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Arra Y, Auguy F, Stiebner M, Chéron S, Wudick MM, Miras M, Schepler‐Luu V, Köhler S, Cunnac S, Frommer WB, Albar L. Rice Yellow Mottle Virus resistance by genome editing of the Oryza sativa L. ssp. japonica nucleoporin gene OsCPR5.1 but not OsCPR5.2. Plant Biotechnol J 2024; 22:1299-1311. [PMID: 38124291 PMCID: PMC11022797 DOI: 10.1111/pbi.14266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment-friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (Oryza glaberrima), however, introgression into Oryza sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss-of-function mutants were fully resistant, while loss-of-function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susceptibility. Notably, edited lines with short in-frame deletions or replacements in the N-terminal domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed plants, oscpr5.1 and oscpr5.2 single and double knockout mutants showed neither substantial growth defects nor symptoms indicative lesion mimic phenotypes, possibly reflecting functional differentiation. The specific editing of OsCPR5.1, while maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV-resistance in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes or other traits.
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Affiliation(s)
- Yugander Arra
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Florence Auguy
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
| | - Melissa Stiebner
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Sophie Chéron
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
| | - Michael M. Wudick
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Manuel Miras
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Van Schepler‐Luu
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Steffen Köhler
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
- Center for Advanced ImagingHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Sébastien Cunnac
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
| | - Wolf B. Frommer
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
- Center for Advanced ImagingHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Transformative Bio‐Molecules (ITbM‐WPI)Nagoya UniversityNagoyaJapan
| | - Laurence Albar
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
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Favilla LD, Herman TS, Goersch CDS, de Andrade RV, Felipe MSS, Bocca AL, Fernandes L. Expanding the Toolbox for Functional Genomics in Fonsecaea pedrosoi: The Use of Split-Marker and Biolistic Transformation for Inactivation of Tryptophan Synthase ( trpB) Gene. J Fungi (Basel) 2023; 9:jof9020224. [PMID: 36836338 PMCID: PMC9963410 DOI: 10.3390/jof9020224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Chromoblastomycosis (CBM) is a disease caused by several dematiaceous fungi from different genera, and Fonsecaea is the most common which has been clinically isolated. Genetic transformation methods have recently been described; however, molecular tools for the functional study of genes have been scarcely reported for those fungi. In this work, we demonstrated that gene deletion and generation of the null mutant by homologous recombination are achievable for Fonsecaea pedrosoi by the use of two approaches: use of double-joint PCR for cassette construction, followed by delivery of the split-marker by biolistic transformation. Through in silico analyses, we identified that F. pedrosoi presents the complete enzymatic apparatus required for tryptophan (trp) biosynthesis. The gene encoding a tryptophan synthase trpB -which converts chorismate to trp-was disrupted. The ΔtrpB auxotrophic mutant can grow with external trp supply, but germination, viability of conidia, and radial growth are defective compared to the wild-type and reconstituted strains. The use of 5-FAA for selection of trp- phenotypes and for counter-selection of strains carrying the trp gene was also demonstrated. The molecular tools for the functional study of genes, allied to the genetic information from genomic databases, significantly boost our understanding of the biology and pathogenicity of CBM causative agents.
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Affiliation(s)
- Luísa Dan Favilla
- Laboratory of Applied Immunology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Molecular Biology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
| | - Tatiana Sobianski Herman
- Laboratory of Applied Immunology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Molecular Patology, Faculty of Medicine, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
| | - Camila da Silva Goersch
- Laboratory of Applied Immunology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Microbial Biology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
| | - Rosangela Vieira de Andrade
- Graduate Program of Genomic Sciences and Biotechnology, Catholic University of Brasilia, Campus Asa Norte, Asa Norte, Federal District, Taguatinga 70790-160, Brazil
| | - Maria Sueli Soares Felipe
- Graduate Program of Genomic Sciences and Biotechnology, Catholic University of Brasilia, Campus Asa Norte, Asa Norte, Federal District, Taguatinga 70790-160, Brazil
| | - Anamélia Lorenzetti Bocca
- Laboratory of Applied Immunology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Molecular Biology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Molecular Patology, Faculty of Medicine, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
| | - Larissa Fernandes
- Laboratory of Applied Immunology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Graduate Program in Microbial Biology, Institute of Biology, Campus Darcy Ribeiro, University of Brasília, Asa Norte, Federal District, Brasilia 70910-900, Brazil
- Centro Metropolitano, Faculty of Ceilândia, Campus UnB Ceilândia, University of Brasília, Ceilândia Sul, Federal District, Brasilia 72220-275, Brazil
- Correspondence:
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Grigorian E, Groisillier A, Thomas F, Leblanc C, Delage L. Functional Characterization of a L-2-Haloacid Dehalogenase From Zobellia galactanivorans Dsij T Suggests a Role in Haloacetic Acid Catabolism and a Wide Distribution in Marine Environments. Front Microbiol 2021; 12:725997. [PMID: 34621253 PMCID: PMC8490876 DOI: 10.3389/fmicb.2021.725997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/31/2021] [Indexed: 12/21/2022] Open
Abstract
L-2-halocid dehalogenases (L-2-HADs) have been mainly characterized from terrestrial polluted environments. By contrast, knowledge is still scarce about their role in detoxification of predominant halocarbons in marine environments. Here, phylogenetic analyses showed a wide diversity of homologous L-2-HADs, especially among those belonging to marine bacteria. Previously characterized terrestrial L-2-HADs were part of a monophyletic group (named group A) including proteins of terrestrial and marine origin. Another branch (named group B) contained mostly marine L-2-HADs, with two distinct clades of Bacteroidetes homologs, closely linked to Proteobacteria ones. This study further focused on the characterization of the only L-2-HAD from the flavobacterium Zobellia galactanivorans DsijT (ZgHAD), belonging to one of these Group B clades. The recombinant ZgHAD was shown to dehalogenate bromo- and iodoacetic acids, and gene knockout in Z. galactanivorans revealed a direct role of ZgHAD in tolerance against both haloacetic acids. Analyses of metagenomic and metatranscriptomic datasets confirmed that L-2-HADs from group A were well-represented in terrestrial and marine bacteria, whereas ZgHAD homologs (group B L-2-HADs) were mainly present in marine bacteria, and particularly in host-associated species. Our results suggest that ZgHAD homologs could be key enzymes for marine Bacteroidetes, by conferring selective advantage for the recycling of toxic halogen compounds produced in particular marine habitats, and especially during interactions with macroalgae.
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Affiliation(s)
- Eugénie Grigorian
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Agnès Groisillier
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - François Thomas
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Catherine Leblanc
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Ludovic Delage
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
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Ballester AR, González-Candelas L. EFE-Mediated Ethylene Synthesis Is the Major Pathway in the Citrus Postharvest Pathogen Penicillium digitatum during Fruit Infection. J Fungi (Basel) 2020; 6:jof6030175. [PMID: 32957714 PMCID: PMC7558865 DOI: 10.3390/jof6030175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022] Open
Abstract
Penicillium digitatum is the main fungal postharvest pathogen of citrus fruit under Mediterranean climate conditions. The role of ethylene in the P. digitatum-citrus fruit interaction is unclear and controversial. We analyzed the involvement of the 2-oxoglutarate-dependent ethylene-forming enzyme (EFE)-encoding gene (efeA) of P. digitatum on the pathogenicity of the fungus. The expression of P. digitatumefeA parallels ethylene production during growth on PDA medium, with maximum levels reached during sporulation. We generated ΔefeA knockout mutants in P. digitatum strain Pd1. These mutants showed no significant defect on mycelial growth or sporulation compared to the parental strain. However, the knockout mutants did not produce ethylene in vitro. Citrus pathogenicity assays showed no differences in virulence between the parental and ΔefeA knockout mutant strains, despite a lack of ethylene production by the knockout mutant throughout the infection process. This result suggests that ethylene plays no role in P. digitatum pathogenicity. Our results clearly show that EFE-mediated ethylene synthesis is the major ethylene synthesis pathway in the citrus postharvest pathogen P. digitatum during both in vitro growth on PDA medium and the infection process, and that this hormone is not necessary for establishing P. digitatum infection in citrus fruit. However, our results also indicate that ethylene produced by P. digitatum during sporulation on the fruit surface may influence the development of secondary fungal infections.
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Kammerscheit X, Chauvat F, Cassier-Chauvat C. From Cyanobacteria to Human, MAPEG-Type Glutathione-S-Transferases Operate in Cell Tolerance to Heat, Cold, and Lipid Peroxidation. Front Microbiol 2019; 10:2248. [PMID: 31681188 PMCID: PMC6798054 DOI: 10.3389/fmicb.2019.02248] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/13/2019] [Indexed: 11/18/2022] Open
Abstract
The MAPEG2 sub-family of glutathione-S-transferase proteins (GST) has been poorly investigated in vivo, even in prokaryotes such as cyanobacteria the organisms that are regarded as having developed glutathione-dependent enzymes to protect themselves against the reactive oxygen species (ROS) often produced by their powerful photosynthesis. We report the first in vivo analysis of a cyanobacterial MAPEG2-like protein (Sll1147) in the model cyanobacterium Synechocystis PCC 6803. While Sll1147 is dispensable to cell growth in standard photo-autotrophic conditions, it plays an important role in the resistance to heat and cold, and to n-tertbutyl hydroperoxide (n-tBOOH) that induces lipid peroxidation. These findings suggest that Sll1147 could be involved in membrane fluidity, which is critical for photosynthesis. Attesting its sensitivity to these stresses, the Δsll1147 mutant lacking Sll1147 challenged by heat, cold, or n-tBOOH undergoes transient accumulation of peroxidized lipids and then of reduced and oxidized glutathione. These results are welcome because little is known concerning the signaling and/or protection mechanisms used by cyanobacteria to cope with heat and cold, two inevitable environmental stresses that limit their growth, and thus their production of biomass for our food chain and of biotechnologically interesting chemicals. Also interestingly, the decreased resistance to heat, cold and n-tBOOH of the Δsll1147 mutant could be rescued back to normal (wild-type) levels upon the expression of synthetic MAPEG2-encoding human genes adapted to the cyanobacterial codon usage. These synthetic hmGST2 and hmGST3 genes were also able to increase the Escherichia coli tolerance to heat and n-tBOOH. Collectively, these finding indicate that the activity of the MAPEG2 proteins have been conserved, at least in part, during evolution from (cyano)bacteria to human.
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Liu S, Wu N, Zhang S, Yuan Y, Zhang W, Zhang Y. Variable Persister Gene Interactions with (p)ppGpp for Persister Formation in Escherichia coli. Front Microbiol 2017; 8:1795. [PMID: 28979246 PMCID: PMC5611423 DOI: 10.3389/fmicb.2017.01795] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/05/2017] [Indexed: 12/01/2022] Open
Abstract
Persisters comprise a group of phenotypically heterogeneous metabolically quiescent bacteria with multidrug tolerance and contribute to the recalcitrance of chronic infections. Although recent work has shown that toxin-antitoxin (TA) system HipAB depends on stringent response effector (p)ppGppin persister formation, whether other persister pathways are also dependent on stringent response has not been explored. Here we examined the relationship of (p)ppGpp with 15 common persister genes (dnaK, clpB, rpoS, pspF, tnaA, sucB, ssrA, smpB, recA, umuD, uvrA, hipA, mqsR, relE, dinJ) using Escherichia coli as a model. By comparing the persister levels of wild type with their single gene knockout and double knockout mutants with relA, we divided their interactions into five types, namely A “dependent” (dnaK, recA), B “positive reinforcement” (rpoS, pspF, ssrA, recA), C “antagonistic” (clpB, sucB, umuD, uvrA, hipA, mqsR, relE, dinJ), D “epistasis” (clpB, rpoS, tnaA, ssrA, smpB, hipA), and E “irrelevant” (dnaK, clpB, rpoS, tnaA, sucB, smpB, umuD, uvrA, hipA, mqsR, relE, dinJ). We found that the persister gene interactions are intimately dependent on bacterial culture age, cell concentrations (diluted versus undiluted culture), and drug classifications, where the same gene may belong to different groups with varying antibiotics, culture age or cell concentrations. Together, this study represents the first attempt to systematically characterize the intricate relationships among the different mechanisms of persistence and as such provide new insights into the complexity of the persistence phenomenon at the level of persister gene network interactions.
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Affiliation(s)
- Shuang Liu
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan UniversityShanghai, China
| | - Nan Wu
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan UniversityShanghai, China
| | - Shanshan Zhang
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan UniversityShanghai, China
| | - Youhua Yuan
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan UniversityShanghai, China
| | - Wenhong Zhang
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan UniversityShanghai, China
| | - Ying Zhang
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan UniversityShanghai, China.,Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, BaltimoreMD, United States
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Rademacher N, Kern R, Fujiwara T, Mettler-Altmann T, Miyagishima SY, Hagemann M, Eisenhut M, Weber APM. Photorespiratory glycolate oxidase is essential for the survival of the red alga Cyanidioschyzon merolae under ambient CO2 conditions. J Exp Bot 2016; 67:3165-75. [PMID: 26994474 PMCID: PMC4867895 DOI: 10.1093/jxb/erw118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Photorespiration is essential for all organisms performing oxygenic photosynthesis. The evolution of photorespiratory metabolism began among cyanobacteria and led to a highly compartmented pathway in plants. A molecular understanding of photorespiration in eukaryotic algae, such as glaucophytes, rhodophytes, and chlorophytes, is essential to unravel the evolution of this pathway. However, mechanistic detail of the photorespiratory pathway in red algae is scarce. The unicellular red alga Cyanidioschyzon merolae represents a model for the red lineage. Its genome is fully sequenced, and tools for targeted gene engineering are available. To study the function and importance of photorespiration in red algae, we chose glycolate oxidase (GOX) as the target. GOX catalyses the conversion of glycolate into glyoxylate, while hydrogen peroxide is generated as a side-product. The function of the candidate GOX from C. merolae was verified by the fact that recombinant GOX preferred glycolate over L-lactate as a substrate. Yellow fluorescent protein-GOX fusion proteins showed that GOX is targeted to peroxisomes in C. merolae The GOX knockout mutant lines showed a high-carbon-requiring phenotype with decreased growth and reduced photosynthetic activity compared to the wild type under ambient air conditions. Metabolite analyses revealed glycolate and glycine accumulation in the mutant cells after a shift from high CO2 conditions to ambient air. In summary, or results demonstrate that photorespiratory metabolism is essential for red algae. The use of a peroxisomal GOX points to a high photorespiratory flux as an ancestral feature of all photosynthetic eukaryotes.
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Affiliation(s)
- Nadine Rademacher
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ramona Kern
- University Rostock, Department Plant Physiology, Albert-Einstein-Straße 3, 18059 Rostock, Germany
| | - Takayuki Fujiwara
- Division of Symbiosis and Cell Evolution, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Shizuoka, Japan
| | - Tabea Mettler-Altmann
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Shin-Ya Miyagishima
- Division of Symbiosis and Cell Evolution, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Shizuoka, Japan Japan Science and Technology Agency, CREST, 4-1-8 Honcho, Kawaguchi 332-0012, Saitama, Japan
| | - Martin Hagemann
- University Rostock, Department Plant Physiology, Albert-Einstein-Straße 3, 18059 Rostock, Germany
| | - Marion Eisenhut
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
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Abstract
Aubergine is an RNA-binding protein of the Piwi clade, functioning in germline in the piRNA pathway that silences transposons and repetitive sequences. Several mutations of this gene exist, but they mostly result in truncated proteins or correspond to mutations that also affect neighboring genes. We have generated complete aubergine knock-out mutants that do not disrupt the neighboring genes. These novel mutants are characterized by PCR and sequencing. Their nature is confirmed by female sterility and by the presence of crystals in testes, common to the aubergine loss of function mutations. These mutants provide novel and more appropriate tools for the study of the piRNA pathway that controls genome stability.
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Affiliation(s)
- H Bahar Sahin
- a IGBMC, CNRS UMR 7104 - Inserm U 964 . Illkirch Cedex / FRANCE.,b Current address: Kadir Has University , Department of Bioinformatics and Genetics , Fatih , İstanbul / TURKEY
| | - Omer Faruk Karatas
- a IGBMC, CNRS UMR 7104 - Inserm U 964 . Illkirch Cedex / FRANCE.,c Current address: Department of Molecular Biology and Genetics, Erzurum Technical University , Erzurum / TURKEY
| | - Valeria Specchia
- d DiSTeBA - Department of Biological and Environmental Science and Technology - University of Salento - Lecce , Italy
| | - Silvia Di Tommaso
- d DiSTeBA - Department of Biological and Environmental Science and Technology - University of Salento - Lecce , Italy
| | - Céline Diebold
- a IGBMC, CNRS UMR 7104 - Inserm U 964 . Illkirch Cedex / FRANCE
| | - Maria Pia Bozzetti
- d DiSTeBA - Department of Biological and Environmental Science and Technology - University of Salento - Lecce , Italy
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Han SH, Yoo SC, Lee BD, An G, Paek NC. Rice FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1) promotes flowering independent of photoperiod. Plant Cell Environ 2015; 38:2527-40. [PMID: 25850808 DOI: 10.1111/pce.12549] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 03/22/2015] [Accepted: 03/23/2015] [Indexed: 05/09/2023]
Abstract
In the facultative long-day (LD) plant Arabidopsis thaliana, FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) is activated by blue light and promotes flowering through the transcriptional and post-translational regulation of CONSTANS under inductive LD conditions. By contrast, the facultative short day (SD) plant rice (Oryza sativa) flowers early under inductive SD and late under non-inductive LD conditions; the regulatory function of OsFKF1 remains elusive. Here we show that osfkf1 mutants flower late under SD, LD and natural LD conditions. Transcriptional analysis revealed that OsFKF1 up-regulates the expression of the floral activator Ehd2 and down-regulates the expression of the floral repressor Ghd7; these regulators up- and down-regulate Ehd1 expression, respectively. Moreover, OsFKF1 can up-regulate Ehd1 expression under blue light treatment, without affecting the expression of Ehd2 and Ghd7. In contrast to the LD-specific floral activator Arabidopsis FKF1, OsFKF1 likely acts as an autonomous floral activator because it promotes flowering independent of photoperiod, probably via its distinct roles in controlling the expression of rice-specific genes including Ehd2, Ghd7 and Ehd1. Like Arabidopsis FKF1, which interacts with GI and CDF1, OsFKF1 also interacts with OsGI and OsCDF1 (also termed OsDOF12). Thus, we have identified similar and distinct roles of FKF1 in Arabidopsis and rice.
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Affiliation(s)
- Su-Hyun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea
| | - Soo-Cheul Yoo
- Department of Plant Life and Environmental Science, Hankyong National University, Ansung, 456-749, South Korea
| | - Byoung-Doo Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology, Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, South Korea
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, South Korea
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Wu N, He L, Cui P, Wang W, Yuan Y, Liu S, Xu T, Zhang S, Wu J, Zhang W, Zhang Y. Ranking of persister genes in the same Escherichia coli genetic background demonstrates varying importance of individual persister genes in tolerance to different antibiotics. Front Microbiol 2015; 6:1003. [PMID: 26483762 PMCID: PMC4588708 DOI: 10.3389/fmicb.2015.01003] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/07/2015] [Indexed: 12/31/2022] Open
Abstract
Despite the identification of many genes and pathways involved in the persistence phenomenon of bacteria, the relative importance of these genes in a single organism remains unclear. Here, using Escherichia coli as a model, we generated mutants of 21 known candidate persister genes and compared the relative importance of these mutants in persistence to various antibiotics (ampicillin, gentamicin, norfloxacin, and trimethoprim) at different times. We found that oxyR, dnaK, sucB, relA, rpoS, clpB, mqsR, and recA were prominent persister genes involved in persistence to multiple antibiotics. These genes map to the following pathways: antioxidative defense pathway (oxyR), global regulators (dnaK, clpB, and rpoS), energy production (sucB), stringent response (relA), toxin-antitoxin (TA) module (mqsR), and SOS response (recA). Among the TA modules, the ranking order was mqsR, lon, relE, tisAB, hipA, and dinJ. Intriguingly, rpoS deletion caused a defect in persistence to gentamicin but increased persistence to ampicillin and norfloxacin. Mutants demonstrated dramatic differences in persistence to different antibiotics at different time points: some mutants (oxyR, dnaK, phoU, lon, recA, mqsR, and tisAB) displayed defect in persistence from early time points, while other mutants (relE, smpB, glpD, umuD, and tnaA) showed defect only at later time points. These results indicate that varying hierarchy and importance of persister genes exist and that persister genes can be divided into those involved in shallow persistence and those involved in deep persistence. Our findings suggest that the persistence phenomenon is a dynamic process with different persister genes playing roles of variable significance at different times. These findings have implications for improved understanding of persistence phenomenon and developing new drugs targeting persisters for more effective cure of persistent infections.
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Affiliation(s)
- Nan Wu
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China
| | - Lei He
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China
| | - Peng Cui
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China
| | - Wenjie Wang
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China
| | - Youhua Yuan
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China
| | - Shuang Liu
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China
| | - Tao Xu
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China
| | - Shanshan Zhang
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China
| | - Jing Wu
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China
| | - Wenhong Zhang
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China
| | - Ying Zhang
- Key Lab of Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University Shanghai, China ; Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA
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Shigeto J, Itoh Y, Hirao S, Ohira K, Fujita K, Tsutsumi Y. Simultaneously disrupting AtPrx2, AtPrx25 and AtPrx71 alters lignin content and structure in Arabidopsis stem. J Integr Plant Biol 2015; 57:349-56. [PMID: 25644691 DOI: 10.1111/jipb.12334] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/20/2015] [Indexed: 05/23/2023]
Abstract
Plant class III heme peroxidases catalyze lignin polymerization. Previous reports have shown that at least three Arabidopsis thaliana peroxidases, AtPrx2, AtPrx25 and AtPrx71, are involved in stem lignification using T-DNA insertion mutants, atprx2, atprx25, and atprx71. Here, we generated three double mutants, atprx2/atprx25, atprx2/atprx71, and atprx25/atprx71, and investigated the impact of the simultaneous deficiency of these peroxidases on lignins and plant growth. Stem tissue analysis using the acetyl bromide method and derivatization followed by reductive cleavage revealed improved lignin characteristics, such as lowered lignin content and increased arylglycerol-β-aryl (β-O-4) linkage type, especially β-O-4 linked syringyl units, in lignin, supporting the roles of these genes in lignin polymerization. In addition, none of the double mutants exhibited severe growth defects, such as shorter plant stature, dwarfing, or sterility, and their stems had improved cell wall degradability. This study will contribute to progress in lignin bioengineering to improve lignocellulosic biomass.
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Affiliation(s)
- Jun Shigeto
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan
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Forsthoefel NR, Klag KA, Simeles BP, Reiter R, Brougham L, Vernon DM. The Arabidopsis Plant Intracellular Ras-group LRR (PIRL) Family and the Value of Reverse Genetic Analysis for Identifying Genes that Function in Gametophyte Development. Plants (Basel) 2013; 2:507-20. [PMID: 27137390 DOI: 10.3390/plants2030507] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/02/2013] [Accepted: 07/24/2013] [Indexed: 12/31/2022]
Abstract
Arabidopsis thaliana has proven a powerful system for developmental genetics, but identification of gametophytic genes with developmental mutants can be complicated by factors such as gametophyte-lethality, functional redundancy, or poor penetrance. These issues are exemplified by the Plant Intracellular Ras-group LRR (PIRL) genes, a family of nine genes encoding a class of leucine-rich repeat proteins structurally related to animal and fungal LRR proteins involved in developmental signaling. Previous analysis of T-DNA insertion mutants showed that two of these genes, PIRL1 and PIRL9, have an essential function in pollen formation but are functionally redundant. Here, we present evidence implicating three more PIRLs in gametophyte development. Scanning electron microscopy revealed that disruption of either PIRL2 or PIRL3 results in a low frequency of pollen morphological abnormalities. In addition, molecular analysis of putative pirl6 insertion mutants indicated that knockout alleles of this gene are not represented in current Arabidopsis mutant populations, suggesting gametophyte lethality may hinder mutant recovery. Consistent with this, available microarray and RNA-seq data have documented strongest PIRL6 expression in developing pollen. Taken together, these results now implicate five PIRLs in gametophyte development. Systematic reverse genetic analysis of this novel LRR family has therefore identified gametophytically active genes that otherwise would likely be missed by forward genetic screens.
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Tamura W, Kojima S, Toyokawa A, Watanabe H, Tabuchi-Kobayashi M, Hayakawa T, Yamaya T. Disruption of a Novel NADH-Glutamate Synthase2 Gene Caused Marked Reduction in Spikelet Number of Rice. Front Plant Sci 2011; 2:57. [PMID: 22645542 PMCID: PMC3355815 DOI: 10.3389/fpls.2011.00057] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 09/09/2011] [Indexed: 05/19/2023]
Abstract
Inorganic ammonium ions are assimilated by a coupled reaction of glutamine synthetase and glutamate synthase (GOGAT). In rice, three genes encoding either ferredoxin (Fd)-GOGAT, NADH-GOGAT1, or NADH-GOGAT2, have been identified. OsNADH-GOGAT2, a newly identified gene, was expressed mainly in fully expanded leaf blades and leaf sheaths. Although the distinct expression profile to OsNADH-GOGAT1, which is mainly detected in root tips, developing leaf blades, and grains, was shown in our previous studies, physiological role of NADH-GOGAT2 is not yet known. Here, we isolated retrotransposon mediated-knockout mutants lacking OsNADH-GOGAT2. In rice grown under paddy field conditions, disruption of the OsNADH-GOGAT2 gene caused a remarkable decrease in spikelet number per panicle associated with a reductions in yield and whole plant biomass, when compared with wild-type (WT) plants. The total nitrogen contents in the senescing leaf blade of the mutants were approximately a half of the WT plants. Expression of this gene was mainly detected in phloem companion cells and phloem parenchyma cells associated with large vascular bundles in fully expanded leaf blades, when the promoter region fused with a β-glucuronidase gene was introduced into the WT rice. These results suggest that the NADH-GOGAT2 is important in the process of glutamine generation in senescing leaves for the remobilization of leaf nitrogen through phloem to the panicle during natural senescence. These results also indicate that other GOGATs, i.e., NADH-GOGAT1 and ferredoxin-GOGAT are not able to compensate the function of NADH-GOGAT2.
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Affiliation(s)
- Wataru Tamura
- Graduate School of Agricultural Science, Tohoku UniversitySendai, Japan
| | - Soichi Kojima
- Graduate School of Agricultural Science, Tohoku UniversitySendai, Japan
| | - Ayako Toyokawa
- Graduate School of Agricultural Science, Tohoku UniversitySendai, Japan
| | - Hideo Watanabe
- Graduate School of Agricultural Science, Tohoku UniversitySendai, Japan
| | | | | | - Tomoyuki Yamaya
- Graduate School of Agricultural Science, Tohoku UniversitySendai, Japan
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