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Junta Sugiyama - One of the best experts on this subject based on the ideXlab platform.
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Group I Introns from Zygomycota: Evolutionary Implications for the Fungal IC1 Intron SubGroup
Journal of Molecular Evolution, 2002Co-Authors: Yuuhiko Tanabe, Akira Yokota, Junta SugiyamaAbstract:The origins of Fungal Group I introns within nuclear small-subunit (nSSU) rDNA are enigmatic. This is partly because they have never been reported in basal Fungal phyla (Zygomycota and Chytridiomycota), which are hypothesized to be ancestral to derived phyla (Ascomycota and Basidiomycota). Here we report Group I introns from the nSSU rDNA of two zygomycete fungi, Zoophagus insidians (Zoopagales) and Coemansia mojavensis (Kickxellales). Secondary structure analyses predicted that both introns belong to the IC1 subGroup and that they are distantly related to each other, which is also suggested by different insertion sites. Molecular phylogenetic analyses indicated that the IC1 intron of Z. insidians is closely related to the IC1 intron inserted in the LSU rDNA of the basidiomycete fungus Clavicorona taxophila , which strongly suggests interphylum horizontal transfer. The IC1 intron of C. mojavensis has a low phylogenetic affinity to other Fungal IC1 introns inserted into site 943 of nSSU rDNA (relative to E. coli 16S rDNA). It is noteworthy that this intron contains a putative ORF containing a His–Cys box motif in the antisense strand, a hallmark for nuclear-encoded homing endonucleases. Overall, molecular phylogenetic analyses do not support the placement of these two introns in basal Fungal IC1 intron lineages. This result leads to the suggestion that Fungal IC1 introns might have invaded or been transferred laterally after the divergence of the four major Fungal phyla.
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multiple origins of Fungal Group i introns located in the same position of nuclear ssu rrna gene
Journal of Molecular Evolution, 1998Co-Authors: Hiromi Nishida, Yoshito Tajiri, Junta SugiyamaAbstract:The archiascomycetous fungus Protomyces pachydermus has two Group I introns within the nuclear small subunit (nSSU) rRNA gene. One of these introns has an internal open reading frame (ORF) that encodes a predicted protein of 228 amino acid residues. On the other hand, Protomyces macrosporus has two Group I introns that insert at the same positions as P. pachydermus, which have no ORF. Each alignment was constructed with Protomyces Group I introns located in the same position and other introns retrieved by the BLAST Search. Each phylogenetic tree based on the alignment shows that Protomyces introns are monophyletic but the relationships among Fungal introns do not reflect on the Fungal phylogeny. Therefore, it is suggested that two different horizontal transfers of Group I introns occurred at the early stage of Protomyces species diversification.
Debashish Bhattacharya - One of the best experts on this subject based on the ideXlab platform.
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phylogenetic analyses suggest reverse splicing spread of Group i introns in Fungal ribosomal dna
BMC Evolutionary Biology, 2005Co-Authors: Debashish Bhattacharya, Valerie Reeb, Dawn M Simon, Francois LutzoniAbstract:Group I introns have spread into over 90 different sites in nuclear ribosomal DNA (rDNA) with greater than 1700 introns reported in these genes. These ribozymes generally spread through endonuclease-mediated intron homing. Another putative pathway is reverse splicing whereby a free Group I intron inserts into a homologous or heterologous RNA through complementary base-pairing between the intron and exon RNA. Reverse-transcription of the RNA followed by general recombination results in intron spread. Here we used phylogenetics to test for reverse splicing spread in a taxonomically broadly sampled data set of Fungal Group I introns including 9 putatively ancient Group I introns in the rDNA of the yeast-like symbiont Symbiotaphrina buchneri. Our analyses reveal a complex evolutionary history of the Fungal introns with many cases of vertical inheritance (putatively for the 9 introns in S. buchneri) and intron lateral transfer. There are several examples in which introns, many of which are still present in S. buchneri, may have spread through reverse splicing into heterologous rDNA sites. If the S. buchneri introns are ancient as we postulate, then Group I intron loss was widespread in Fungal rDNA evolution. On the basis of these results, we suggest that the extensive distribution of Fungal Group I introns is at least partially explained by the reverse splicing movement of existing introns into ectopic rDNA sites.
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vertical evolution and intragenic spread of lichen Fungal Group i introns
Journal of Molecular Evolution, 2002Co-Authors: Debashish Bhattacharya, Thomas Friedl, Gert HelmsAbstract:One family within the Euascomycetes (Ascomycota), the lichen-forming Physciaceae, is particularly rich in nuclear ribosomal [r]DNA Group I introns. We used phylogenetic analyses of Group I introns and lichen-Fungal host cells to address four questions about Group I intron evolution in lichens, and generally in all eukaryotes: I ) Is intron spread in the lichens associated with the intimate association of the Fungal and photosynthetic cells that make up the lichen thallus? 2) Are the multiple Group I introns in the lichen-fungi of independent origins, or have existing introns spread into novel sites in the rDNA? 3) If introns have moved to novel sites, then does the exon context of these sites provide insights into the mechanism of intron spread? and 4) What is the pattern of intron loss in the small subunit rDNA gene of lichen-fungi? Our analyses show that Group I introns in the lichen-fungi and in the lichen-algae (and lichenized cyanobacteria) do not share a close evolutionary relationship, suggesting that these introns do not move between the symbionts. Many Group I introns appear to have originated in the common ancestor of the Lecanorales, whereas others have spread within this lineage (particularly in the Physciaceae) putatively through reverse-splicing into novel rRNA sites. We suggest that the evolutionary history of most lichen-Fungal Group I introns is characterized by rare gains followed by extensive losses in descendants, resulting in a sporadic intron distribution. Detailed phylogenetic analyses of the introns and host cells are required, therefore, to distinguish this scenario from the alternative hypothesis of widespread and independent intron gains in the different lichen-Fungal lineages.
Francois Lutzoni - One of the best experts on this subject based on the ideXlab platform.
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phylogenetic analyses suggest reverse splicing spread of Group i introns in Fungal ribosomal dna
BMC Evolutionary Biology, 2005Co-Authors: Debashish Bhattacharya, Valerie Reeb, Dawn M Simon, Francois LutzoniAbstract:Group I introns have spread into over 90 different sites in nuclear ribosomal DNA (rDNA) with greater than 1700 introns reported in these genes. These ribozymes generally spread through endonuclease-mediated intron homing. Another putative pathway is reverse splicing whereby a free Group I intron inserts into a homologous or heterologous RNA through complementary base-pairing between the intron and exon RNA. Reverse-transcription of the RNA followed by general recombination results in intron spread. Here we used phylogenetics to test for reverse splicing spread in a taxonomically broadly sampled data set of Fungal Group I introns including 9 putatively ancient Group I introns in the rDNA of the yeast-like symbiont Symbiotaphrina buchneri. Our analyses reveal a complex evolutionary history of the Fungal introns with many cases of vertical inheritance (putatively for the 9 introns in S. buchneri) and intron lateral transfer. There are several examples in which introns, many of which are still present in S. buchneri, may have spread through reverse splicing into heterologous rDNA sites. If the S. buchneri introns are ancient as we postulate, then Group I intron loss was widespread in Fungal rDNA evolution. On the basis of these results, we suggest that the extensive distribution of Fungal Group I introns is at least partially explained by the reverse splicing movement of existing introns into ectopic rDNA sites.
Dawn M Simon - One of the best experts on this subject based on the ideXlab platform.
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phylogenetic analyses suggest reverse splicing spread of Group i introns in Fungal ribosomal dna
BMC Evolutionary Biology, 2005Co-Authors: Debashish Bhattacharya, Valerie Reeb, Dawn M Simon, Francois LutzoniAbstract:Group I introns have spread into over 90 different sites in nuclear ribosomal DNA (rDNA) with greater than 1700 introns reported in these genes. These ribozymes generally spread through endonuclease-mediated intron homing. Another putative pathway is reverse splicing whereby a free Group I intron inserts into a homologous or heterologous RNA through complementary base-pairing between the intron and exon RNA. Reverse-transcription of the RNA followed by general recombination results in intron spread. Here we used phylogenetics to test for reverse splicing spread in a taxonomically broadly sampled data set of Fungal Group I introns including 9 putatively ancient Group I introns in the rDNA of the yeast-like symbiont Symbiotaphrina buchneri. Our analyses reveal a complex evolutionary history of the Fungal introns with many cases of vertical inheritance (putatively for the 9 introns in S. buchneri) and intron lateral transfer. There are several examples in which introns, many of which are still present in S. buchneri, may have spread through reverse splicing into heterologous rDNA sites. If the S. buchneri introns are ancient as we postulate, then Group I intron loss was widespread in Fungal rDNA evolution. On the basis of these results, we suggest that the extensive distribution of Fungal Group I introns is at least partially explained by the reverse splicing movement of existing introns into ectopic rDNA sites.
Konečný Jan - One of the best experts on this subject based on the ideXlab platform.
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Plant sugar metabolism and arbuscular mycorrhizal symbiosis
2017Co-Authors: Konečný JanAbstract:The study of arbuscular mycorrhizal symbiosis (AMS) - the mutualist relationship between the most of land plants and evolutionary old Fungal Group Glomeromycota - is becoming a prestigious topic. The prevalence of and extent of physiological action of AMS on plants is very interesting for the plant biology itself, but its importance grows, notably in time of global climate change, frequent soil degradation and ascending exhaustion of mineral fertilizer reserves. Although the flows in AMS of some minerals, like of phosphorus was enlightened, carbon exchange between the symbionts is still poorly understood. In this experimental work, I utilized the boom of molecular and bioinformatic methods in the quest for completely unexplained carbon flows. The organisms used include barrel medic (Medicago truncatula), the model legume for symbiotic relationships, biotic, and abiotic stresses; Rhizophagus irregularis, the widely used fungus for such experimental studies of AMS; and Sinorhizobium meliloti, the nodulating nitrogen-fixing bacterium compatible with the barrel medic. Two variants - mycorrhizal (M+) and non-mycorrhizal (NM) plants were subjected to several levels of analysis. I have checked the variants, did the measurements of phosphorus and nitrogen contents, as well as I probed the plants with..
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Plant sugar metabolism and arbuscular mycorrhizal symbiosis
Univerzita Karlova Přírodovědecká fakulta, 2017Co-Authors: Konečný JanAbstract:The study of arbuscular mycorrhizal symbiosis (AMS) - the mutualist relationship between the most of land plants and evolutionary old Fungal Group Glomeromycota - is becoming a prestigious topic. The prevalence of and extent of physiological action of AMS on plants is very interesting for the plant biology itself, but its importance grows, notably in time of global climate change, frequent soil degradation and ascending exhaustion of mineral fertilizer reserves. Although the flows in AMS of some minerals, like of phosphorus was enlightened, carbon exchange between the symbionts is still poorly understood. In this experimental work, I utilized the boom of molecular and bioinformatic methods in the quest for completely unexplained carbon flows. The organisms used include barrel medic (Medicago truncatula), the model legume for symbiotic relationships, biotic, and abiotic stresses; Rhizophagus irregularis, the widely used fungus for such experimental studies of AMS; and Sinorhizobium meliloti, the nodulating nitrogen-fixing bacterium compatible with the barrel medic. Two variants - mycorrhizal (M+) and non-mycorrhizal (NM) plants were subjected to several levels of analysis. I have checked the variants, did the measurements of phosphorus and nitrogen contents, as well as I probed the plants with...Studium arbuskulární mykorhizní symbiózy (AMS) - mutualistického vztahu mezi většinou suchozemských rostlin a evolučně starou skupinou hub z oddělení Glomeromycota - je v poslední době prestižní záležitostí. Její rozšířenost a rozsah fyziologického působení AMS na rostliny je zajímavou pro rostlinnou biologii samotnou, ale její důležitost narůstá v době změny klimatu, časté degradace půd a snižujícím se zásobám minerálních hnojiv. Přestože toky některých minerálních látek v AMS, zejména fosforu, byly osvětleny, výměna uhlíku mezi symbionty je stále velkou neznámou. V této experimentální práci jsem využil rozmachu molekulárních a bioinformatických metod při pátrání v doposavad zcela neobjasněných tocích uhlíku. Použitými organismy jsou tolice Medicago truncatula, modelová rostlina pro studium symbiotických vztahů, biotických i abiotických stresů, Rhizophagus irregularis, široce využívaná arbuskulárně mykorhizní houba pro experimentální studia AMS, a Sinorhizobium meliloti, hlízkovitá bakterie fixující vzdušný dusík komaptibilní s M. truncatula. Dvě varianty - mykorhizní (M+) a nemykorhizní (NM) tolice byly analyzovány na několika úrovních. Provedl jsem kontrolu variant, měření obsahu makroprvků fosforu a dusíku a také značení stabilním izotopem uhlíku 13 C a sledování jeho toku v experimentálním...Katedra experimentální biologie rostlinDepartment of Experimental Plant BiologyFaculty of SciencePřírodovědecká fakult
