST demonstrated that the three TALEs bind Xa5 and OsTFIIAγ1 with a stronger affinity than xa5. These results provide insights into the complex roles of OsTFIIAγ1 and OsTFIIAγ5 in TALE-mediated host gene transcription.
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Affiliation(s)
- Wenxiu Ma
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Lifang Zou
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - JI Zhiyuan
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
- Present address:
Present address: National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop ScienceChinese Academy of Agriculture Sciences (CAAS)Beijing 100081China
| | - XU Xiameng
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - XU Zhengyin
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Yangyang Yang
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - James R. Alfano
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- The Center for Plant Science Innovation, University of NebraskaLincolnNE68588‐0660USA
| | - Gongyou Chen
- School of Agriculture and BiologyShanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of AgricultureShanghai200240China
- State Key Laboratory of Microbial Metabolism, School of Life Science & BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
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Denancé N, Szurek B, Doyle EL, Lauber E, Fontaine-Bodin L, Carrère S, Guy E, Hajri A, Cerutti A, Boureau T, Poussier S, Arlat M, Bogdanove AJ, Noël LD. Two ancestral genes shaped the Xanthomonas campestris TAL effector gene repertoire. THE NEW PHYTOLOGIST 2018; 219:391-407. [PMID: 29677397 DOI: 10.1111/nph.15148] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/06/2018] [Indexed: 06/08/2023]
Abstract
Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome). The 53 sequenced tal genes encode 21 distinct DNA binding domains that sort into seven major DNA binding specificities. In silico analysis of the Brassica rapa promoterome identified a repertoire of predicted TALE targets, five of which were experimentally validated using quantitative reverse transcription polymerase chain reaction. The Xc TALome shows multiple signs of DNA rearrangements that probably drove its evolution from two ancestral tal genes. We discovered that Tal12a and Tal15a of Xcc strain Xca5 contribute together in the development of disease symptoms on susceptible B. oleracea var. botrytis cv Clovis. This large and polymorphic repertoire of TALEs opens novel perspectives for elucidating TALE-mediated susceptibility of Brassicaceae to black rot disease and for understanding the molecular processes underlying TALE evolution.
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Affiliation(s)
- Nicolas Denancé
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Boris Szurek
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Erin L Doyle
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
- Department of Biology, Doane University, Crete, NE, 68333, USA
| | - Emmanuelle Lauber
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | | | - Sébastien Carrère
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Endrick Guy
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Ahmed Hajri
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Aude Cerutti
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Tristan Boureau
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Stéphane Poussier
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 49071, Beaucouzé Cedex, France
| | - Matthieu Arlat
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
| | - Adam J Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Laurent D Noël
- LIPM, Université de Toulouse, INRA, CNRS, UPS, F-31326, Castanet-Tolosan Cedex, France
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Wang J, Zeng X, Tian D, Yang X, Wang L, Yin Z. The pepper Bs4C proteins are localized to the endoplasmic reticulum (ER) membrane and confer disease resistance to bacterial blight in transgenic rice. MOLECULAR PLANT PATHOLOGY 2018; 19:2025-2035. [PMID: 29603592 PMCID: PMC6638055 DOI: 10.1111/mpp.12684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/21/2018] [Accepted: 03/25/2018] [Indexed: 05/07/2023]
Abstract
Transcription activator-like effector (TALE)-dependent dominant disease resistance (R) genes in plants, also referred to as executor R genes, are induced on infection by phytopathogenic bacteria of the genus Xanthomonas harbouring the corresponding TALE genes. Unlike the traditional R proteins, the executor R proteins do not determine the resistance specificity and may function broadly in different plant species. The executor R gene Bs4C-R in the resistant genotype PI 235047 of the pepper species Capsicum pubescens (CpBs4C-R) confers disease resistance to Xanthomonas campestris pv. vesicatoria (Xcv) harbouring the TALE genes avrBsP/avrBs4. In this study, the synthetic genes of CpBs4C-R and two other Bs4C-like genes, the susceptible allele in the genotype PI585270 of C. pubescens (CpBs4C-S) and the CaBs4C-R homologue gene in the cultivar 'CM334' of Capsicum annum (CaBs4C), were characterized in tobacco (Nicotiana benthamiana) and rice (Oryza sativa). The Bs4C genes induced cell death in N. benthamiana. The functional Bs4C-eCFP fusion proteins were localized to the endoplasmic reticulum (ER) membrane in the leaf epidermal cells of N. benthamiana. The Xa10 promoter-Bs4C fusion genes in transgenic rice conferred strain-specific disease resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight in rice, and were specifically induced by the Xa10-incompatible Xoo strain PXO99A (pHM1avrXa10). The results indicate that the Bs4C proteins from pepper species function broadly in rice and the Bs4C protein-mediated cell death from the ER is conserved between dicotyledonous and monocotyledonous plants, which can be utilized to engineer novel and enhanced disease resistance in heterologous plants.
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Affiliation(s)
- Jun Wang
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore 117604Singapore
| | - Xuan Zeng
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore 117604Singapore
| | - Dongsheng Tian
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore 117604Singapore
| | - Xiaobei Yang
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore 117604Singapore
| | - Lanlan Wang
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore 117604Singapore
| | - Zhongchao Yin
- Temasek Life Sciences LaboratoryNational University of SingaporeSingapore 117604Singapore
- Department of Biological SciencesNational University of SingaporeSingapore 117543Singapore
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Bano S, Khan AU, Asghar F, Usman M, Badshah A, Ali S. Computational and Pharmacological Evaluation of Ferrocene-Based Acyl Ureas and Homoleptic Cadmium Carboxylate Derivatives for Anti-diabetic Potential. Front Pharmacol 2018; 8:1001. [PMID: 29387011 PMCID: PMC5776112 DOI: 10.3389/fphar.2017.01001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/29/2017] [Indexed: 02/03/2023] Open
Abstract
We investigated possible anti-diabetic effect of ferrocene-based acyl ureas: 4-ferrocenyl aniline (PFA), 1-(4-chlorobenzoyl)-3-(4-ferrocenylphenyl) urea (DPC1), 1-(3-chlorobenzoyl)-3-(4-ferrocenylphenyl) urea (DMC1), 1-(2-chlorobenzoyl)-3-(4-ferrocenylphenyl) urea (DOC1) and homoleptic cadmium carboxylates: bis (diphenylacetato) cadmium (II) (DPAA), bis (4-chlorophenylacetato) cadmium (II) (CPAA), using in silico and in vivo techniques. PFA, DPC1, DMC1, DOC1, DPAA and CPAA exhibited high binding affinities (ACE ≥ −350 Kcal/mol) against targets: aldose reductase, peroxisome proliferator-activated receptor γ, 11β-hydroxysteroid dehydrogenase-1, C-alpha glucosidase and glucokinase, while showed moderate affinities (ACE ≥ −250 Kcal/mol) against N-alpha glucosidase, dipeptidyl peptidase-IV, phosphorylated-Akt, glycogen synthase kinase-3β, fructose-1,6-bisphosphatase and phosphoenolpyruvate carboxykinase, whereas revealed lower affinities (ACE < −250 Kcal/mol) vs. alpha amylase, protein tyrosine phosphatases 1B, glycogen phosphorylase and phosphatidylinositol 3 kinase. In alloxan (300 mg/Kg)-induced diabetic mice, DPAA and DPC1 (1–10 mg/Kg) at day 1, 5, 10, 15, and 20th decreased blood glucose levels, compared to diabetic control group and improved the treated animals body weight. DPAA (10 mg/Kg) and DPC1 (5 mg/Kg) in time-dependent manner (30–120 min.) enhanced tolerance of oral glucose overload in mice. DPAA and DPCI dose-dependently at 1, 5, and 10 mg/Kg decreased glycosylated hemoglobin levels in diabetic animals, as caused by metformin. These results indicate that aforementioned derivatives of ferrocene and cadmium possess anti-diabetic potential.
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Affiliation(s)
- Shahar Bano
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Arif-Ullah Khan
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad, Pakistan
| | - Faiza Asghar
- Department of Chemistry, Quaid-e-Azam University, Islamabad, Pakistan.,Department of Chemistry, University of Wah, Wah, Pakistan
| | - Muhammad Usman
- Department of Chemistry, Quaid-e-Azam University, Islamabad, Pakistan
| | - Amin Badshah
- Department of Chemistry, Quaid-e-Azam University, Islamabad, Pakistan
| | - Saqib Ali
- Department of Chemistry, Quaid-e-Azam University, Islamabad, Pakistan
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Büttner D. Behind the lines-actions of bacterial type III effector proteins in plant cells. FEMS Microbiol Rev 2018; 40:894-937. [PMID: 28201715 PMCID: PMC5091034 DOI: 10.1093/femsre/fuw026] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/31/2016] [Accepted: 07/03/2016] [Indexed: 01/30/2023] Open
Abstract
Pathogenicity of most Gram-negative plant-pathogenic bacteria depends on the type III secretion (T3S) system, which translocates bacterial effector proteins into plant cells. Type III effectors modulate plant cellular pathways to the benefit of the pathogen and promote bacterial multiplication. One major virulence function of type III effectors is the suppression of plant innate immunity, which is triggered upon recognition of pathogen-derived molecular patterns by plant receptor proteins. Type III effectors also interfere with additional plant cellular processes including proteasome-dependent protein degradation, phytohormone signaling, the formation of the cytoskeleton, vesicle transport and gene expression. This review summarizes our current knowledge on the molecular functions of type III effector proteins with known plant target molecules. Furthermore, plant defense strategies for the detection of effector protein activities or effector-triggered alterations in plant targets are discussed.
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Affiliation(s)
- Daniela Büttner
- Genetics Department, Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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Kachroo A, Vincelli P, Kachroo P. Signaling Mechanisms Underlying Resistance Responses: What Have We Learned, and How Is It Being Applied? PHYTOPATHOLOGY 2017; 107:1452-1461. [PMID: 28609156 DOI: 10.1094/phyto-04-17-0130-rvw] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plants have evolved highly specific mechanisms to resist pathogens including preformed barriers and the induction of elaborate signaling pathways. Induced signaling requires recognition of the pathogen either via conserved pathogen-derived factors or specific pathogen-encoded proteins called effectors. Recognition of these factors by host encoded receptor proteins can result in the elicitation of different tiers of resistance at the site of pathogen infection. In addition, plants induce a type of systemic immunity which is effective at the whole plant level and protects against a broad spectrum of pathogens. Advances in our understanding of pathogen-recognition mechanisms, identification of the underlying molecular components, and their significant conservation across diverse plant species has enabled the development of novel strategies to combat plant diseases. This review discusses key advances in plant defense signaling that have been adapted or have the potential to be adapted for plant protection against microbial diseases.
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Affiliation(s)
- Aardra Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington 40546
| | - Paul Vincelli
- Department of Plant Pathology, University of Kentucky, Lexington 40546
| | - Pradeep Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington 40546
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24
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Ruh M, Briand M, Bonneau S, Jacques MA, Chen NWG. Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors. BMC Genomics 2017; 18:670. [PMID: 28854875 PMCID: PMC5577687 DOI: 10.1186/s12864-017-4087-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/24/2017] [Indexed: 12/25/2022] Open
Abstract
Background Common bacterial blight is a devastating bacterial disease of common bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause similar symptoms on common bean, suggesting that they have acquired common genetic determinants of adaptation to common bean. Transcription Activator-Like (TAL) effectors are bacterial type III effectors that are able to induce the expression of host genes to promote infection or resistance. Their capacity to bind to a specific host DNA sequence suggests that they are potential candidates for host adaption. Results To study the diversity of tal genes from Xanthomonas strains responsible for common bacterial blight of bean, whole genome sequences of 17 strains representing the diversity of X. citri pv. fuscans and X. phaseoli pv. phaseoli were obtained by single molecule real time sequencing. Analysis of these genomes revealed the existence of four tal genes named tal23A, tal20F, tal18G and tal18H, respectively. While tal20F and tal18G were chromosomic, tal23A and tal18H were carried on plasmids and shared between phylogenetically distant strains, therefore suggesting recent horizontal transfers of these genes between X. citri pv. fuscans and X. phaseoli pv. phaseoli strains. Strikingly, tal23A was present in all strains studied, suggesting that it played an important role in adaptation to common bean. In silico predictions of TAL effectors targets in the common bean genome suggested that TAL effectors shared by X. citri pv. fuscans and X. phaseoli pv. phaseoli strains target the promoters of genes of similar functions. This could be a trace of convergent evolution among TAL effectors from different phylogenetic groups, and comforts the hypothesis that TAL effectors have been implied in the adaptation to common bean. Conclusions Altogether, our results favour a model where plasmidic TAL effectors are able to contribute to host adaptation by being horizontally transferred between distant lineages. Electronic supplementary material The online version of this article (10.1186/s12864-017-4087-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mylène Ruh
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France.
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Perycz M, Krwawicz J, Bochtler M. A TALE-inspired computational screen for proteins that contain approximate tandem repeats. PLoS One 2017; 12:e0179173. [PMID: 28617832 PMCID: PMC5472282 DOI: 10.1371/journal.pone.0179173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/24/2017] [Indexed: 11/18/2022] Open
Abstract
TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.
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Affiliation(s)
- Malgorzata Perycz
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Joanna Krwawicz
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Matthias Bochtler
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Poland
- * E-mail:
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Li W, Zheng M, Wu S, Gao S, Yang M, Li Z, Min Q, Sun W, Chen L, Xiang G, Li H. Benserazide, a dopadecarboxylase inhibitor, suppresses tumor growth by targeting hexokinase 2. J Exp Clin Cancer Res 2017; 36:58. [PMID: 28427443 PMCID: PMC5399312 DOI: 10.1186/s13046-017-0530-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Hexokinase (HK) is the rate-limiting enzyme in the first reaction of glycolysis. And Hexokinase 2 (HK2) is most closely related to malignant tumor which expresses at higher level compared with normal cells. HK2 plays a pivotal role in tumor initiation and maintenance, which provides a new target for cancer therapy. METHODS Structure-based virtual ligand screening was used in hit identification from ZINC Drug Database. Microscale thermophoresis assay was performed to evaluate the binding affinity. Enzyme inhibition, cytotoxicity, apoptosis, intracellular ATP level, mitochondrial membrane potential (MMP), glucose uptake and lactate production experiments were undertaken in SW480 cells to identify Benz as a HK2 inhibitor. Western blot was used to test protein expression. SW480 cells xenograft mouse models were used for in vivo study. Nano-particles of Benz were prepared to improve the antitumor efficacy and tumor targeting of Benz. HPLC was used to measure the concentration of free Benz in tumor tissues. RESULTS Benserazide (Benz), was identified as a selective HK2 inhibitor, could specifically bind to HK2 and significantly inhibit HK2 enzymatic activity in vitro. In addition, Benz reduced glucose uptake, lactate production and intracellular ATP level, and could cause cell apoptosis and an increased loss of MMP as well. In vivo study indicated that intraperitoneal (ip) injection of Benz at 300 and 600 mg/Kg suppressed cancer growth in tumor-bearing mice and no toxicity shown. To further improve the antitumor efficacy and tumor targeting of Benz, nano-particles of Benz was prepared. Liposomal Benz at 100 and 200 mg/Kg performed potent inhibitory effects on tumor-bearing mice, showing reduced dose and better efficacy. CONCLUSIONS Our study provides a new direction for the development of Benz and its analogues as novel antitumor agents for cancer therapy.
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Affiliation(s)
- Wei Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Mengzhu Zheng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Shuangping Wu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Suyu Gao
- School of Traditional Chinese Materia Medica, Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016 China
| | - Mei Yang
- School of Public Health, Wuhan University of Science and Technology, Wuhan, 430081 China
| | - Zhimei Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Qiuxia Min
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Weiguang Sun
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Lixia Chen
- School of Traditional Chinese Materia Medica, Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016 China
| | - Guangya Xiang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Hua Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
- School of Traditional Chinese Materia Medica, Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016 China
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27
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Identification of mangiferin as a potential Glucokinase activator by structure-based virtual ligand screening. Sci Rep 2017; 7:44681. [PMID: 28317897 PMCID: PMC5357792 DOI: 10.1038/srep44681] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/10/2017] [Indexed: 12/19/2022] Open
Abstract
The natural product mangiferin (compound 7) has been identified as a potential glucokinase activator by structure-based virtual ligand screening. It was proved by enzyme activation experiment and cell-based assays in vitro, with potency in micromolar range. Meanwhile, this compound showed good antihyperglycemic activity in db/db mice without obvious side effects such as excessive hypoglycaemia.
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Mehrotra R, Renganaath K, Kanodia H, Loake GJ, Mehrotra S. Towards combinatorial transcriptional engineering. Biotechnol Adv 2017; 35:390-405. [PMID: 28300614 DOI: 10.1016/j.biotechadv.2017.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/22/2017] [Accepted: 03/09/2017] [Indexed: 01/31/2023]
Abstract
The modular nature of the transcriptional unit makes it possible to design robust modules with predictable input-output characteristics using a ‘parts- off a shelf’ approach. Customized regulatory circuits composed of multiple such transcriptional units have immense scope for application in diverse fields of basic and applied research. Synthetic transcriptional engineering seeks to construct such genetic cascades. Here, we discuss the three principle strands of transcriptional engineering: promoter and transcriptional factor engineering, and programming inducibilty into synthetic modules. In this context, we review the scope and limitations of some recent technologies that seek to achieve these ends. Our discussion emphasizes a requirement for rational combinatorial engineering principles and the promise this approach holds for the future development of this field.
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Affiliation(s)
- Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani 333031, Rajasthan, India.
| | - Kaushik Renganaath
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani 333031, Rajasthan, India
| | - Harsh Kanodia
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani 333031, Rajasthan, India
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani 333031, Rajasthan, India
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de Lange O, Schandry N, Wunderlich M, Berendzen KW, Lahaye T. Exploiting the sequence diversity of TALE-like repeats to vary the strength of dTALE-promoter interactions. Synth Biol (Oxf) 2017; 2:ysx004. [PMID: 32995505 PMCID: PMC7445789 DOI: 10.1093/synbio/ysx004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 06/13/2017] [Accepted: 06/16/2017] [Indexed: 11/13/2022] Open
Abstract
Designer transcription activator-like effectors (dTALEs) are programmable transcription factors used to regulate user-defined promoters. The TALE DNA-binding domain is a tandem series of amino acid repeats that each bind one DNA base. Each repeat is 33-35 amino acids long. A residue in the center of each repeat is responsible for defining DNA base specificity and is referred to as the base specificying residue (BSR). Other repeat residues are termed non-BSRs and can contribute to TALE DNA affinity in a non-base-specific manner. Previous dTALE engineering efforts have focused on BSRs. Non-BSRs have received less attention, perhaps because there is almost no non-BSR sequence diversity in natural TALEs. However, more sequence diverse, TALE-like proteins are found in diverse bacterial clades. Here, we show that natural non-BSR sequence diversity of TALEs and TALE-likes can be used to modify DNA-binding strength in a new form of dTALE repeat array that we term variable sequence TALEs (VarSeTALEs). We generated VarSeTALE repeat modules through random assembly of repeat sequences from different origins, while holding BSR composition, and thus base preference, constant. We used two different VarSeTALE design approaches combing either whole repeats from different TALE-like sources (inter-repeat VarSeTALEs) or repeat subunits corresponding to secondary structural elements (intra-repeat VarSeTALEs). VarSeTALE proteins were assayed in bacteria, plant protoplasts and leaf tissues. In each case, VarSeTALEs activated or repressed promoters with a range of activities. Our results indicate that natural non-BSR diversity can be used to diversify the binding strengths of dTALE repeat arrays while keeping target sequences constant.
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Affiliation(s)
- Orlando de Lange
- Department of General Genetics, Center for Plant Molecular Biology (ZMBP), Eberhard Karls Universitat Tübingen, Tübingen, Germany
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | - Niklas Schandry
- Department of General Genetics, Center for Plant Molecular Biology (ZMBP), Eberhard Karls Universitat Tübingen, Tübingen, Germany
| | - Markus Wunderlich
- Department of General Genetics, Center for Plant Molecular Biology (ZMBP), Eberhard Karls Universitat Tübingen, Tübingen, Germany
| | - Kenneth Wayne Berendzen
- ZMBP Central Facilities, Center for Plant Molecular Biology (ZMBP), Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Thomas Lahaye
- Department of General Genetics, Center for Plant Molecular Biology (ZMBP), Eberhard Karls Universitat Tübingen, Tübingen, Germany
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30
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Yuan M, Ke Y, Huang R, Ma L, Yang Z, Chu Z, Xiao J, Li X, Wang S. A host basal transcription factor is a key component for infection of rice by TALE-carrying bacteria. eLife 2016; 5:e19605. [PMID: 27472897 PMCID: PMC4993585 DOI: 10.7554/elife.19605] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 07/21/2016] [Indexed: 01/27/2023] Open
Abstract
Transcription activator-like effectors (TALEs) are sequence-specific DNA binding proteins found in a range of plant pathogenic bacteria, where they play important roles in host-pathogen interactions. However, it has been unclear how TALEs, after they have been injected into the host cells, activate transcription of host genes required for infection success. Here, we show that the basal transcription factor IIA gamma subunit TFIIAγ5 from rice is a key component for infection by the TALE-carrying bacterium Xanthomonas oryzae pv. oryzae, the causal agent for bacterial blight. Direct interaction of several TALEs with TFIIAγ5 is required for activation of disease susceptibility genes. Conversely, reduced expression of the TFIIAγ5 host gene limits the induction of susceptibility genes and thus decreases bacterial blight symptoms. Suppression or mutation of TFIIAγ5 can also reduce bacterial streak, another devastating disease of rice caused by TALE-carrying X. oryzae pv. oryzicola. These results have important implications for formulating a widely applicable strategy with which to improve resistance of plants to TALE-carrying pathogens.
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Affiliation(s)
- Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yinggen Ke
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Renyan Huang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Zeyu Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Taian, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
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31
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Yuan M, Ke Y, Huang R, Ma L, Yang Z, Chu Z, Xiao J, Li X, Wang S. A host basal transcription factor is a key component for infection of rice by TALE-carrying bacteria. eLife 2016; 5. [PMID: 27472897 DOI: 10.7554/elife.19605.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 07/21/2016] [Indexed: 05/20/2023] Open
Abstract
Transcription activator-like effectors (TALEs) are sequence-specific DNA binding proteins found in a range of plant pathogenic bacteria, where they play important roles in host-pathogen interactions. However, it has been unclear how TALEs, after they have been injected into the host cells, activate transcription of host genes required for infection success. Here, we show that the basal transcription factor IIA gamma subunit TFIIAγ5 from rice is a key component for infection by the TALE-carrying bacterium Xanthomonas oryzae pv. oryzae, the causal agent for bacterial blight. Direct interaction of several TALEs with TFIIAγ5 is required for activation of disease susceptibility genes. Conversely, reduced expression of the TFIIAγ5 host gene limits the induction of susceptibility genes and thus decreases bacterial blight symptoms. Suppression or mutation of TFIIAγ5 can also reduce bacterial streak, another devastating disease of rice caused by TALE-carrying X. oryzae pv. oryzicola. These results have important implications for formulating a widely applicable strategy with which to improve resistance of plants to TALE-carrying pathogens.
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Affiliation(s)
- Meng Yuan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yinggen Ke
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Renyan Huang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Zeyu Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Taian, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
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(±)-Japonones A and B, two pairs of new enantiomers with anti-KSHV activities from Hypericum japonicum. Sci Rep 2016; 6:27588. [PMID: 27270221 PMCID: PMC4897785 DOI: 10.1038/srep27588] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/20/2016] [Indexed: 11/08/2022] Open
Abstract
Two pairs of new enantiomers with unusual 5,5-spiroketal cores, termed (±)-japonones A and B [(±)-1 and (±)-2], were obtained from Hypericum japonicum Thunb. The absolute configurations of (±)-1 and (±)-2 were characterized by extensive analyses of spectroscopic data and calculated electronic circular dichroism (ECD) spectra, the application of modified Mosher’s methods, and the assistance of quantum chemical predictions (QCP) of 13C NMR chemical shifts. Among these metabolites, (+)-1 exhibited some inhibitory activity on Kaposi’s sarcoma associated herpesvirus (KSHV). Virtual screening of (±)-1 and (±)-2 were conducted using the Surflex-Dock module in the Sybyl software, and (+)-1 exhibited ability to bind with ERK to form key interactions with residues Lys52, Pro56, Ile101, Asp165, Gly167 and Val99.
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Hu L, Zhang Y, Zhu H, Liu J, Li H, Li XN, Sun W, Zeng J, Xue Y, Zhang Y. Filicinic Acid Based Meroterpenoids with Anti-Epstein-Barr Virus Activities from Hypericum japonicum. Org Lett 2016; 18:2272-5. [PMID: 27116597 DOI: 10.1021/acs.orglett.6b00906] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Seven filicinic acid-based meroterpenoids (1-7), possessing 6/6/11, 6/6/7/5, or 6/6/10 ring systems, were isolated from Hypericum japonicum. All of them have novel skeletons with the incorporation of sesquiterpenoid moieties to an acylated filicinic acid. Compounds 2a and 4 exhibited significant efficacy on anti-Epstein-Barr virus, with EC50 values of 0.57 and 0.49 μM, respectively. Furthermore, compounds 2a and 4 were well accommodated to the binding pocket of 2GV9 predicted by the molecular docking.
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Affiliation(s)
- Linzhen Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030, P. R. China.,Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430022, P. R. China
| | - Yu Zhang
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430022, P. R. China
| | - Hucheng Zhu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030, P. R. China
| | - Junjun Liu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030, P. R. China
| | - Hua Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030, P. R. China
| | - Xiao-Nian Li
- Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650204, P. R. China
| | - Weiguang Sun
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030, P. R. China
| | - Junfen Zeng
- Department of Pharmacy, Renmin Hospital of Wuhan University , Wuhan 430060, P. R. China
| | - Yongbo Xue
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030, P. R. China
| | - Yonghui Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030, P. R. China
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The Use and Development of TAL Effector Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Schandry N, de Lange O, Prior P, Lahaye T. TALE-Like Effectors Are an Ancestral Feature of the Ralstonia solanacearum Species Complex and Converge in DNA Targeting Specificity. FRONTIERS IN PLANT SCIENCE 2016; 7:1225. [PMID: 27582755 PMCID: PMC4987410 DOI: 10.3389/fpls.2016.01225] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/02/2016] [Indexed: 05/19/2023]
Abstract
Ralstonia solanacearum, a species complex of bacterial plant pathogens divided into four monophyletic phylotypes, causes plant diseases in tropical climates around the world. Some strains exhibit a broad host range on solanaceous hosts, while others are highly host-specific as for example some banana-pathogenic strains. Previous studies showed that transcription activator-like (TAL) effectors from Ralstonia, termed RipTALs, are capable of activating reporter genes in planta, if these are preceded by a matching effector binding element (EBE). RipTALs target DNA via their central repeat domain (CRD), where one repeat pairs with one DNA-base of the given EBE. The repeat variable diresidue dictates base repeat specificity in a predictable fashion, known as the TALE code. In this work, we analyze RipTALs across all phylotypes of the Ralstonia solanacearum species complex. We find that RipTALs are prevalent in phylotypes I and IV but absent from most phylotype III and II strains (10/12, 8/14, 1/24, and 1/5 strains contained a RipTAL, respectively). RipTALs originating from strains of the same phylotype show high levels of sequence similarity (>98%) in the N-terminal and C-terminal regions, while RipTALs isolated from different phylotypes show 47-91% sequence similarity in those regions, giving rise to four RipTAL classes. We show that, despite sequence divergence, the base preference for guanine, mediated by the N-terminal region, is conserved across RipTALs of all classes. Using the number and order of repeats found in the CRD, we functionally sub-classify RipTALs, introduce a new simple nomenclature, and predict matching EBEs for all seven distinct RipTALs identified. We experimentally study RipTAL EBEs and uncover that some RipTALs are able to target the EBEs of other RipTALs, referred to as cross-reactivity. In particular, RipTALs from strains with a broad host range on solanaceous hosts cross-react on each other's EBEs. Investigation of sequence divergence between RipTAL repeats allows for a reconstruction of repeat array biogenesis, for example through slipped strand mispairing or gene conversion. Using these studies we show how RipTALs of broad host range strains evolved convergently toward a shared target sequence. Finally, we discuss the differences between TALE-likes of plant pathogens in the context of disease ecology.
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Affiliation(s)
- Niklas Schandry
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
| | - Orlando de Lange
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
| | - Philippe Prior
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement – Institut National de la Recherche AgronomiqueSaint-Pierre, France
| | - Thomas Lahaye
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
- *Correspondence: Thomas Lahaye,
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Abstract
Transcription activator-like effectors (TALEs) are proteins with a unique DNA-binding domain that confers both a predictable and programmable specificity. The DNA-binding domain consists typically of 34-amino acid near-identical repeats. The repeats form a right-handed superhelical structure that wraps around the DNA double helix and exposes the variable amino acids at position 13 of each repeat to the sense strand DNA bases. Each repeat binds one base in a highly specific, non-overlapping, and comma-free fashion. Although TALE specificities are encoded in a simple way, sophisticated rules can be taken into account to build highly efficient DNA-binding modules for biotechnological use.
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Budhagatapalli N, Schedel S, Gurushidze M, Pencs S, Hiekel S, Rutten T, Kusch S, Morbitzer R, Lahaye T, Panstruga R, Kumlehn J, Hensel G. A simple test for the cleavage activity of customized endonucleases in plants. PLANT METHODS 2016; 12:18. [PMID: 26962325 PMCID: PMC4784412 DOI: 10.1186/s13007-016-0118-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/24/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although customized endonucleases [transcription activator-like effector nucleases (TALENs) and RNA-guided endonucleases (RGENs)] are known to be effective agents of mutagenesis in various host plants, newly designed endonuclease constructs require some pre-validation with respect to functionality before investing in the creation of stable transgenic plants. RESULTS A simple, biolistics-based leaf epidermis transient expression test has been developed, based on reconstituting the translational reading frame of a mutated, non-functional yfp reporter gene. Quantification of mutation efficacy was made possible by co-bombarding the explant with a constitutive mCherry expression cassette, thereby allowing the ratio between the number of red and yellow fluorescing cells to serve as a metric for mutation efficiency. Challenging either stable mutant alleles of a compromised version of gfp in tobacco and barley or the barley MLO gene with TALENs/RGENs confirmed the capacity to induce site-directed mutations. CONCLUSIONS A convenient procedure to assay the cleavage activity of customized endonucleases has been established. The system is independent of the endonuclease platform and operates in both di- and monocotyledonous hosts. It not only enables the validation of a TALEN/RGEN's functionality prior to the creation of stable mutants, but also serves as a suitable tool to optimize the design of endonuclease constructs.
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Affiliation(s)
- Nagaveni Budhagatapalli
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Sindy Schedel
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Maia Gurushidze
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Stefanie Pencs
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
- />Chair of Plant Breeding, Martin Luther University, Betty-Heimann-Str. 3, 06120 Halle (Saale), Germany
| | - Stefan Hiekel
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Twan Rutten
- />Structural Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Stefan Kusch
- />Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
| | - Robert Morbitzer
- />ZMBP-General Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Thomas Lahaye
- />ZMBP-General Genetics, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Ralph Panstruga
- />Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
| | - Jochen Kumlehn
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
| | - Goetz Hensel
- />Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland/OT Gatersleben, Germany
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de Lange O, Wolf C, Thiel P, Krüger J, Kleusch C, Kohlbacher O, Lahaye T. DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats. Nucleic Acids Res 2015; 43:10065-10080. [PMID: 26481363 DOI: 10.1093/nar.gkv1053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/14/2015] [Indexed: 05/28/2023] Open
Abstract
Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats.
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Affiliation(s)
- Orlando de Lange
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Christina Wolf
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Philipp Thiel
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Jens Krüger
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | | | - Oliver Kohlbacher
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany Quantitative Biology Centre and Faculty of Medicine, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Thomas Lahaye
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
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de Lange O, Wolf C, Thiel P, Krüger J, Kleusch C, Kohlbacher O, Lahaye T. DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats. Nucleic Acids Res 2015; 43:10065-80. [PMID: 26481363 PMCID: PMC4787788 DOI: 10.1093/nar/gkv1053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/14/2015] [Indexed: 12/24/2022] Open
Abstract
Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats.
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Affiliation(s)
- Orlando de Lange
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Christina Wolf
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Philipp Thiel
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Jens Krüger
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | | | - Oliver Kohlbacher
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany Quantitative Biology Centre and Faculty of Medicine, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Thomas Lahaye
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
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Venken KJT, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. Genome engineering: Drosophila melanogaster and beyond. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:233-67. [PMID: 26447401 DOI: 10.1002/wdev.214] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 08/03/2015] [Accepted: 08/20/2015] [Indexed: 12/26/2022]
Abstract
A central challenge in investigating biological phenomena is the development of techniques to modify genomic DNA with nucleotide precision that can be transmitted through the germ line. Recent years have brought a boon in these technologies, now collectively known as genome engineering. Defined genomic manipulations at the nucleotide level enable a variety of reverse engineering paradigms, providing new opportunities to interrogate diverse biological functions. These genetic modifications include controlled removal, insertion, and substitution of genetic fragments, both small and large. Small fragments up to a few kilobases (e.g., single nucleotide mutations, small deletions, or gene tagging at single or multiple gene loci) to large fragments up to megabase resolution can be manipulated at single loci to create deletions, duplications, inversions, or translocations of substantial sections of whole chromosome arms. A specialized substitution of chromosomal portions that presumably are functionally orthologous between different organisms through syntenic replacement, can provide proof of evolutionary conservation between regulatory sequences. Large transgenes containing endogenous or synthetic DNA can be integrated at defined genomic locations, permitting an alternative proof of evolutionary conservation, and sophisticated transgenes can be used to interrogate biological phenomena. Precision engineering can additionally be used to manipulate the genomes of organelles (e.g., mitochondria). Novel genome engineering paradigms are often accelerated in existing, easily genetically tractable model organisms, primarily because these paradigms can be integrated in a rigorous, existing technology foundation. The Drosophila melanogaster fly model is ideal for these types of studies. Due to its small genome size, having just four chromosomes, the vast amount of cutting-edge genetic technologies, and its short life-cycle and inexpensive maintenance requirements, the fly is exceptionally amenable to complex genetic analysis using advanced genome engineering. Thus, highly sophisticated methods developed in the fly model can be used in nearly any sequenced organism. Here, we summarize different ways to perform precise inheritable genome engineering using integrases, recombinases, and DNA nucleases in the D. melanogaster. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Koen J T Venken
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | | | - Paul J Vandeventer
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Audrey E Christiansen
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Kristi L Hoffman
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
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Müller TM, Böttcher C, Morbitzer R, Götz CC, Lehmann J, Lahaye T, Glawischnig E. TRANSCRIPTION ACTIVATOR-LIKE EFFECTOR NUCLEASE-Mediated Generation and Metabolic Analysis of Camalexin-Deficient cyp71a12 cyp71a13 Double Knockout Lines. PLANT PHYSIOLOGY 2015; 168:849-58. [PMID: 25953104 PMCID: PMC4741344 DOI: 10.1104/pp.15.00481] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/05/2015] [Indexed: 05/05/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), a number of defense-related metabolites are synthesized via indole-3-acetonitrile (IAN), including camalexin and indole-3-carboxylic acid (ICOOH) derivatives. Cytochrome P450 71A13 (CYP71A13) is a key enzyme for camalexin biosynthesis and catalyzes the conversion of indole-3-acetaldoxime (IAOx) to IAN. The CYP71A13 gene is located in tandem with its close homolog CYP71A12, also encoding an IAOx dehydratase. However, for CYP71A12, indole-3-carbaldehyde and cyanide were identified as major reaction products. To clarify CYP71A12 function in vivo and to better understand IAN metabolism, we generated two cyp71a12 cyp71a13 double knockout mutant lines. CYP71A12-specific transcription activator-like effector nucleases were introduced into the cyp71a13 background, and very efficient somatic mutagenesis was achieved. We observed stable transmission of the cyp71a12 mutation to the following generations, which is a major challenge for targeted mutagenesis in Arabidopsis. In contrast to cyp71a13 plants, in which camalexin accumulation is partially reduced, double mutants synthesized only traces of camalexin, demonstrating that CYP71A12 contributes to camalexin biosynthesis in leaf tissue. A major role of CYP71A12 was identified for the inducible biosynthesis of ICOOH. Specifically, the ICOOH methyl ester was reduced to 12% of the wild-type level in AgNO3-challenged cyp71a12 leaves. In contrast, indole-3-carbaldehyde derivatives apparently are synthesized via alternative pathways, such as the degradation of indole glucosinolates. Based on these results, we present a model for this surprisingly complex metabolic network with multiple IAN sources and channeling of IAOx-derived IAN into camalexin biosynthesis. In conclusion, transcription activator-like effector nuclease-mediated mutation is a powerful tool for functional analysis of tandem genes in secondary metabolism.
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Affiliation(s)
- Teresa M Müller
- Lehrstuhl für Genetik, Technische Universität München, 85354 Freising, Germany (T.M.M., C.C.G., J.L., E.G.);Julius Kühn-Institut, Institut für Ökologische Chemie, Pflanzenanalytik, und Vorratsschutz, 14195 Berlin, Germany (C.B.); andCenter for Plant Molecular Biology-General Genetics, University of Tübingen, 72076 Tuebingen, Germany (R.M., T.L.)
| | - Christoph Böttcher
- Lehrstuhl für Genetik, Technische Universität München, 85354 Freising, Germany (T.M.M., C.C.G., J.L., E.G.);Julius Kühn-Institut, Institut für Ökologische Chemie, Pflanzenanalytik, und Vorratsschutz, 14195 Berlin, Germany (C.B.); andCenter for Plant Molecular Biology-General Genetics, University of Tübingen, 72076 Tuebingen, Germany (R.M., T.L.)
| | - Robert Morbitzer
- Lehrstuhl für Genetik, Technische Universität München, 85354 Freising, Germany (T.M.M., C.C.G., J.L., E.G.);Julius Kühn-Institut, Institut für Ökologische Chemie, Pflanzenanalytik, und Vorratsschutz, 14195 Berlin, Germany (C.B.); andCenter for Plant Molecular Biology-General Genetics, University of Tübingen, 72076 Tuebingen, Germany (R.M., T.L.)
| | - Cornelia C Götz
- Lehrstuhl für Genetik, Technische Universität München, 85354 Freising, Germany (T.M.M., C.C.G., J.L., E.G.);Julius Kühn-Institut, Institut für Ökologische Chemie, Pflanzenanalytik, und Vorratsschutz, 14195 Berlin, Germany (C.B.); andCenter for Plant Molecular Biology-General Genetics, University of Tübingen, 72076 Tuebingen, Germany (R.M., T.L.)
| | - Johannes Lehmann
- Lehrstuhl für Genetik, Technische Universität München, 85354 Freising, Germany (T.M.M., C.C.G., J.L., E.G.);Julius Kühn-Institut, Institut für Ökologische Chemie, Pflanzenanalytik, und Vorratsschutz, 14195 Berlin, Germany (C.B.); andCenter for Plant Molecular Biology-General Genetics, University of Tübingen, 72076 Tuebingen, Germany (R.M., T.L.)
| | - Thomas Lahaye
- Lehrstuhl für Genetik, Technische Universität München, 85354 Freising, Germany (T.M.M., C.C.G., J.L., E.G.);Julius Kühn-Institut, Institut für Ökologische Chemie, Pflanzenanalytik, und Vorratsschutz, 14195 Berlin, Germany (C.B.); andCenter for Plant Molecular Biology-General Genetics, University of Tübingen, 72076 Tuebingen, Germany (R.M., T.L.)
| | - Erich Glawischnig
- Lehrstuhl für Genetik, Technische Universität München, 85354 Freising, Germany (T.M.M., C.C.G., J.L., E.G.);Julius Kühn-Institut, Institut für Ökologische Chemie, Pflanzenanalytik, und Vorratsschutz, 14195 Berlin, Germany (C.B.); andCenter for Plant Molecular Biology-General Genetics, University of Tübingen, 72076 Tuebingen, Germany (R.M., T.L.)
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Schreiber T, Sorgatz A, List F, Blüher D, Thieme S, Wilmanns M, Bonas U. Refined requirements for protein regions important for activity of the TALE AvrBs3. PLoS One 2015; 10:e0120214. [PMID: 25781334 PMCID: PMC4363659 DOI: 10.1371/journal.pone.0120214] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 01/20/2015] [Indexed: 11/25/2022] Open
Abstract
AvrBs3, the archetype of the family of transcription activator-like (TAL) effectors from phytopathogenic Xanthomonas bacteria, is translocated by the type III secretion system into the plant cell. AvrBs3 localizes to the plant cell nucleus and activates the transcription of target genes. Crucial for this is the central AvrBs3 region of 17.5 34-amino acid repeats that functions as a DNA-binding domain mediating recognition in a “one-repeat-to-one base pair” manner. Although AvrBs3 forms homodimers in the plant cell cytosol prior to nuclear import, it binds DNA as a monomer. Here, we show that complex formation of AvrBs3 proteins negatively affects their DNA-binding affinity in vitro. The conserved cysteine residues at position 30 of each repeat facilitate AvrBs3 complexes via disulfide bonds in vitro but are also required for the gene-inducing activity of the AvrBs3 monomer, i.e., activation of plant gene promoters. Our data suggest that the latter is due to a contribution to protein plasticity and that cysteine substitutions to alanine or serine result in a different DNA-binding mode. In addition, our studies revealed that extended parts of both the N-terminal and C-terminal regions of AvrBs3 contribute to DNA binding and, hence, gene-inducing activity in planta.
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Affiliation(s)
- Tom Schreiber
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Anika Sorgatz
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Felix List
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, Hamburg, Germany
| | - Doreen Blüher
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sabine Thieme
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, Hamburg, Germany
| | - Ulla Bonas
- Institute for Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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Wang C, Zhang X, Fan Y, Gao Y, Zhu Q, Zheng C, Qin T, Li Y, Che J, Zhang M, Yang B, Liu Y, Zhao K. XA23 is an executor R protein and confers broad-spectrum disease resistance in rice. MOLECULAR PLANT 2015; 8:290-302. [PMID: 25616388 DOI: 10.1016/j.molp.2014.10.010] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 10/10/2014] [Accepted: 10/28/2014] [Indexed: 05/03/2023]
Abstract
The majority of plant disease resistance (R) genes encode proteins that share common structural features. However, the transcription activator-like effector (TALE)-associated executor type R genes show no considerable sequence homology to any known R genes. We adopted a map-based cloning approach and TALE-based technology to isolate and characterize Xa23, a new executor R gene derived from wild rice (Oryza rufipogon) that confers an extremely broad spectrum of resistance to bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo). Xa23 encodes a 113 amino acid protein that shares 50% identity with the known executor R protein XA10. The predicted transmembrane helices in XA23 also overlap with those of XA10. Unlike Xa10, however, Xa23 transcription is specifically activated by AvrXa23, a TALE present in all examined Xoo field isolates. Moreover, the susceptible xa23 allele has an identical open reading frame of Xa23 but differs in promoter region by lacking the TALE binding element (EBE) for AvrXa23. XA23 can trigger a strong hypersensitive response in rice, tobacco, and tomato. Our results provide the first evidence that plant genomes have an executor R gene family of which members execute their function and spectrum of disease resistance by recognizing the cognate TALEs in the pathogen.
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Affiliation(s)
- Chunlian Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China
| | - Xiaoping Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China
| | - Yinglun Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China
| | - Ying Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Chongke Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China
| | - Tengfei Qin
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China
| | - Yanqiang Li
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China
| | - Jinying Che
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China
| | - Mingwei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China
| | - Bing Yang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100081, China.
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Hutin M, Pérez-Quintero AL, Lopez C, Szurek B. MorTAL Kombat: the story of defense against TAL effectors through loss-of-susceptibility. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 26236326 DOI: 10.3389/fpls.2015.0053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Many plant-pathogenic xanthomonads rely on Transcription Activator-Like (TAL) effectors to colonize their host. This particular family of type III effectors functions as specific plant transcription factors via a programmable DNA-binding domain. Upon binding to the promoters of plant disease susceptibility genes in a sequence-specific manner, the expression of these host genes is induced. However, plants have evolved specific strategies to counter the action of TAL effectors and confer resistance. One mechanism is to avoid the binding of TAL effectors by mutations of their DNA binding sites, resulting in resistance by loss-of-susceptibility. This article reviews our current knowledge of the susceptibility hubs targeted by Xanthomonas TAL effectors, possible evolutionary scenarios for plants to combat the pathogen with loss-of-function alleles, and how this knowledge can be used overall to develop new pathogen-informed breeding strategies and improve crop resistance.
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Affiliation(s)
- Mathilde Hutin
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2 Montpellier, France
| | - Alvaro L Pérez-Quintero
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2 Montpellier, France
| | - Camilo Lopez
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2 Montpellier, France ; Biology Department, Universidad Nacional de Colombia Bogota, Colombia
| | - Boris Szurek
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2 Montpellier, France
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Pérez-Quintero AL, Lamy L, Gordon JL, Escalon A, Cunnac S, Szurek B, Gagnevin L. QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically. FRONTIERS IN PLANT SCIENCE 2015; 6:545. [PMID: 26284082 PMCID: PMC4522561 DOI: 10.3389/fpls.2015.00545] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/06/2015] [Indexed: 05/20/2023]
Abstract
Transcription Activator-Like (TAL) effectors from Xanthomonas plant pathogenic bacteria can bind to the promoter region of plant genes and induce their expression. DNA-binding specificity is governed by a central domain made of nearly identical repeats, each determining the recognition of one base pair via two amino acid residues (a.k.a. Repeat Variable Di-residue, or RVD). Knowing how TAL effectors differ from each other within and between strains would be useful to infer functional and evolutionary relationships, but their repetitive nature precludes reliable use of traditional alignment methods. The suite QueTAL was therefore developed to offer tailored tools for comparison of TAL effector genes. The program DisTAL considers each repeat as a unit, transforms a TAL effector sequence into a sequence of coded repeats and makes pair-wise alignments between these coded sequences to construct trees. The program FuncTAL is aimed at finding TAL effectors with similar DNA-binding capabilities. It calculates correlations between position weight matrices of potential target DNA sequence predicted from the RVD sequence, and builds trees based on these correlations. The programs accurately represented phylogenetic and functional relationships between TAL effectors using either simulated or literature-curated data. When using the programs on a large set of TAL effector sequences, the DisTAL tree largely reflected the expected species phylogeny. In contrast, FuncTAL showed that TAL effectors with similar binding capabilities can be found between phylogenetically distant taxa. This suite will help users to rapidly analyse any TAL effector genes of interest and compare them to other available TAL genes and should improve our understanding of TAL effectors evolution. It is available at http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi.
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Affiliation(s)
| | - Léo Lamy
- UMR IPME, IRD-CIRAD-Université MontpellierMontpellier, France
| | | | - Aline Escalon
- UMR PVBMT, CIRAD-Université de la RéunionSaint-Pierre, France
| | | | - Boris Szurek
- UMR IPME, IRD-CIRAD-Université MontpellierMontpellier, France
- *Correspondence: Boris Szurek and Lionel Gagnevin, UMR IPME, IRD-CIRAD-UM, 911, Av. Agropolis BP 64501, 34394 Montpellier, France ;
| | - Lionel Gagnevin
- UMR IPME, IRD-CIRAD-Université MontpellierMontpellier, France
- *Correspondence: Boris Szurek and Lionel Gagnevin, UMR IPME, IRD-CIRAD-UM, 911, Av. Agropolis BP 64501, 34394 Montpellier, France ;
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Hutin M, Pérez-Quintero AL, Lopez C, Szurek B. MorTAL Kombat: the story of defense against TAL effectors through loss-of-susceptibility. FRONTIERS IN PLANT SCIENCE 2015; 6:535. [PMID: 26236326 PMCID: PMC4500901 DOI: 10.3389/fpls.2015.00535] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/30/2015] [Indexed: 05/21/2023]
Abstract
Many plant-pathogenic xanthomonads rely on Transcription Activator-Like (TAL) effectors to colonize their host. This particular family of type III effectors functions as specific plant transcription factors via a programmable DNA-binding domain. Upon binding to the promoters of plant disease susceptibility genes in a sequence-specific manner, the expression of these host genes is induced. However, plants have evolved specific strategies to counter the action of TAL effectors and confer resistance. One mechanism is to avoid the binding of TAL effectors by mutations of their DNA binding sites, resulting in resistance by loss-of-susceptibility. This article reviews our current knowledge of the susceptibility hubs targeted by Xanthomonas TAL effectors, possible evolutionary scenarios for plants to combat the pathogen with loss-of-function alleles, and how this knowledge can be used overall to develop new pathogen-informed breeding strategies and improve crop resistance.
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Affiliation(s)
- Mathilde Hutin
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2Montpellier, France
| | - Alvaro L. Pérez-Quintero
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2Montpellier, France
| | - Camilo Lopez
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2Montpellier, France
- Biology Department, Universidad Nacional de ColombiaBogota, Colombia
| | - Boris Szurek
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2Montpellier, France
- *Correspondence: Boris Szurek, UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2, 911 Avenue Agropolis BP 64501, 34394 Montpellier Cedex 5, France,
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Boch J, Bonas U, Lahaye T. TAL effectors--pathogen strategies and plant resistance engineering. THE NEW PHYTOLOGIST 2014; 204:823-32. [PMID: 25539004 DOI: 10.1111/nph.13015] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transcription activator-like effectors (TALEs) from plant pathogenic Xanthomonas spp. and the related RipTALs from Ralstonia solanacearum are DNA-binding proteins with a modular DNA-binding domain. This domain is both predictable and programmable, which simplifies elucidation of TALE function in planta and facilitates generation of DNA-binding modules with desired specificity for biotechnological approaches. Recently identified TALE host target genes that either promote or stop bacterial disease provide new insights into how expression of TALE genes affects the plant–pathogen interaction. Since its elucidation the TALE code has been continuously refined and now provides a mature tool that, in combination with transcriptome profiling, allows rapid isolation of novel TALE target genes. The TALE code is also the basis for synthetic promoter-traps that mediate recognition of TALE or RipTAL proteins in engineered plants. In this review, we will summarize recent findings in plant-focused TALE research. In addition, we will provide an outline of the newly established gene isolation approach for TALE or RipTAL host target genes with an emphasis on potential pitfalls.
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