Pyret, a Ty3/Gypsy retrotransposon in Magnaporthe grisea contains an extra domain between the nucleocapsid and protease domains

Nakayashiki, Hitoshi; Matsuo, Hideki; Chuma, Izumi; Ikeda, Kenichi; Betsuyaku, Shigeyuki; Kusaba, Motoaki; Tosa, Yukio; Mayama, Shigeyuki

doi:10.1093/nar/29.20.4106

Cited by 40 publications

(26 citation statements)

References 46 publications

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“…This resulted in the identification of a number of different repeats (.100 bp) whose copy numbers ranged from 2 to 498 (show as gray boxes in Figure 4). Only two of the repeats showed BLASTX similarity to known transposable elements: one that corresponded to the Pogo element previously identified at Tel-VR (Schechtman 1990) and another that exhibited similarity to the retrotransposons MAGGY (Farman et al 1996), MGLR-3 (Kang 2001), and Pyret (Nakayashiki et al 2001) in M. oryzae and Skippy in Fusarium oxysporum (Anaya and Roncero 1995).…”

Section: Resultsmentioning

confidence: 94%

Characterization of Chromosome Ends in the Filamentous FungusNeurospora crassa

Kim

Smith

et al. 2009

Genetics

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Telomeres and subtelomere regions have vital roles in cellular homeostasis and can facilitate niche adaptation. However, information on telomere/subtelomere structure is still limited to a small number of organisms. Prior to initiation of this project, the Neurospora crassa genome assembly contained only 3 of the 14 telomeres. The missing telomeres were identified through bioinformatic mining of raw sequence data from the genome project and from clones in new cosmid and plasmid libraries. Their chromosomal locations were assigned on the basis of paired-end read information and/or by RFLP mapping. One telomere is attached to the ribosomal repeat array. The remaining chromosome ends have atypical structures in that they lack distinct subtelomere domains or other sequence features that are associated with telomeres in other organisms. Many of the chromosome ends terminate in highly AT-rich sequences that appear to be products of repeat-induced point mutation, although most are not currently repeated sequences. Several chromosome termini in the standard Oak Ridge wild-type strain were compared to their counterparts in an exotic wild type, Mauriceville. This revealed that the sequences immediately adjacent to the telomeres are usually genome specific. Finally, despite the absence of many features typically found in the telomere regions of other organisms, the Neurospora chromosome termini still retain the dynamic nature that is characteristic of chromosome ends.

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Section: Resultsmentioning

confidence: 94%

Characterization of Chromosome Ends in the Filamentous FungusNeurospora crassa

Kim

Smith

et al. 2009

Genetics

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“…Homologues with the best hit were aligned using ClustalW and the amino acid per cent identity for each pair was calculated. M. grisea and N. crassa genes were considered 50 .…”

Section: Annotation and Analysismentioning

confidence: 99%

The genome sequence of the rice blast fungus Magnaporthe grisea

Dean

Talbot

Ebbole

et al. 2005

Nature

1,502

1,194

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Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.Outbreaks of rice blast disease are a serious and recurrent problem in all rice-growing regions of the world, and the disease is extremely difficult to control 1,2 . Rice blast, caused by the fungus Magnaporthe grisea, is therefore a significant economic and humanitarian problem. It is estimated that each year enough rice is destroyed by rice blast disease to feed 60 million people 3 . The life cycle of the rice blast fungus is shown in Fig. 1. Infections occur when fungal spores land and attach themselves to leaves using a special adhesive released from the tip of each spore 4 . The germinating spore develops an appressorium-a specialized infection cell-which generates enormous turgor pressure (up to 8 MPa) that ruptures the leaf cuticle, allowing invasion of the underlying leaf tissue 5,6 . Subsequent colonization of the leaf produces disease lesions from which the fungus sporulates and spreads to new plants. When rice blast infects young rice seedlings, whole plants often die, whereas spread of the disease to the stems, nodes or panicle of older plants results in nearly total loss of the rice grain 2 . Different host-limited forms of M. grisea also infect a broad range of grass species including wheat, barley and millet. Recent reports have shown that the fungus has the capacity to infect plant roots 7 .Here we present our preliminary analysis of the draft genome sequence of M. grisea, which has emerged as a model system for understanding plant-microbe interactions because of both its economic significance and genetic tractability 1,2 . Acquisition of the M. grisea genome sequenceThe genome of a rice pathogenic strain of M. grisea, 70-15, was sequenced through a whole-genome shotgun approach. In all, greater than sevenfold sequence coverage was produced, and a summary of the principal genome sequence data is provided in Table 1 and Supplementary Table S1. The draft genome sequence consists of 2,273 sequence contigs longer than 2 kilobases (kb), ordered and orientated within 159 scaffolds. The total length of all sequence contigs is 38.8 mega...

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“…The hypothetical protein products of the ORFs of CrREM1 include the domains Retro-gag, zinc finger, protease and reverse transcriptase conserved among autonomously active retrotransposons and retroviruses (3,29), though typical RNase H and integrase domains could not be identified (Fig. 1).…”

Section: Discussionmentioning

confidence: 99%

REM1, a New Type of Long Terminal Repeat Retrotransposon in Chlamydomonas reinhardtii

Pérez-Alegre

Dubus

Fernández

2005

Molecular and Cellular Biology

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A new long terminal repeat (LTR) retrotransposon, named REM1, has been identified in the green alga Chlamydomonas reinhardtii. It was found in low copy number, highly methylated, and with an inducible transpositional activity. This retrotransposon is phylogenetically related to Ty3-gypsy LTR retrotransposons and possesses new and unusual structural features. A regulatory module, ORF3p, is present in an inverse transcriptional orientation to that of the polyprotein and contains PHD-finger and chromodomains, which might confer specificity of the target site and are highly conserved in proteins involved in transcriptional regulation by chromatin remodeling. By using different wild-type and mutant strains, we show that CrREM1 was active with a strong transcriptional activity and amplified its copy number in strains that underwent foreign DNA integration and/or genetic crosses. However, integration of CrREM1 was restricted to these events even though the expression of its full-length transcripts remained highly activated. A regulatory mechanism of CrREM1 retrotransposition which would help to minimize its deleterious effects in the host genome is proposed.Transposable elements are a powerful source of change in eukaryotic and prokaryotic genomes since they provide an important flexibility and evolutionary capacity on the host genome. Their capacity for duplication and mobilization from one site to another, causing mutations and reorganizations, affects the regulation of genes where they integrate, so that they have been positively selected and maintained during evolution (4, 16).Class I of mobile elements includes long terminal repeat (LTR) retrotransposons whose genome has structural features very similar to those of retroviruses. They are bounded by two long terminal repeats and possess a coding region that is normally divided in a single gag-pol or two separate gag and pol open reading frames (ORFs) that determine several mature proteins. The former, named gag (specific antigen group), encodes an RNA binding protein (Gag) and other proteins involved in maturation and packaging of retrotransposons, and it usually presents zinc finger CCHC motifs similar to those described in eukaryotic transcription factors. The latter, named pol (polymerase), encodes several proteins, such as protease, integrase, reverse transcriptase, and RNase H. The retrotranscriptase and RNase H activities are required for cDNA synthesis and the integrase activity is required for the integration of the cDNA into a new chromosomal location (3). The polencoded protease is necessary for cleavage of the polyproteins into functional peptides.Two families of LTR elements (Ty1-copia and Ty3-gypsy) have been differentiated in terms of structure and known protein sequences (mainly reverse transcriptase). Both of them are ancient and ubiquitous constituents of eukaryotic genomes. The main difference among them concerns the relative position of the integrase domain with respect to the ORF homologous to the pol gene (28). Some members of the Ty3-gypsy gro...

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Pyret, a Ty3/Gypsy retrotransposon in Magnaporthe grisea contains an extra domain between the nucleocapsid and protease domains

Cited by 40 publications

References 46 publications

Characterization of Chromosome Ends in the Filamentous FungusNeurospora crassa

Characterization of Chromosome Ends in the Filamentous FungusNeurospora crassa

The genome sequence of the rice blast fungus Magnaporthe grisea

REM1, a New Type of Long Terminal Repeat Retrotransposon in Chlamydomonas reinhardtii

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