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Chimeric retrogenes suggest a role for the nucleolus in LINE amplification
2007
FEBS Letters
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Chimeric retrogenes, found in mammalian and fungal genomes, are bipartite elements composed of DNA copies of cellular transcripts either directly fused to each other or fused to the 3 0 part of a LINE retrotransposon. These cellular transcripts correspond to messenger RNAs, ribosomal RNAs, small nuclear RNAs and 7SL RNA. The chimeras are likely formed by RNA template switches during reverse transcription of LINE elements by their retrotranspositional machinery. The 5 0 part of chimeras are
doi:10.1016/j.febslet.2007.05.034
pmid:17560999
fatcat:dvxxommibnbuhbldcfxrbmdimu
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... s of nucleolar RNAs, suggesting that the nucleolus plays a significant role in LINE retrotransposition. RNAs from the nucleolus might have protective function against retroelement invasion or, alternatively, the nucleolus may be required for retrotranspositional complex assembly and maturation. These hypotheses will be discussed in this review.
Fungi have three tetraspanin families with distinct functions
2008
BMC Genomics
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Tetraspanins are small membrane proteins that belong to a superfamily encompassing 33 members in human and mouse. These proteins act as organizers of membrane-signalling complexes. So far only two tetraspanin families have been identified in fungi. These are Pls1, which is required for pathogenicity of the plant pathogenic ascomycetes, Magnaporthe grisea, Botrytis cinerea and Colletotrichum lindemuthianum, and Tsp2, whose function is unknown. In this report, we describe a third family of
doi:10.1186/1471-2164-9-63
pmid:18241352
pmcid:PMC2278132
fatcat:sxrstlrptvewhiu3txopjj2vjm
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... anins (Tsp3) and a new family of tetraspanin-like proteins (Tpl1) in fungi. We also describe expression of some of these genes in M. grisea and a basidiomycete, Laccaria bicolor, and also their functional analysis in M. grisea. Results: The exhaustive search for tetraspanins in fungal genomes reveals that higher fungi (basidiomycetes and ascomycetes) contain three families of tetraspanins (Pls1, Tsp2 and Tsp3) with different distribution amongst phyla. Pls1 is found in ascomycetes and basidiomycetes, whereas Tsp2 is restricted to basidiomycetes and Tsp3 to ascomycetes. A unique copy of each of PLS1 and TSP3 was found in ascomycetes in contrast to TSP2, which has several paralogs in the basidiomycetes, Coprinus cinereus and Laccaria bicolor. A tetraspanin-like family (Tpl1) was also identified in ascomycetes. Transcriptional analyses in various tissues of L. bicolor and M. grisea showed that PLS1 and TSP2 are expressed in all tissues in L. bicolor and that TSP3 and TPL1 are overexpressed in the sexual fruiting bodies (perithecia) and mycelia of M. grisea, suggesting that these genes are not pseudogenes. Phenotypic analysis of gene replacementmutants Δtsp3 and Δtpl1 of M. grisea revealed a reduction of the pathogenicity only on rice, in contrast to Δpls1 mutants, which are completely non-pathogenic on barley and rice. Conclusion: A new tetraspanin family (Tsp3) and a tetraspanin-like protein family (Tpl1) have been identified in fungi. Functional analysis by gene replacement showed that these proteins, as well as Pls1, are involved in the infection process of the plant pathogenic fungus M. grisea. The next challenge will be to decipher the role(s) of tetraspanins in a range of symbiotic, saprophytic and human pathogenic fungi.
Convergent evolution of morphogenetic processes in fungi
2008
Communicative & Integrative Biology
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Addendum to: Lambou K, Malagnac F, Barbisan C, Tharreau D, Lebrun MH, Silar P. ...
morphogenetic processes in fungi Role of tetraspanins and NADPH oxidases 2 in plant pathogens and saprobes Fabienne Malagnac, 1,2 Frédérique Bidard, 2 Hervé Lalucque, 1,2 Sylvain Brun, 1,2 Karine Lambou, 3 Marc-Henri ...
Lebrun 3 and Philippe Silar 1,2, * evolution. ...
doi:10.4161/cib.1.2.7198
pmid:19704887
pmcid:PMC2686016
fatcat:rifgdeln6je23ghezjakki6nv4
Funybase: a Fungal phylogenomic database
2008
BMC Bioinformatics
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The increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotation and the difficulty of retrieving true orthologs, makes such investigations challenging. The aim of this study was to provide a reliable and integrated resource of orthologous gene families to perform comparative and phylogenetic analyses in fungi. Description: FUNYBASE is a database
doi:10.1186/1471-2105-9-456
pmid:18954438
pmcid:PMC2600828
fatcat:vedb7iomvrcyfcsflkfvhswnlq
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... cated to the analysis of fungal single-copy genes extracted from available fungal genomes sequences, their classification into reliable clusters of orthologs, and the assessment of their informative value for phylogenetic reconstruction based on amino acid sequences. The current release of FUNYBASE contains two types of protein data: (i) a complete set of protein sequences extracted from 30 public fungal genomes and classified into clusters of orthologs using a robust automated procedure, and (ii) a subset of 246 reliable ortholog clusters present as single copy genes in 21 fungal genomes. For each of these 246 ortholog clusters, phylogenetic trees were reconstructed based on their amino acid sequences. To assess the informative value of each ortholog cluster, each was compared to a reference species tree constructed using a concatenation of roughly half of the 246 sequences that are best approximated by the WAG evolutionary model. The orthologs were classified according to a topological score, which measures their ability to recover the same topology as the reference species tree. The full results of these analyses are available on-line with a user-friendly interface that allows for searches to be performed by species name, the ortholog cluster, various keywords, or using the BLAST algorithm. Examples of fruitful utilization of FUNYBASE for investigation of fungal phylogenetics are also presented. Conclusion: FUNYBASE constitutes a novel and useful resource for two types of analyses: (i) comparative studies can be greatly facilitated by reliable clusters of orthologs across sets of user-defined fungal genomes, and (ii) phylogenetic reconstruction can be improved by identifying genes with the highest informative value at the desired taxonomic level.
Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi
2008
Genome Biology
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Expression ofMagnaporthe griseaAvirulence GeneACE1Is Connected to the Initiation of Appressorium-Mediated Penetration
2006
Eukaryotic Cell
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Magnaporthe griseais responsible for a devastating fungal disease of rice called blast. Current control of this disease relies on resistant rice cultivars that recognizeM. griseasignals corresponding to specific secreted proteins encoded by avirulence genes. TheM. grisea ACE1avirulence gene differs from others, since it controls the biosynthesis of a secondary metabolite likely recognized by rice cultivars carrying thePi33resistance gene. Using a transcriptional fusion betweenACE1promoter
doi:10.1128/ec.00330-05
pmid:17142568
pmcid:PMC1828936
fatcat:cxrmhp5hrncfzel453bpatta5e
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... P, we showed thatACE1is only expressed in appressoria during fungal penetration into rice and barley leaves, onion skin, and cellophane membranes.ACE1is almost not expressed in appressoria differentiated on Teflon and Mylar artificial membranes.ACE1expression is not induced by cellophane and plant cell wall components, demonstrating that it does not require typical host plant compounds. Cyclic AMP (cAMP) signaling mutants ΔcpkAand Δmac1 sum1-99and tetraspanin mutant Δpls1::hphdifferentiate melanized appressoria with normal turgor but are unable to penetrate host plant leaves.ACE1is normally expressed in these mutants, suggesting that it does not require cAMP signaling or a successful penetration event.ACE1is not expressed in appressoria of thebuf1::hphmutant defective for melanin biosynthesis and appressorial turgor. The addition of hyperosmotic solutes tobuf1::hphappressoria restores appressorial development andACE1expression. Treatments of young wild-type appressoria with actin and tubulin inhibitors reduce both fungal penetration andACE1expression. These experiments suggest thatACE1appressorium-specific expression does not depend on host plant signals but is connected to the onset of appressorium-mediated penetration.
Impacts of Sodium Arsenite on Wood Microbiota of Esca-Diseased Grapevines
2021
Journal of Fungi
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Although sodium arsenite was widely used in Europe until its ban in 2003, its effects on microorganisms is not clearly understood. To improve our understanding of sodium arsenite curative effect on GTDs, grapevines displaying esca-foliar symptoms from different French regions (Alsace, Champagne, Languedoc) were treated or not with sodium arsenite, and analyzed for their wood microbiota. Using metabarcoding, we identified the fungal and bacterial taxa composition of microbiota colonizing woody
doi:10.3390/jof7070498
fatcat:vhc5ug5swzfi7es3fskptkyjp4
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... unk tissues. Large differences in fungal microbiota composition between treated and untreated grapevines were observed while no major impacts were observed on bacteria microbiota. The main fungal species detected in untreated necrotic woody tissues was Fomitiporia mediterranea (63–94%), a fungal pathogen associated with esca. The relative abundance of this fungal species significantly decreased after sodium arsenite treatment in the three vineyards, in particular in white-rot necrotic tissues and their borders (−90%). F. mediterranea was the most sensitive to sodium arsenite among fungi from grapevine woody tissues. These results strongly suggest that the effect of sodium arsenite on GTDs is due to its ability to efficiently and almost specifically eliminate F. mediterranea from white-rot necrotic tissues, allowing saprobic fungi to colonize the tissues previously occupied by this pathogenic fungus.
Editorial: How Can Secretomics Help Unravel the Secrets of Plant-Microbe Interactions?
2016
Frontiers in Plant Science
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Copyright © 2016 Vincent, Plummer, Solomon, Lebrun, Job and Rafiqi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). ...
doi:10.3389/fpls.2016.01777
pmid:27965687
pmcid:PMC5127848
fatcat:75zyig6cjjggtf5dhmtuxzpoee
Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes
2015
BMC Genomics
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Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. Fungi have developed defense mechanisms against TE invasion such as RIP (Repeat-Induced Point mutation), MIP (Methylation Induced Premeiotically) and Quelling (RNA interference). RIP inactivates repeated sequences by promoting Cytosine to Thymine mutations, whereas MIP only methylates TEs at C residues. Both mechanisms require specific cytosine DNA Methyltransferases (RID1/Masc1) of the Dnmt1
doi:10.1186/s12864-015-1347-1
pmid:25766680
pmcid:PMC4352252
fatcat:2p3iv6wdkfeurovsj2kvwgtzvm
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... erfamily. Results: We annotated TE sequences from 10 fungal genomes with different TE content (1-70%). We then used these TE sequences to carry out a genome-wide analysis of C to T mutations biases. Genomes from either Ascomycota or Basidiomycota that were massively invaded by TEs (Blumeria, Melampsora, Puccinia) were characterized by a low frequency of C to T mutation bias (10-20%), whereas other genomes displayed intermediate to high frequencies (25-75%). We identified several dinucleotide signatures at these C to T mutation sites (CpA, CpT, and CpG). Phylogenomic analysis of fungal Dnmt1 MTases revealed a previously unreported association between these dinucleotide signatures and the presence/absence of sub-classes of Dnmt1. Conclusions: We identified fungal genomes containing large numbers of TEs with many C to T mutations associated with species-specific dinucleotide signatures. This bias suggests that a basic defense mechanism against TE invasion similar to RIP is widespread in fungi, although the efficiency and specificity of this mechanism differs between species. Our analysis revealed that dinucleotide signatures are associated with the presence/absence of specific Dnmt1 subfamilies. In particular, an RID1-dependent RIP mechanism was found only in Ascomycota.
Association Genetics in Plant Pathogens: Minding the Gap between the Natural Variation and the Molecular Function
2017
Frontiers in Plant Science
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Copyright © 2017 Genissel, Confais, Lebrun and Gout. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). ...
doi:10.3389/fpls.2017.01301
pmid:28791038
pmcid:PMC5524819
fatcat:3rqinfu6hrgwhm7yaiuz2t6bte
Post-genomic approaches to understanding interactions between fungi and their environment
2011
IMA Fungus
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Fungi inhabit every natural and anthropogenic environment on Earth. They have highly varied life-styles including saprobes (using only dead biomass as a nutrient source), pathogens (feeding on living biomass), and symbionts (co-existing with other organisms). These distinctions are not absolute as many species employ several life styles (e.g. saprobe and opportunistic pathogen, saprobe and mycorrhiza). To efficiently survive in these different and often changing environments, fungi need to be
doi:10.5598/imafungus.2011.02.01.11
pmid:22679591
pmcid:PMC3317359
fatcat:g7f6nagjwbgrzbguxxzs7tid6a
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... le to modify their physiology and in some cases will even modify their local environment. Understanding the interaction between fungi and their environments has been a topic of study for many decades. However, recently these studies have reached a new dimension. The availability of fungal genomes and development of postgenomic technologies for fungi, such as transcriptomics, proteomics and metabolomics, have enabled more detailed studies into this topic resulting in new insights. Based on a Special Interest Group session held during IMC9, this paper provides examples of the recent advances in using (post-)genomic approaches to better understand fungal interactions with their environments.
Methionine Biosynthesis is Essential for Infection in the Rice Blast Fungus Magnaporthe oryzae
2015
PLoS ONE
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Methionine is a sulfur amino acid standing at the crossroads of several biosynthetic pathways. In fungi, the last step of methionine biosynthesis is catalyzed by a cobalamine-independent methionine synthase (Met6, EC 2.1.1.14). In the present work, we studied the role of Met6 in the infection process of the rice blast fungus, Magnaporthe oryzae. To this end MET6 null mutants were obtained by targeted gene replacement. On minimum medium, MET6 null mutants were auxotrophic for methionine. Even
doi:10.1371/journal.pone.0111108
pmid:25856162
pmcid:PMC4391826
fatcat:a6p4jbgpvjc5dkdoibfucxlspi
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... n grown in presence of excess methionine, these mutants displayed developmental defects, such as reduced mycelium pigmentation, aerial hypha formation and sporulation. They also displayed characteristic metabolic signatures such as increased levels of cysteine, cystathionine, homocysteine, S-adenosylmethionine, S-adenosylhomocysteine while methionine and glutathione levels remained unchanged. These metabolic perturbations were associated with the over-expression of MgCBS1 involved in the reversed transsulfuration pathway that metabolizes homocysteine into cysteine and MgSAM1 and MgSAHH1 involved in the methyl cycle. This suggests a physiological adaptation of M. oryzae to metabolic defects induced by the loss of Met6, in particular an increase in homocysteine levels. Pathogenicity assays showed that MET6 null mutants were non-pathogenic on both barley and rice leaves. These mutants were defective in appressorium-mediated penetration and invasive infectious growth. These pathogenicity defects were rescued by addition of exogenous methionine and S-methylmethionine. These results show that M. oryzae cannot assimilate sufficient methionine from plant tissues and must synthesize this amino acid de novo to fulfill its sulfur amino acid requirement during infection.
Draft Genome Sequence of Diplodia seriata F98.1, a Fungal Species Involved in Grapevine Trunk Diseases
2017
Genome Announcements
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The ascomycete Diplodia seriata is a causal agent of grapevine trunk diseases. Here, we present the draft genome sequence of D. seriata isolate F98.1 (37.27 Mb, 512 contigs, 112 scaffolds, and 8,087 predicted protein-coding genes).
doi:10.1128/genomea.00061-17
pmid:28385831
pmcid:PMC5383879
fatcat:x7bdv3fdcrbvpb332ekzoxyj44
The pentose catabolic pathway of the rice-blast fungusMagnaporthe oryzaeinvolves a novel pentose reductase restricted to few fungal species
2013
FEBS Letters
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Edited by Judit Ovadi Keywords: Pentose catabolism Pentose reductase D-Xylose L-Arabinose Magnaporthe oryzae a b s t r a c t A gene (MoPRD1), related to xylose reductases, was identified in Magnaporthe oryzae. Recombinant MoPRD1 displays its highest specific reductase activity toward L-arabinose and D-xylose. K m and V max values using L-arabinose and D-xylose are similar. MoPRD1 was highly overexpressed 2-8 h after transfer of mycelium to D-xylose or L-arabinose, compared to D-glucose.
doi:10.1016/j.febslet.2013.03.003
pmid:23499935
fatcat:mf5yxtai7jhmtmqi56xgp257z4
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... e, we conclude that MoPDR1 is a novel pentose reductase, which combines the activities and expression patterns of fungal L-arabinose and D-xylose reductases. Phylogenetic analysis shows that PRD1 defines a novel family of pentose reductases related to fungal D-xylose reductases, but distinct from fungal L-arabinose reductases. The presence of PRD1, L-arabinose and D-xylose reductases encoding genes in a given species is variable and likely related to their life style.
Infection cushions of Fusarium graminearum are fungal arsenals for wheat infection
2020
Molecular plant pathology
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Fusarium graminearum is one of the most destructive plant pathogens worldwide, causing fusarium head blight (FHB) on cereals. F. graminearum colonizes wheat plant surfaces with specialized unbranched hyphae called runner hyphae (RH), which develop multicelled complex appressoria called infection cushions (IC). IC generate multiple penetration sites, allowing the fungus to enter the plant cuticle. Complex infection structures are typical for several economically important plant pathogens, yet
doi:10.1111/mpp.12960
pmid:32573086
fatcat:ktej4qwqbfbetlus2s75pdvkcq
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... h unknown molecular basis. In this study, RH and IC formed on the surface of wheat paleae were isolated by laser capture microdissection. RNA-Seq-based transcriptomic analyses were performed on RH and IC and compared to mycelium grown in complete medium (MY). Both RH and IC displayed a high number of infection up-regulated genes (982), encoding, among others, carbohydrate-active enzymes (CAZymes: 140), putative effectors (PE: 88), or secondary metabolism gene clusters (SMC: 12 of 67 clusters). RH specifically up-regulated one SMC corresponding to aurofusarin biosynthesis, a broad activity antibiotic. IC specifically up-regulated 248 genes encoding mostly putative virulence factors such as 7 SMC, including the mycotoxin deoxynivalenol and the newly identified fusaoctaxin A, 33 PE, and 42 CAZymes. Furthermore, we studied selected candidate virulence factors using cellular biology and reverse genetics. Hence, our results demonstrate that IC accumulate an arsenal of proven and putative virulence factors to facilitate the invasion of epidermal cells.
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