28 results on '"Julio Rodríguez-Romero"'
Search Results
2. Construction and Characterization of a Botrytis Virus F Infectious Clone
- Author
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Laura Córdoba, Ana Ruiz-Padilla, Julio Rodríguez-Romero, and María A. Ayllón
- Subjects
Botrytis cinerea ,infectious clones ,mycovirus ,Botrytis virus F ,biological control ,functional fungal genomics ,Biology (General) ,QH301-705.5 - Abstract
Botrytis virus F (BVF) is a positive-sense, single-stranded RNA (+ssRNA) virus within the Gammaflexiviridae family of the plant-pathogenic fungus Botrytis cinerea. In this study, the complete sequence of a BVF strain isolated from B. cinerea collected from grapevine fields in Spain was analyzed. This virus, in this work BVF-V448, has a genome of 6827 nt in length, excluding the poly(A) tail, with two open reading frames encoding an RNA dependent RNA polymerase (RdRP) and a coat protein (CP). The 5′- and 3′-terminal regions of the genome were determined by rapid amplification of cDNA ends (RACE). Furthermore, a yet undetected subgenomic RNA species in BVF-V448 was identified, indicating that the CP is expressed via 3′ coterminal subgenomic RNAs (sgRNAs). We also report the successful construction of the first BVF full-length cDNA clone and synthesized in vitro RNA transcripts using the T7 polymerase, which could efficiently transfect two different strains of B. cinerea, B05.10 and Pi258.9. The levels of growth in culture and virulence on plants of BVF-V448 transfected strains were comparable to BVF-free strains. The infectious clones generated in this work provide a useful tool for the future development of an efficient BVF foreign gene expression vector and a virus-induced gene silencing (VIGS) vector as a biological agent for the control of B. cinerea.
- Published
- 2022
- Full Text
- View/download PDF
3. Tpc1 is an important Zn(II)2Cys6 transcriptional regulator required for polarized growth and virulence in the rice blast fungus.
- Author
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Rita Galhano, Adriana Illana, Lauren S Ryder, Julio Rodríguez-Romero, Marie Demuez, Muhammad Badaruddin, Ana Lilia Martinez-Rocha, Darren M Soanes, David J Studholme, Nicholas J Talbot, and Ane Sesma
- Subjects
Immunologic diseases. Allergy ,RC581-607 ,Biology (General) ,QH301-705.5 - Abstract
The establishment of polarity is a critical process in pathogenic fungi, mediating infection-related morphogenesis and host tissue invasion. Here, we report the identification of TPC1 (Transcription factor for Polarity Control 1), which regulates invasive polarized growth in the rice blast fungus Magnaporthe oryzae. TPC1 encodes a putative transcription factor of the fungal Zn(II)2Cys6 family, exclusive to filamentous fungi. Tpc1-deficient mutants show severe defects in conidiogenesis, infection-associated autophagy, glycogen and lipid metabolism, and plant tissue colonisation. By tracking actin-binding proteins, septin-5 and autophagosome components, we show that Tpc1 regulates cytoskeletal dynamics and infection-associated autophagy during appressorium-mediated plant penetration. We found that Tpc1 interacts with Mst12 and modulates its DNA-binding activity, while Tpc1 nuclear localisation also depends on the MAP kinase Pmk1, consistent with the involvement of Tpc1 in this signalling pathway, which is critical for appressorium development. Importantly, Tpc1 directly regulates NOXD expression, the p22phox subunit of the fungal NADPH oxidase complex via an interaction with Mst12. Tpc1 therefore controls spatial and temporal regulation of cortical F-actin through regulation of the NADPH oxidase complex during appressorium re-polarisation. Consequently, Tpc1 is a core developmental regulator in filamentous fungi, linking the regulated synthesis of reactive oxygen species and the Pmk1 pathway, with polarity control during host invasion.
- Published
- 2017
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- View/download PDF
4. A relationship between carotenoid accumulation and the distribution of species of the fungus Neurospora in Spain.
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Eva M Luque, Gabriel Gutiérrez, Laura Navarro-Sampedro, María Olmedo, Julio Rodríguez-Romero, Carmen Ruger-Herreros, Víctor G Tagua, and Luis M Corrochano
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Medicine ,Science - Abstract
The ascomycete fungus Neurospora is present in many parts of the world, in particular in tropical and subtropical areas, where it is found growing on recently burned vegetation. We have sampled the Neurospora population across Spain. The sampling sites were located in the region of Galicia (northwestern corner of the Iberian peninsula), the province of Cáceres, the city of Seville, and the two major islands of the Canary Islands archipelago (Tenerife and Gran Canaria, west coast of Africa). The sites covered a latitude interval between 27.88° and 42.74°. We have identified wild-type strains of N. discreta, N. tetrasperma, N. crassa, and N. sitophila and the frequency of each species varied from site to site. It has been shown that after exposure to light Neurospora accumulates the orange carotenoid neurosporaxanthin, presumably for protection from UV radiation. We have found that each Neurospora species accumulates a different amount of carotenoids after exposure to light, but these differences did not correlate with the expression of the carotenogenic genes al-1 or al-2. The accumulation of carotenoids in Neurospora shows a correlation with latitude, as Neurospora strains isolated from lower latitudes accumulate more carotenoids than strains isolated from higher latitudes. Since regions of low latitude receive high UV irradiation we propose that the increased carotenoid accumulation may protect Neurospora from high UV exposure. In support of this hypothesis, we have found that N. crassa, the species that accumulates more carotenoids, is more resistant to UV radiation than N. discreta or N. tetrasperma. The photoprotection provided by carotenoids and the capability to accumulate different amounts of carotenoids may be responsible, at least in part, for the distribution of Neurospora species that we have observed across a range of latitudes.
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- 2012
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5. Molecular Data of a Novel Penoulivirus Associated with the Plant-Pathogenic Fungus Erysiphe necator
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Rocío Galán-Cubero, Laura Córdoba, Julio Rodríguez-Romero, Marco Chiapello, Massimo Turina, María A. Ayllón, European Commission, Galán-Cubero, Rocío, Rodríguez-Romero, Julio, Chiapello, Marco, Turina, Massimo, Ayllón, María A, Galán-Cubero, Rocío [0000-0001-5157-0562], Rodríguez-Romero, Julio [0000-0001-8304-4014], Chiapello, Marco [0000-0001-7768-3047], Turina, Massimo [0000-0002-9659-9470], and Ayllón, María A [0000-0001-7893-6106]
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Powdery mildew ,Virology ,Penoulivirus ,Grapevine ,Plant Science ,Erysiphe necator ,Ambisense genome ,Agronomy and Crop Science ,Fungal pathogens ,Botourmiaviridae - Abstract
5 Pág., Project VIROPLANT, European Union's Horizon 2020 Research and Innovation Programme Grant/Award Number: 773567
- Published
- 2022
6. Molecular Data of a Novel Penoulivirus Associated with the Plant-Pathogenic Fungus
- Author
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Rocío, Galán-Cubero, Laura, Córdoba, Julio, Rodríguez-Romero, Marco, Chiapello, Massimo, Turina, and María A, Ayllón
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Ascomycota ,Vitis ,Erysiphe ,Plant Diseases - Published
- 2022
7. Putative new plant viruses associated withPlasmopara viticola‐infected grapevine samples
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Massimo Turina, Luca Nerva, Marco Chiapello, Marco Forgia, Walter Chitarra, María A. Ayllón, and Julio Rodríguez-Romero
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Ilarvirus ,jivivirus ,biology ,fungi ,food and beverages ,biology.organism_classification ,oomycetes ,Virology ,grapevine ,Plasmopara viticola ,Plant virus ,ilarvirus ,Agronomy and Crop Science ,coguvirus - Abstract
In this study, we analysed a total of 16 libraries from over 150 grapevine leaf and grape samples infected with Plasmopara viticola (downy mildew of grapevine) to characterise the virome associated to this oomycete. Samples were collected in five distinct regions in Italy and in four different regions in Spain, representative of different pedoclimatic conditions and different grapevine cultivars during 2018 growing season. Due to the metagenomics nature of the samples (containing at least both downy mildew hyphae and spores, and grapevine cells residues), we were able to assemble several plant viruses and a few possible novel plant virus genomes with our in silico analysis. We detected several plant virus variants already reported in grapevine, and a putative new ilarvirus previously unreported in grapevine. Furthermore, we characterised three new phenui-like viruses (in the order Bunyavirales), one of which shares some commonalities with plant coguviruses. Finally, we report a new strict association of three viral segments (one flavi-like and two virga-like) that we propose to be a new virus taxon named jivivirus.
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- 2020
8. Virulence- and signaling-associated genes display a preference for long 3′UTRs during rice infection and metabolic stress in the rice blast fungus
- Author
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Víctor Ortega-Campayo, Marie Demuez, Marco Marconi, Julio Rodríguez-Romero, Mark Wilkinson, and Ane Sesma
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0106 biological sciences ,0301 basic medicine ,Transposable element ,RNA, Untranslated ,Polyadenylation ,Physiology ,Virulence ,Plant Science ,Biology ,01 natural sciences ,Genome ,Fungal Proteins ,03 medical and health sciences ,Stress, Physiological ,Gene Expression Regulation, Fungal ,Gene expression ,3' Untranslated Regions ,Gene ,Pathogen ,Plant Diseases ,Genetics ,Messenger RNA ,Oryza ,Carbon ,Magnaporthe ,030104 developmental biology ,Host-Pathogen Interactions ,Mutation ,DNA Transposable Elements ,Poly A ,Signal Transduction ,010606 plant biology & botany - Abstract
Generation of mRNA isoforms by alternative polyadenylation (APA) and their involvement in regulation of fungal cellular processes, including virulence, remains elusive. Here, we investigated genome-wide polyadenylation site (PAS) selection in the rice blast fungus to understand how APA regulates pathogenicity. More than half of Magnaporthe oryzae transcripts undergo APA and show novel motifs in their PAS region. Transcripts with shorter 3'UTRs are more stable and abundant in polysomal fractions, suggesting they are being translated more efficiently. Importantly, rice colonization increases the use of distal PASs of pathogenicity genes, especially those participating in signalling pathways like 14-3-3B, whose long 3'UTR is required for infection. Cleavage factor I (CFI) Rbp35 regulates expression and distal PAS selection of virulence and signalling-associated genes, tRNAs and transposable elements, pointing its potential to drive genomic rearrangements and pathogen evolution. We propose a noncanonical PAS selection mechanism for Rbp35 that recognizes UGUAH, unlike humans, without CFI25. Our results showed that APA controls turnover and translation of transcripts involved in fungal growth and environmental adaptation. Furthermore, these data provide useful information for enhancing genome annotations and for cross-species comparisons of PASs and PAS usage within the fungal kingdom and the tree of life.
- Published
- 2018
9. Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae
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Mark Wilkinson, Marco Marconi, Ping Xu, Tamas Dalmay, Ane Sesma, Adriana Illana, Julio Rodríguez-Romero, and María A. Ayllón
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0301 basic medicine ,Untranslated region ,viruses ,Molecular Sequence Data ,030106 microbiology ,Genome, Viral ,Fungal Viruses ,Virus ,Ourmiavirus ,Open Reading Frames ,Viral Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,Rapid amplification of cDNA ends ,Virology ,Plant virus ,RNA polymerase ,RNA Viruses ,Amino Acid Sequence ,3' Untranslated Regions ,Phylogeny ,Plant Diseases ,Genetics ,biology ,RNA ,Oryza ,General Medicine ,biology.organism_classification ,Magnaporthe ,030104 developmental biology ,chemistry ,Mycovirus ,RNA, Viral ,Sequence Alignment - Abstract
In this study we characterize a novel positive and single stranded RNA (ssRNA) mycovirus isolated from the rice field isolate of Magnaporthe oryzae Guy11. The ssRNA contains a single open reading frame (ORF) of 2,373 nucleotides in length and encodes an RNA-dependent RNA polymerase (RdRp) closely related to ourmiaviruses (plant viruses) and ourmia-like mycoviruses. Accordingly, we name this virus Magnaporthe oryzae ourmia-like virus 1 (MOLV1). Although phylogenetic analysis suggests that MOLV1 is closely related to ourmia and ourmia-like viruses, it has some features never reported before within the Ourmiavirus genus. 3' RLM-RACE (RNA ligase-mediated rapid amplification of cDNA ends) and extension poly(A) tests (ePAT) suggest that the MOLV1 genome contains a poly(A) tail whereas the three cytosine and the three guanine residues present in 5' and 3' untranslated regions (UTRs) of ourmia viruses are not observed in the MOLV1 sequence. The discovery of this novel viral genome supports the hypothesis that plant pathogenic fungi may have acquired this type of viruses from their host plants.
- Published
- 2016
10. Inferring roles in defense from metabolic allocation of rice diterpenoids
- Author
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Benjamin Brown, Zhiqiang Pan, Julio Rodríguez-Romero, Bo Liu, Aileen Berasategui, Scott R. Baerson, Dangping Luo, Ane Sesma, Zhaohu Li, Riqing Li, Reuben J. Peters, Bing Yang, Juan Zhang, Xuan Lu, Jonathan Gershenzon, and Meimei Xu
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0301 basic medicine ,Rhizosphere ,Oryza sativa ,biology ,food and beverages ,Oryza ,Cell Biology ,Plant Science ,Plant disease resistance ,biology.organism_classification ,Microbiology ,Magnaporthe ,03 medical and health sciences ,030104 developmental biology ,Xanthomonas oryzae ,Gene Expression Regulation, Plant ,Blight ,Arabidopsis thaliana ,Diterpenes ,Pathogen ,Gene ,Research Articles ,Disease Resistance ,Plant Diseases - Abstract
Among their responses to microbial infection, plants deploy an arsenal of natural antibiotic products. These historically have been identified on the basis of their antibiotic activity in vitro, which leaves open the question of their relevance to defense in planta. The vast majority of such natural products from the important crop plant rice (Oryza sativa) are diterpenoids whose biosynthesis proceeds via either ent- or syn- copalyl diphosphate (CPP) intermediates, and which were isolated on the basis of their antibiotic activity against the fungal blast pathogen Magnaporthe oryzae. However, rice plants in which the gene for the syn-CPP synthase Os-CPS4 is knocked-out do not exhibit increased susceptibility to M. oryzae. Here we show that knocking-out or knocking-down Os-CPS4 actually decreases susceptibility to the bacterial leaf blight pathogen Xanthomonas oryzae. By contrast, genetic manipulation of the gene for the ent-CPP synthase Os-CPS2 alters susceptibility to both M. oryzae and X. oryzae. Despite the secretion of diterpenoids dependent on Os-CPS2 or Os-CPS4 from roots, neither knock-out exhibited significant changes in the composition of their rhizosphere bacterial communities. Nevertheless, rice plants allocate substantial metabolic resources towards syn- and ent-CPP derived diterpenoids upon infection/induction. Further investigation revealed that Os-CPS4 plays a role in fungal non-host disease resistance. Thus, examination of metabolic allocation provides important clues into physiological function.
- Published
- 2018
11. Genome-wide polyadenylation site mapping datasets in the rice blast fungus Magnaporthe oryzae
- Author
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Ane Sesma, Mark Wilkinson, Marco Marconi, María Lourdes Rosano González, and Julio Rodríguez-Romero
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0301 basic medicine ,Statistics and Probability ,Data Descriptor ,Polyadenylation ,Sequence analysis ,Virulence ,Fungus ,Library and Information Sciences ,Genome informatics ,Genome ,Education ,03 medical and health sciences ,Polyadenylation site ,Plant Diseases ,Genetics ,Regulation of gene expression ,biology ,Sequence Analysis, RNA ,RNA ,Chromosome Mapping ,food and beverages ,RNA sequencing ,Oryza ,biology.organism_classification ,RNA modification ,Computer Science Applications ,Gene regulation ,Magnaporthe ,030104 developmental biology ,Statistics, Probability and Uncertainty ,Genome, Fungal ,Information Systems - Abstract
Polyadenylation plays an important role in gene regulation, thus affecting a wide variety of biological processes. In the rice blast fungus Magnaporthe oryzae the cleavage factor I protein Rpb35 is required for pre-mRNA polyadenylation and fungal virulence. Here we present the bioinformatic approach and output data related to a global survey of polyadenylation site usage in M. oryzae wild-type and Δrbp35 strains under a variety of nutrient conditions, some of which simulate the conditions experienced by the fungus during part of its infection cycle., Scientific Data, 5, ISSN:2052-4463
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- 2018
- Full Text
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12. Light-dependent gene activation inAspergillus nidulansis strictly dependent on phytochrome and involves the interplay of phytochrome and white collar-regulated histone H3 acetylation
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Maren Hedtke, Stefan Rauscher, Julio Rodríguez-Romero, Julian Röhrig, Zhenzhong Yu, and Reinhard Fischer
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Regulation of gene expression ,biology ,Phytochrome ,Microbiology ,Molecular biology ,Cell biology ,Histone H3 ,Histone ,Acetylation ,biology.protein ,Histone deacetylase ,Histone H3 acetylation ,Molecular Biology ,Transcription factor - Abstract
The ability for light sensing is found from bacteria to humans but relies only on a small number of evolutionarily conserved photoreceptors. A large number of fungi react to light, mostly to blue light. Aspergillus nidulans also responds to red light using a phytochrome light sensor, FphA, for the control of hundreds of light-regulated genes. Here, we show that photoinduction of one light-induced gene, ccgA, occurs mainly through red light. Induction strictly depends on phytochrome and its histidine-kinase activity. Full light activation also depends on the Velvet protein, VeA. This putative transcription factor binds to the ccgA promoter in an fphA-dependent manner but independent of light. In addition, the blue light receptor LreA binds to the ccgA promoter in the dark but is released after blue or red light illumination and together with FphA modulates gene expression through histone H3 modification. LreA interacts with the acetyltransferase GcnE and with the histone deacetylase HdaA. ccgA induction is correlated to an increase of the acetylation level of lysine 9 in histone H3. Our results suggest regulation of red light-induced genes at the transcriptional level involving transcription factor(s) and epigenetic control through modulation of the acetylation level of histone H3.
- Published
- 2015
13. Multilayer regulatory mechanisms control cleavage factor I proteins in filamentous fungi
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Julio Rodríguez-Romero, Emilio Bueno, Marina Franceschetti, and Ane Sesma
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Magnaporthe ,Polyadenylation ,Complement factor I ,Biology ,Fungal Proteins ,Open Reading Frames ,03 medical and health sciences ,0302 clinical medicine ,Protein structure ,Gene Expression Regulation, Fungal ,Upstream open reading frame ,Genetics ,Plant Diseases ,030304 developmental biology ,mRNA Cleavage and Polyadenylation Factors ,Regulation of gene expression ,0303 health sciences ,Fungal protein ,TOR Serine-Threonine Kinases ,Gene regulation, Chromatin and Epigenetics ,biology.organism_classification ,Protein Structure, Tertiary ,Cell biology ,Proteolysis ,RNA splicing ,5' Untranslated Regions ,030217 neurology & neurosurgery - Abstract
Cleavage factor I (CFI) proteins are core components of the polyadenylation machinery that can regulate several steps of mRNA life cycle, including alternative polyadenylation, splicing, export and decay. Here, we describe the regulatory mechanisms that control two fungal CFI protein classes in Magnaporthe oryzae: Rbp35/CfI25 complex and Hrp1. Using mutational, genetic and biochemical studies we demonstrate that cellular concentration of CFI mRNAs is a limited indicator of their protein abundance. Our results suggest that several post-transcriptional mechanisms regulate Rbp35/CfI25 complex and Hrp1 in the rice blast fungus, some of which are also conserved in other ascomycetes. With respect to Rbp35, these include C-terminal processing, RGG-dependent localization and cleavage, C-terminal autoregulatory domain and regulation by an upstream open reading frame of Rbp35-dependent TOR signalling pathway. Our proteomic analyses suggest that Rbp35 regulates the levels of proteins involved in melanin and phenylpropanoids synthesis, among others. The drastic reduction of fungal CFI proteins in carbon-starved cells suggests that the pre-mRNA processing pathway is altered. Our findings uncover broad and multilayer regulatory mechanisms controlling fungal polyadenylation factors, which have profound implications in pre-mRNA maturation. This area of research offers new avenues for fungicide design by targeting fungal-specific proteins that globally affect thousands of mRNAs.
- Published
- 2014
14. Regulation of Conidiation by Light in Aspergillus nidulans
- Author
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María Teresa Camacho Olmedo, David Cánovas, Luis M. Corrochano, Raul Fernández-Barranco, Carmen Ruger-Herreros, Reinhard Fischer, and Julio Rodríguez-Romero
- Subjects
Transcriptional Activation ,Genetics ,Fungal protein ,Light ,Phytochrome ,biology ,Regulator ,Conidiation ,Spores, Fungal ,Investigations ,Photoreceptors, Microbial ,biology.organism_classification ,Aspergillus nidulans ,Fungal Proteins ,Gene Expression Regulation, Fungal ,Reproduction, Asexual ,Genome, Fungal ,Gene ,Mycelium ,Regulator gene - Abstract
Light regulates several aspects of the biology of many organisms, including the balance between asexual and sexual development in some fungi. To understand how light regulates fungal development at the molecular level we have used Aspergillus nidulans as a model. We have performed a genome-wide expression analysis that has allowed us to identify >400 genes upregulated and >100 genes downregulated by light in developmentally competent mycelium. Among the upregulated genes were genes required for the regulation of asexual development, one of the major biological responses to light in A. nidulans, which is a pathway controlled by the master regulatory gene brlA. The expression of brlA, like conidiation, is induced by light. A detailed analysis of brlA light regulation revealed increased expression after short exposures with a maximum after 60 min of light followed by photoadaptation with longer light exposures. In addition to brlA, genes flbA–C and fluG are also light regulated, and flbA–C are required for the correct light-dependent regulation of the upstream regulator fluG. We have found that light induction of brlA required the photoreceptor complex composed of a phytochrome FphA, and the white-collar homologs LreA and LreB, and the fluffy genes flbA–C. We propose that the activation of regulatory genes by light is the key event in the activation of asexual development by light in A. nidulans.
- Published
- 2011
15. Spotlight on Aspergillus nidulans photosensory systems
- Author
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Gerhard H. Braus, Özgür Bayram, Reinhard Fischer, and Julio Rodríguez-Romero
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0303 health sciences ,Opsin ,Light ,Mycelium ,biology ,Phytochrome ,030306 microbiology ,biology.organism_classification ,Microbiology ,Aspergillus nidulans ,Cell biology ,Fungal Proteins ,03 medical and health sciences ,Cryptochrome ,Gene Expression Regulation, Fungal ,Botany ,Genetics ,Signal transduction ,Photolyase ,Secondary metabolism ,Signal Transduction ,Transcription Factors ,030304 developmental biology - Abstract
Aspergilli are ubiquitous soil-borne fungi growing within or on the surface of numerous organic substrates. Growth within a substrate or growth on the surface correlates to different growth conditions for the hyphae due to significant changes in oxygen or reactive oxygen species levels and variations in humidity or temperature. The production of air-borne spores is supported by the substrate-air interphase and also requires a sensing system to adapt appropriately. Here we focus on light as important parameter for the mycelium to discriminate between different habitats. The fungal 'eye' includes several light sensors which react to a broad plethora of wavelengths. Aspergillus nidulans light receptors comprise a phytochrome for red-light sensing, white collar-like blue-light signaling proteins, a putative green-light sensing opsin and a cryptochrome/photolyase as distinct sensory systems. Red- and blue-light receptors are assembled into a light-sensing protein complex. Light receptors transmit their signal to a number of other regulatory proteins including a bridging protein, VeA, as part of a trimeric complex. VeA plays a central role in the balance of asexual and sexual development and in the coordination of morphogenesis and secondary metabolism.
- Published
- 2010
16. Fungi, Hidden in Soil or Up in the Air: Light Makes a Difference
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Reinhard Fischer, Sylvia Müller, Christian Kastner, Maren Hedtke, and Julio Rodríguez-Romero
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Light Signal Transduction ,Light ,Hypha ,Phytochrome ,biology ,Fungi ,Flavin group ,Fungi imperfecti ,Chromophore ,Photoreceptors, Microbial ,biology.organism_classification ,Microbiology ,Fungal Proteins ,Botany ,Secondary metabolism ,Bacteria ,Function (biology) - Abstract
Light is one of the most important environmental factors for orientation of almost all organisms on Earth. Whereas light sensing is of crucial importance in plants to optimize light-dependent energy conservation, in nonphotosynthetic organisms, the synchronization of biological clocks to the length of a day is an important function. Filamentous fungi may use the light signal as an indicator for the exposure of hyphae to air and adapt their physiology to this situation or induce morphogenetic pathways. Although a yes/no decision appears to be sufficient for the light-sensing function in fungi, most species apply a number of different, wavelength-specific receptors. The core of all receptor types is a chromophore, a low-molecular-weight organic molecule, such as flavin, retinal, or linear tetrapyrrols for blue-, green-, or red-light sensing, respectively. Whereas the blue-light response in fungi is one of the best-studied light responses, all other light-sensing mechanisms are less well studied or largely unknown. The discovery of phytochrome in bacteria and fungi in recent years not only advanced the scientific field significantly, but also had great impact on our view of the evolution of phytochrome-like photoreceptors.
- Published
- 2010
17. Phycomyces MADB interacts with MADA to form the primary photoreceptor complex for fungal phototropism
- Author
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Luis M. Corrochano, John M. Christie, Julio Rodríguez-Romero, Arturo P. Eslava, Catalina Sanz, Alexander Idnurm, Joseph Heitman, and Universidad de Sevilla. Departamento de Genética
- Subjects
Transcription, Genetic ,White Collar-1 ,Molecular Sequence Data ,Color ,Transcription factor complex ,White Collar protein ,Neurospora ,Fungal Proteins ,Phycomyces ,Photoreceptor Cells ,Phototropism ,LOV domain ,Phylogeny ,Genetics ,Fungal protein ,Multidisciplinary ,Base Sequence ,zinc finger ,biology ,gene duplication ,Fungal genetics ,Biological Sciences ,biology.organism_classification ,blue light ,Cell biology ,DNA-Binding Proteins ,Alternative Splicing ,Mutation ,Phycomyces blakesleeanus ,Genome, Fungal ,Sequence Alignment ,Transcription Factors - Abstract
The fungus Phycomyces blakesleeanus reacts to environmental signals, including light, gravity, touch, and the presence of nearby objects, by changing the speed and direction of growth of its fruiting body (sporangiophore). Phototropism, growth toward light, shares many features in fungi and plants but the molecular mechanisms remain to be fully elucidated. Phycomyces mutants with altered phototropism were isolated ≈40 years ago and found to have mutations in the mad genes. All of the responses to light in Phycomyces require the products of the madA and madB genes. We showed that madA encodes a protein similar to the Neurospora blue-light photoreceptor, zinc-finger protein WC-1. We show here that madB encodes a protein similar to the Neurospora zinc-finger protein WC-2. MADA and MADB interact to form a complex in yeast 2-hybrid assays and when coexpressed in E. coli , providing evidence that phototropism and other responses to light are mediated by a photoresponsive transcription factor complex. The Phycomyces genome contains 3 genes similar to wc-1 , and 4 genes similar to wc-2 , many of which are regulated by light in a madA or madB dependent manner. We did not detect any interactions between additional WC proteins in yeast 2-hybrid assays, which suggest that MADA and MADB form the major photoreceptor complex in Phycomyces . However, the presence of multiple wc genes in Phycomyces may enable perception across a broad range of light intensities, and may provide specialized photoreceptors for distinct photoresponses.
- Published
- 2009
18. Light-dependent gene activation in Aspergillus nidulans is strictly dependent on phytochrome and involves the interplay of phytochrome and white collar-regulated histone H3 acetylation
- Author
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Maren, Hedtke, Stefan, Rauscher, Julian, Röhrig, Julio, Rodríguez-Romero, Zhenzhong, Yu, and Reinhard, Fischer
- Subjects
Fungal Proteins ,Histones ,Light ,Gene Expression Regulation, Fungal ,Acetylation ,Phytochrome ,Photoreceptors, Microbial ,Aspergillus nidulans ,Transcription Factors - Abstract
The ability for light sensing is found from bacteria to humans but relies only on a small number of evolutionarily conserved photoreceptors. A large number of fungi react to light, mostly to blue light. Aspergillus nidulans also responds to red light using a phytochrome light sensor, FphA, for the control of hundreds of light-regulated genes. Here, we show that photoinduction of one light-induced gene, ccgA, occurs mainly through red light. Induction strictly depends on phytochrome and its histidine-kinase activity. Full light activation also depends on the Velvet protein, VeA. This putative transcription factor binds to the ccgA promoter in an fphA-dependent manner but independent of light. In addition, the blue light receptor LreA binds to the ccgA promoter in the dark but is released after blue or red light illumination and together with FphA modulates gene expression through histone H3 modification. LreA interacts with the acetyltransferase GcnE and with the histone deacetylase HdaA. ccgA induction is correlated to an increase of the acetylation level of lysine 9 in histone H3. Our results suggest regulation of red light-induced genes at the transcriptional level involving transcription factor(s) and epigenetic control through modulation of the acetylation level of histone H3.
- Published
- 2015
19. The Phycomyces madA gene encodes a blue-light photoreceptor for phototropism and other light responses
- Author
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Alexander Idnurm, Enrique A. Iturriaga, Catalina Sanz, Julio Rodríguez-Romero, Arturo P. Eslava, Luis M. Corrochano, Joseph Heitman, and Universidad de Sevilla. Departamento de Genética
- Subjects
Phototropin ,Light ,Transcription, Genetic ,White Collar-1 ,Molecular Sequence Data ,Mutant ,Fungal Proteins ,White Collar 1 ,Cryptochrome ,Genes, Duplicate ,Phycomyces ,evolution ,Photoreceptor Cells ,Phototropism ,Max Delbrück ,Genetics ,photosensor ,Fungal protein ,Multidisciplinary ,Base Sequence ,Flavoproteins ,biology ,Biological Sciences ,biology.organism_classification ,Cell biology ,Cryptochromes ,DNA-Binding Proteins ,Mutation ,Phycomyces blakesleeanus ,light ,oxygen ,or voltage domain ,Transcription Factors - Abstract
Phycomyces blakesleeanus is a filamentous zygomycete fungus that produces striking elongated single cells that extend up to 10 cm into the air, with each such sporangiophore supporting a sphere containing the spores for dispersal. This organism has served as a model for the detection of environmental signals as diverse as light, chemicals, touch, wind, gravity, and adjacent objects. In particular, sporangiophore growth is regulated by light, and it exhibits phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses. The Phycomyces madA mutants were first isolated more than 40 years ago, and they exhibit reduced sensitivity to light. Here, we identify two (duplicated) homologs in the White Collar 1 family of blue-light photoreceptors in Phycomyces . We describe that the madA mutant strains contain point mutations in one of these genes and that these mutations cosegregate with a defect in phototropism after genetic crosses. Thus, the phototropic responses of fungi through madA and plants through phototropin rely on diverse proteins; however, these proteins share a conserved flavin-binding domain for photon detection.
- Published
- 2006
20. Flavin und lineare Tetrapyrrole als Lichtsensoren in Pilzen
- Author
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Julio Rodríguez-Romero and Reinhard Fischer
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Turn (biochemistry) ,Primary (chemistry) ,Biochemistry ,Stereochemistry ,Chemistry ,Pharmacology toxicology ,Moiety ,Light sensing ,Flavin group ,Molecular Biology ,Biotechnology ,Organic molecules - Abstract
Light sensing in organisms is conferred by a small number of light-absorbing, organic molecules. The primary light reaction is transmitted to the protein moiety, which in turn triggers cellular reactions. In filamentous fungi a large number of different morphogenetic and physiological processes is controlled by light; flavine- and tetrapyrrol-containing photoreceptors are main players.
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- 2012
21. Transcriptional changes in the transition from vegetative cells to asexual development in the model fungus Aspergillus nidulans
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Unai Ugalde, Aitor Garzia, Eduardo A. Espeso, Julio Rodríguez-Romero, Reinhard Fischer, and Oier Etxebeste
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Transcription, Genetic ,MAP Kinase Signaling System ,Genes, Fungal ,Morphogenesis ,mRNA sequencing ,Microbiology ,Aspergillus nidulans ,Fungal Proteins ,Transcriptome ,Cell Wall ,Stress, Physiological ,Gene Expression Regulation, Fungal ,Reproduction, Asexual ,Gene expression ,Transcriptional regulation ,Asexual development ,Molecular Biology ,Transcription factor ,Gene ,Genetics ,biology ,Biological Transport ,Articles ,General Medicine ,biology.organism_classification ,MRNA Sequencing ,Multigene Family ,Polyketide synthase ,Chromosomes, Fungal ,Secondary metabolism ,Oxidation-Reduction ,Metabolic Networks and Pathways - Abstract
32 p.-6 fig.-2 tab., Morphogenesis encompasses programmed changes in gene expression that lead to the development of specialized cell types. In the model fungus Aspergillus nidulans, asexual development involves the formation of characteristic cell types, collectively known as the conidiophore. With the aim of determining the transcriptional changes that occur upon induction of asexual development, we have applied massive mRNA sequencing to compare the expression pattern of 19-h-old submerged vegetative cells (hyphae) with that of similar hyphae after exposure to the air for 5 h. We found that the expression of 2,222 (20.3%) of the predicted 10,943 A. nidulans transcripts was significantly modified after air exposure, 2,035 being downregulated and 187 upregulated. The activation during this transition of genes that belong specifically to the asexual developmental pathway was confirmed. Another remarkable quantitative change occurred in the expression of genes involved in carbon or nitrogen primary metabolism. Genes participating in polar growth or sexual development were transcriptionally repressed, as were those belonging to the HogA/SakA stress response mitogen-activated protein (MAP) kinase pathway. We also identified significant expression changes in several genes purportedly involved in redox balance, transmembrane transport, secondary metabolite production, or transcriptional regulation, mainly binuclear-zinc cluster transcription factors. Genes coding for these four activities were usually grouped in metabolic clusters, which may bring regulatory implications for the induction of asexual development. These results provide a blueprint for further stage-specific gene expression studies during conidiophore development. © 2013, American Society for Microbiology. All Rights Reserved., This work has been supported by the Basque Government through grant (IT393-10) and the Ministerio de Economía y Competitividad (formerly Ministerio de Ciencia e Innovación) through grant (BFU2010-17528) to U.U., grant (BFU2009- 08701) to E.A.E. and grants from the German Science Foundation (DFG Fi 459), the Fonds der Chemischen Industrie, the Baden-Württemberg Stiftung, and the Centre for Functional Nanostructures to R.F. A. G. is now a contract researcher from The University of The Basque Country. J.R. was a postdoctoral fellow of the Ministerio de Ciencia e Innovación. O.E is a contract researcher associated to grant BFU2010- 17528.
- Published
- 2013
22. Major Plant Pathogens of the Magnaporthaceae Family
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Adriana Illana, Ane Sesma, and Julio Rodríguez-Romero
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Colonisation ,Magnaporthe poae ,biology ,Magnaporthaceae ,fungi ,Botany ,Root pathogens ,food and beverages ,Leaf spot ,Germ tube ,Fungus ,biology.organism_classification ,Genetic pathways - Abstract
The Magnaporthaceae family includes fungal species that cause devastating diseases on cereals and grasses. The causal agent of take-all disease of wheat Gaeumannomyces graminis, the rice blast fungus Magnaporthe oryzae, and Magnaporthe poae which causes the grey leaf spot on turfgrasses, belong to this family. M. poae and G. graminis are considered root pathogens, whereas M. oryzae is found on aerial plant tissues. Remarkably, M. oryzae can also infect roots and distinct mechanisms control its root infection ability compared to leaf colonisation. Since G. graminis and M. poae are genetically intractable, M. oryzae underground infection process can be used to dissect genetic pathways and molecular mechanisms underlying root infection in other members of Magnaporthaceae. Interestingly, M. oryzae root infection process also shares similarities with ancient mycorrhizal associations. Here, we highlight the latest advances on the mechanisms regulating pathogenicity in these economically significant plant pathogens.
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- 2013
23. A relationship between carotenoid accumulation and the distribution of species of the fungus Neurospora in Spain
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María Teresa Camacho Olmedo, Laura Navarro-Sampedro, Julio Rodríguez-Romero, Gabriel Gutiérrez, Carmen Ruger-Herreros, Víctor G. Tagua, Luis M. Corrochano, Eva M. Luque, and Universidad de Sevilla. Departamento de Genética
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Unclassified drug ,lcsh:Medicine ,Yeast and Fungal Models ,Biochemistry ,Radiation Tolerance ,DNA, Fungal ,lcsh:Science ,Carotenoid ,Phylogeny ,chemistry.chemical_classification ,education.field_of_study ,Multidisciplinary ,Geography ,biology ,Physics ,Electromagnetic Radiation ,Messenger RNA ,Fungal genetics ,Pigment ,Research Article ,Neurosporaxanthin ,Fungal RNA ,Ultraviolet Rays ,Genes, Fungal ,Population ,Mycology ,Subtropics ,Real-Time Polymerase Chain Reaction ,Microbiology ,Neurospora ,Neurospora crassa ,Model Organisms ,Botany ,RNA, Messenger ,education ,Biology ,Population Biology ,lcsh:R ,fungi ,Crassa ,RNA, Fungal ,Pigments, Biological ,biology.organism_classification ,Carotenoids ,Metabolism ,Fungal DNA ,chemistry ,Spain ,Photoprotection ,lcsh:Q - Abstract
The ascomycete fungus Neurospora is present in many parts of the world, in particular in tropical and subtropical areas, where it is found growing on recently burned vegetation. We have sampled the Neurospora population across Spain. The sampling sites were located in the region of Galicia (northwestern corner of the Iberian peninsula), the province of Ca´ceres, the city of Seville, and the two major islands of the Canary Islands archipelago (Tenerife and Gran Canaria, west coast of Africa). The sites covered a latitude interval between 27.88u and 42.74u. We have identified wild-type strains of N. discreta, N. tetrasperma, N. crassa, and N. sitophila and the frequency of each species varied from site to site. It has been shown that after exposure to light Neurospora accumulates the orange carotenoid neurosporaxanthin, presumably for protection from UV radiation. We have found that each Neurospora species accumulates a different amount of carotenoids after exposure to light, but these differences did not correlate with the expression of the carotenogenic genes al-1 or al-2. The accumulation of carotenoids in Neurospora shows a correlation with latitude, as Neurospora strains isolated from lower latitudes accumulate more carotenoids than strains isolated from higher latitudes. Since regions of low latitude receive high UV irradiation we propose that the increased carotenoid accumulation may protect Neurospora from high UV exposure. In support of this hypothesis, we have found that N. crassa, the species that accumulates more carotenoids, is more resistant to UV radiation than N. discreta or N. tetrasperma. The photoprotection provided by carotenoids and the capability to accumulate different amounts of carotenoids may be responsible, at least in part, for the distribution of Neurospora species that we have observed across a range of latitudes.
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- 2012
24. Regulation by blue light and heat shock of gene transcription in the fungus Phycomyces: proteins required for photoinduction and mechanism for adaptation to light
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Julio Rodríguez-Romero and Luis M. Corrochano
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Light ,Transcription, Genetic ,Fungus ,Regulatory Sequences, Nucleic Acid ,Microbiology ,DNA sequencing ,Fungal Proteins ,chemistry.chemical_compound ,Transcription (biology) ,Phycomyces ,Gene Expression Regulation, Fungal ,Photoreceptor Cells ,Cloning, Molecular ,Phototropism ,Promoter Regions, Genetic ,Molecular Biology ,Gene ,Heat-Shock Proteins ,Genetics ,biology ,Zinc Fingers ,biology.organism_classification ,Cell biology ,chemistry ,Phycomyces blakesleeanus ,Signal transduction ,Transcription Initiation Site ,DNA ,Heat-Shock Response - Abstract
Summary The gene hspA for the heat-shock protein HSP100 is induced by blue light and heat shock in the zygomycete fungus Phycomyces blakesleeanus. We have investigated the molecular details of the regulation of hspA gene transcription. We have cloned 1.9 kb of hspA upstream DNA sequence and identified many DNA segments possibly involved in heat-shock and blue-light regulation. We have identified several gene products required for hspA photoactivation and found that they are also required for mycelial photoresponses, a suggestion for a common signal transduction pathway. In addition, we have found that beta-carotene, or a chemical derivative, is required for hspA gene photoactivation. The activation of hspA after blue light-exposure or a heat shock is transient, suggesting the adaptation to the stimulus. The adaptation of hspA photoactivation seems to be the result of a novel mechanism causing a light-dependent loss of gene transcription. We propose that a reduction in the amount of MADA, a putative flavin-binding zinc-finger protein, in light-exposed mycelia may cause a reduced hspA photoactivation, providing a simple explanation for adaptation to light.
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- 2006
25. The gene for the heat-shock protein HSP100 is induced by blue light and heat-shock in the fungus Phycomyces blakesleeanus
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Luis M. Corrochano and Julio Rodríguez-Romero
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Hot Temperature ,Light ,Transcription, Genetic ,Photochemistry ,Molecular Sequence Data ,Gene product ,Bacterial Proteins ,Transcription (biology) ,Phycomyces ,Heat shock protein ,Gene Expression Regulation, Fungal ,Genetics ,Amino Acid Sequence ,Cloning, Molecular ,Promoter Regions, Genetic ,Transcription factor ,Gene ,Heat-Shock Proteins ,Adenosine Triphosphatases ,Binding Sites ,biology ,Base Sequence ,Sequence Homology, Amino Acid ,General Medicine ,biology.organism_classification ,Carotenoids ,Biochemistry ,Phycomyces blakesleeanus ,CLPB ,Heat-Shock Response - Abstract
We cloned and sequenced the Phycomyces hspA gene. The hspA gene product is a 901-amino-acid protein member of the clpB/HSP100 family. HSP100 proteins are ATPases involved in high-temperature tolerance, proteolysis, and protein disaggregation. Phycomyces HSP100 is composed of a domain presumably involved in protein-protein interactions and two ATP-binding domains. The hspA promoter contains three heat-shock elements that are presumably involved in the activation of hspA after heat-shock. In addition, four short sequences are present in the hspA promoter and in the promoter of the photoinducible genes carB and carRA; and these are candidates as binding sites for light-regulated transcription factors. Blue light can increase transcription of the hspA gene 10-fold, with a threshold of 1 J/m2. The threshold for hspA photoactivation is 10(4) times higher than the thresholds for blue-light regulation of sporangiophore development and photocarotenogenesis, which suggests that there are differences in the photosensory systems for gene photoactivation and mycelial photoresponses. A heat-shock of 30 min at 34 degrees C or 42 degrees C increased hspA gene activity 160-fold. The differences in maximum hspA gene transcription by blue light and heatshock suggest the presence of different regulatory mechanisms.
- Published
- 2004
26. Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages
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Marco Chiapello, Massimo Turina, María A. Ayllón, and Julio Rodríguez-Romero
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[mycovirus ,virome ,Plasmopara ,narnavirus ,Microbiology ,Virus ,03 medical and health sciences ,mycovirus ,Virology ,Human virome ,AcademicSubjects/MED00860 ,Clade ,Polymerase ,030304 developmental biology ,Genetics ,0303 health sciences ,biology ,030306 microbiology ,Phylum ,AcademicSubjects/SCI01130 ,AcademicSubjects/SCI02285 ,RNA ,Ribosomal RNA ,biology.protein ,Mycovirus ,Research Article - Abstract
The obligatory biotrophic oomycetes Plasmopara viticola is the causal agent of downy mildew, a destructive disease of grapevine worldwide. So far, chemical fungicides are widely employed to limit this pathogen, but their adverse effects are stimulating the quest for environmentally friendly alternative approaches. Here, we report on the search for mycoviruses that might be later developed as biocontrol agents for this pathogen. Symptomatic leaves were collected from various regions in Spain and Italy and mycelia associated to leaf lesions was harvested. Total RNA extractions were depleted of rRNA and metatranscriptomes were generated using a high-throughput sequencing approach. The virome associated to leaf lesions was then characterized through a bioinformatic pipeline relying on blast searches against current viral databases. Here, we present an inventory of 283 new RNA viruses: 222 positive strand RNA viruses, 29 negative strand RNA viruses, 27 double-stranded RNA viruses and 5 ORFan virus RdRP segments, which could not be reliably assigned to any existing group in the Riboviria. In addition to ORFan viruses, we found other surprising new evolutionary trajectories in this wide inventory of viruses. The most represented viruses in our collection are those in phylum Lenarviricota, and, among them, a group of mycovirus segments distantly related to narnaviruses, but characterized by a polymerase palm domain lacking subdomain C, with the putative GDD catalytic triad. We also provided evidence of a strict association between two RNA segments that form a new mycovirus clade of positive strand RNA in the phylum Kitrinoviricota, order Martellivirales. In the phylum Negarnaviricota, we report for the first time in the order Mononegavirales a clade of viruses that is ambisense, a feature that so far was present only in the order Bunyavirales. Furthermore, in the same phylum we detected the widespread occurrence and abundant accumulation in our libraries of a distinct mycovirus clade distantly related to the Muvirales and Goujanvirales orders, which so far include only viruses infecting invertebrates. Possible new oomycetes-specific virus clades are also described in the phylum Duplornaviricota. These data greatly expand the evolutionary history of mycoviruses adding new layers of diversity to the realm Riboviria.
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27. Novel Mycoviruses Discovered in the Mycovirome of a Necrotrophic Fungus
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D. Pacifico, María A. Ayllón, Ana Ruiz-Padilla, Julio Rodríguez-Romero, Irene Gómez-Cid, Agencia Estatal de Investigación (España), Comunidad de Madrid, European Commission, Ruiz-Padilla, Ana, Rodríguez-Romero, Julio, Pacifico, Davide, Ayllón, María A, Ruiz-Padilla, Ana [0000-0001-9165-2845], Rodríguez-Romero, Julio [0000-0001-8304-4014], Pacifico, Davide [0000-0003-3620-9829], and Ayllón, María A [0000-0001-7893-6106]
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trisegmented ssRNA- virus ,Binarnavirus ,Trisegmented ssRNA– virus ,Fungus ,Genome, Viral ,Fungal Viruses ,plant pathogens ,Microbiology ,Genome ,03 medical and health sciences ,Botrytis cinerea ,Virology ,virus metagenomics ,Human virome ,Vitis ,Clade ,Phylogeny ,030304 developmental biology ,Plant Diseases ,Genetics ,trisegmented ssRNA– virus ,0303 health sciences ,virome ,biology ,Virome ,030306 microbiology ,Mycovirome ,fungi ,Fungi ,RNA ,respiratory system ,biology.organism_classification ,QR1-502 ,grapevine ,Virus metagenomics ,RNA silencing ,Italy ,mycovirome ,Mycovirus ,ssDNA mycovirus ,RNA, Viral ,Grapevine ,Plant pathogens ,Botrytis ,binarnavirus ,human activities ,Research Article - Abstract
Centro de Biotecnología y Genómica de Plantas (CBGP), Botrytis cinerea is one of the most important plant-pathogenic fungus. Products based on microorganisms can be used in biocontrol strategies alternative to chemical control, and mycoviruses have been explored as putative biological agents in such approaches. Here, we have explored the mycovirome of B. cinerea isolates from grapevine of Italy and Spain to increase the knowledge about mycoviral diversity and evolution, and to search for new widely distributed mycoviruses that could be active ingredients in biological products to control this hazardous fungus. A total of 248 B. cinerea field isolates were used for our metatranscriptomic study. Ninety-two mycoviruses were identified: 62 new mycoviral species constituting putative novel viral genera and families. Of these mycoviruses, 57 had a positive-sense single-stranded RNA (ssRNA) genome, 19 contained a double-stranded RNA (dsRNA) genome, 15 had a negative-sense ssRNA genome, and 1 contained a single-stranded DNA (ssDNA) genome. In general, ssRNA mycoviruses were widely distributed in all sampled regions, the ssDNA mycovirus was more frequently found in Spain, and dsRNA mycoviruses were scattered in some pools of both countries. Some of the identified mycoviruses belong to clades that have never been found associated with Botrytis species: Botrytis-infecting narnaviruses; alpha-like, umbra-like, and tymo-like ssRNA+ mycoviruses; trisegmented ssRNA- mycovirus; bisegmented and tetrasegmented dsRNA mycoviruses; and finally, an ssDNA mycovirus. Among the results obtained in this massive mycovirus screening, the discovery of novel bisegmented viruses, phylogenetically related to narnaviruses, is remarkable.IMPORTANCE The results obtained here have expanded our knowledge of mycoviral diversity, horizontal transfers, and putative cross-kingdom events. To date, this study presents the most extensive and wide diversity collection of mycoviruses infecting the necrotrophic fungus B. cinerea The collection included all types of mycoviruses, with dsRNA, ssRNA+, ssRNA-, and ssDNA genomes, most of which were discovered here, and some of which were previously reported as infecting B. cinerea or other plant-pathogenic fungi. Some of these mycoviruses are reported for the first time here associated with B. cinerea, as a trisegmented ssRNA- mycovirus and as an ssDNA mycovirus, but even more remarkablly, we also describe here four novel bisegmented viruses (binarnaviruses) not previously described in nature. The present findings significantly contribute to general knowledge in virology and more particularly in the field of mycovirology., J.R.-R. was partially supported by a postdoctoral fellowship from the Severo Ochoa Program for Centers of Excellence in R&D (2017–2021) from the Agencia Estatal de Investigación of Spain (grant SEV-2016-0672 to the Centro de Biotecnología y Genómica de Plantas). I.G.-C. was supported by contract PEJ-2018-TL/BIO-11747 from Comunidad de Madrid, Spain. This study was completely supported financially by VIROPLANT, a project that received funding from the European Union’s Horizon 2020 Research and Innovation Program (grant agreement number 773567)
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28. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.
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Li-Jun Ma, Ashraf S Ibrahim, Christopher Skory, Manfred G Grabherr, Gertraud Burger, Margi Butler, Marek Elias, Alexander Idnurm, B Franz Lang, Teruo Sone, Ayumi Abe, Sarah E Calvo, Luis M Corrochano, Reinhard Engels, Jianmin Fu, Wilhelm Hansberg, Jung-Mi Kim, Chinnappa D Kodira, Michael J Koehrsen, Bo Liu, Diego Miranda-Saavedra, Sinead O'Leary, Lucila Ortiz-Castellanos, Russell Poulter, Julio Rodriguez-Romero, José Ruiz-Herrera, Yao-Qing Shen, Qiandong Zeng, James Galagan, Bruce W Birren, Christina A Cuomo, and Brian L Wickes
- Subjects
Genetics ,QH426-470 - Abstract
Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic basal group of the fungal kingdom called "zygomycetes," R. oryzae is also used as a model to study fungal evolution. Here we report the genome sequence of R. oryzae strain 99-880, isolated from a fatal case of mucormycosis. The highly repetitive 45.3 Mb genome assembly contains abundant transposable elements (TEs), comprising approximately 20% of the genome. We predicted 13,895 protein-coding genes not overlapping TEs, many of which are paralogous gene pairs. The order and genomic arrangement of the duplicated gene pairs and their common phylogenetic origin provide evidence for an ancestral whole-genome duplication (WGD) event. The WGD resulted in the duplication of nearly all subunits of the protein complexes associated with respiratory electron transport chains, the V-ATPase, and the ubiquitin-proteasome systems. The WGD, together with recent gene duplications, resulted in the expansion of multiple gene families related to cell growth and signal transduction, as well as secreted aspartic protease and subtilase protein families, which are known fungal virulence factors. The duplication of the ergosterol biosynthetic pathway, especially the major azole target, lanosterol 14alpha-demethylase (ERG11), could contribute to the variable responses of R. oryzae to different azole drugs, including voriconazole and posaconazole. Expanded families of cell-wall synthesis enzymes, essential for fungal cell integrity but absent in mammalian hosts, reveal potential targets for novel and R. oryzae-specific diagnostic and therapeutic treatments.
- Published
- 2009
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