Basidiomycetes Telomeres – A Bioinformatics Approach

Ramı́rez, Lucı́a; Pérez, Gúmer; Castanera, Raúl; Santoyo, Francisco; Pisabarro, Antonio G.

doi:10.5772/21620

Cited by 6 publications

(5 citation statements)

References 153 publications

(146 reference statements)

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“…Table S9): two clusters mapping to the subterminal region of chromosome 4 and to an internal region of chromosome 8 were mainly formed by proteins without a predicted function, a cluster formed by six laccase genes (out of 12 in PC15) appeared to be located at the subterminal region of chromosome 6, six CBM13 genes (out of eight in PC15) appeared to be clustered at a subterminal region of chromosome 1, and a cluster that included seven genes encoding cerato‐platanin‐related proteins was found at the subterminal region of chromosome 3. The occurrence of clusters of genes involved in environmental adaptation (species‐specific) at subterminal chromosomal locations has been reported in several organisms and could be the result of the exploitation of the high variability associated with these chromosomal regions (Pérez et al ., ; Ramírez et al ., ).…”

Section: Resultsmentioning

confidence: 97%

Comparative and transcriptional analysis of the predicted secretome in the lignocellulose‐degrading basidiomycete fungus Pleurotus ostreatus

Alfaro

Castanera

Lavín

et al. 2016

Environmental Microbiology

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SummaryFungi interact with their environment by secreting proteins to obtain nutrients, elicit responses and modify their surroundings. Because the set of proteins secreted by a fungus is related to its lifestyle, it should be possible to use it as a tool to predict fungal lifestyle. To test this hypothesis, we bioinformatically identified 538 and 554 secretable proteins in the monokaryotic strains PC9 and PC15 of the white rot basidiomycete Pleurotus ostreatus. Functional annotation revealed unknown functions (37.2%), glycosyl hydrolases (26.5%) and redox enzymes (11.5%) as the main groups in the two strains. When these results were combined with RNA-seq analyses, we found that the relative importance of each group was different in different strains and culture conditions and the relevance of the unknown function proteins was enhanced. Only a few genes were actively expressed in a given culture condition in expanded multigene families, suggesting that family expansi on could increase adaptive opportunities rather than activity under a specific culture condition. Finally, we used the set of P. ostreatus secreted proteins as a query to search their counterparts in other fungal genomes and found that the secretome profiles cluster the tested basidiomycetes into lifestyle rather than phylogenetic groups.

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Section: Resultsmentioning

confidence: 97%

Comparative and transcriptional analysis of the predicted secretome in the lignocellulose‐degrading basidiomycete fungus Pleurotus ostreatus

Alfaro

Castanera

Lavín

et al. 2016

Environmental Microbiology

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“…2013 ). Similarly to some plants and insects, both longer (5′-TTTAGGG-3′ in Phanerochaete chrysosporium ) and shorter (5′-TTAGG-3′ in Postia placenta , Heterobasidion annosum ) variants are present, providing evidence for a slight variability of telomeric repeats in the phylum ( Guzmán and Sánchez 1994 ; Ramírez et al. 2011 ).…”

Section: Introductionmentioning

confidence: 92%

“…In Basidiomycota, canonical 5′-TTAGGG-3′ telomeric repeat is typical for most species ( Guzmán and Sánchez 1994 ; Ramírez et al. 2011 ; Fulnečková et al.…”

Section: Introductionmentioning

confidence: 99%

Step-by-Step Evolution of Telomeres: Lessons from Yeasts

Červenák

Sepšiová

Nosek

et al. 2020

Genome Biology and Evolution

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In virtually every eukaryotic species, the ends of nuclear chromosomes are protected by telomeres, nucleoprotein structures counteracting the end-replication problem and suppressing recombination and undue DNA repair. Although in most cases, the primary structure of telomeric DNA is conserved, there are several exceptions to this rule. One is represented by the telomeric repeats of ascomycetous yeasts, which encompass a great variety of sequences, whose evolutionary origin has been puzzling for several decades. At present, the key questions concerning the driving force behind their rapid evolution and the means of co-evolution of telomeric repeats and telomere-binding proteins remain largely unanswered. Previously published studies addressed mostly the general concepts of the evolutionary origin of telomeres, key properties of telomeric proteins as well as the molecular mechanisms of telomere maintenance; however, the evolutionary process itself has not been analyzed thoroughly. Here, we aimed to inspect the evolution of telomeres in ascomycetous yeasts from the subphyla Saccharomycotina and Taphrinomycotina, with special focus on the evolutionary origin of species-specific telomeric repeats. We analyzed the sequences of telomeric repeats from 204 yeast species classified into 20 families and as a result, we propose a step-by-step model, which integrates the diversity of telomeric repeats, telomerase RNAs, telomere-binding protein complexes and explains a propensity of certain species to generate the repeat heterogeneity within a single telomeric array.

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“…The refined gapless assembly is high quality, consisting of 21 megabases on 30 scaffolds (N50 = 6, L50 = 1.4 Mb) and a complete 112 Kb mitochondrial genome. Seven de novo scaffolds have telomeric repeats ( Ramirez et al, 2011 ) at both ends, suggesting they represent complete chromosomes, and seven scaffolds have a telomeric repeat at one end ( Supplementary file 1 ). For comparison, electrophoretic karyotyping of R. toruloides NP11 indicated 16 total chromosomes ( Zhu et al, 2012 ).…”

Section: Refining the R Toruloides Ifo 08mentioning

confidence: 99%

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

Coradetti

Pinel

Geiselman

et al. 2018

eLife

115

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The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.

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Basidiomycetes Telomeres – A Bioinformatics Approach

Cited by 6 publications

References 153 publications

Comparative and transcriptional analysis of the predicted secretome in the lignocellulose‐degrading basidiomycete fungus Pleurotus ostreatus

Comparative and transcriptional analysis of the predicted secretome in the lignocellulose‐degrading basidiomycete fungus Pleurotus ostreatus

Step-by-Step Evolution of Telomeres: Lessons from Yeasts

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

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