Telomere Organization in the Ligninolytic Basidiomycete Pleurotus ostreatus

Abstract

Telomeres are structural and functional chromosome regions that are essential for the cell cycle to proceed normally. They are, however, difficult to map genetically and to identify in genome-wide sequence programs because of their structure and repetitive nature. We studied the telomeric and subtelomeric organization in the basidiomycete Pleurotus ostreatus using a combination of molecular and bioinformatics tools that permitted us to determine 19 out of the 22 telomeres expected in this fungus. The telomeric repeating unit in P. ostreatus is TTAGGG, and the numbers of repetitions of this unit range between 25 and 150. The mapping of the telomere restriction fragments to linkage groups 6 and 7 revealed polymorphisms compatible with those observed by pulsed field gel electrophoresis separation of the corresponding chromosomes. The subtelomeric regions in Pleurotus contain genes similar to those described in other eukaryotic systems. The presence of a cluster of laccase genes in chromosome 6 and a bipartite structure containing a Het-related protein and an alcohol dehydrogenase are especially relevant; this bipartite structure is characteristic of the Pezizomycotina fungi Neurospora crassa and Aspergillus terreus. As far as we know, this is the first report describing the presence of such structures in basidiomycetes and the location of a laccase gene cluster in the subtelomeric region, where, among others, species-specific genes allowing the organism to adapt rapidly to the environment usually map.Pleurotus ostreatus (Jacq.: Fr) Kumm. (Dikarya, Basidiomycota, Agaricomycotina, Agaricales) (52) is an active lignin degrader that lives as a saprophyte on dead or decaying wood. P. ostreatus (oyster mushroom) has been industrially cultivated for food production because of its flavor and its nutritional (49) and health-stimulating (8) properties. In addition, it produces various secondary metabolites of medical interest (33). P. ostreatus ligninolytic activity and enzymes have been used in the bioconversion of agricultural wastes (1); in the biodegradation of organopollutants, xenobiotics, and industrial contaminants (12); and in paper pulp bleaching (65), among other applications (10).The whole genome sequence of P. ostreatus is currently being assembled at the Joint Genome Institute (California). P. ostreatus is the first edible and the second lignin-degrading basidiomycete to be sequenced. The sequences of other basidiomycetes, such as Phanerochaete chrysosporium (48), Cryptococcus neoformans (44), Ustilago maydis (38), and Laccaria bicolor (47) have been published, and others (Postia placenta, Heterobasidion annosum, Agaricus bisporus, Serpula lacrymans, etc.) are in progress.Telomeres are the protective DNA-protein complexes found at chromosome termini (6, 13, 76). In most eukaryotes, telomeric DNA consists of tandem arrays of 5-to 8-bp direct repeats where specific telomere-capping proteins bind to ensure chromosomal-end integrity. Telomeres are essential for genome stability, and their shortening (attrition) can...

Basidiomycetes Telomeres – A Bioinformatics Approach

“…This sequence has been described in Aspergillus nidulans (Bhattacharyya & Blackburn, 1997), Beauveria bassiana (Padmavathi et al, 2003), Botrytis cinerea (Levis et al, 1997), Cladosporium fulvum (Coleman et al, 1993), Fusarium oxysporum (Inglis et al, 2000), Glomus intraradices (Hijri et al, 2007), Magnaporthe grisea (Gao et al, 2002), Metarrhizium anisopliae (Inglis et al, 2005), N. crassa (Wu et al, 2009), Pestalotiopsis microspora (Long et al, 1998), Pleurotus ostreatus (Perez et al, 2009), Pneumocystis carinii (Keely et al, 2001), and Ustilago maydis (Sanchez-Alonso & Guzman, 2008). However, variations of this sequence can be found in other fungi such as A. oryzae that has dodecanucleotide telomere repeats (Kusumoto et al, 2003) Incomplete and imperfect telomere units have been reported in: A. oryzae, Candida albicans, Kluyveromyces lactis, S. cerevisiae and S. pombe.…”

“…A similar situation is observed when the sequences immediately adjacent to the TTAGGG repeats were compared between strains. Consistent with the absence of distinct subtelomere elements, N. crassa lacks the TLH genes that are present in the subtelomere regions of diverse fungi (Gao et al, 2002;Inglis et al, 2005;Louis & Haber, 1992;Mandell et al, 2005;Perez et al, 2009;Rehmeyer et al, 2006;Sanchez-Alonso & Guzman, 1998). As in other fungi, the terminal regions of N. crassa chromosomes ferry genes related to secondary metabolism such as a monooyygenase (CYP450), a FAD-binding domain containing protein, a second CYP450, an Omethyltransferase, a polyketide synthase, a major facilitator superfamily efflux pump, a putative transcription factor, and an oxidoreductase.…”

“…It could be that the high evolutive potential of the subtelomeric regions were used by these organisms to create variability aimed to avoid the detection by the host. In fungi the genes more frequently found in subtelomere regions are transposons, telomere-linked RecQ helicases, clusters of secondarymetabolites, cytochrome oxidases, hydrolases, molecular transporters, and genes encoding secreted proteins (Perez et al, 2009). These genes could undergo transcriptional silencing (subtelomere silencing) due to its close proximity to telomeres.…”

“…A consequence of the difficulty in cloning telomeres is that, for most organisms, there is limited information on the organization of chromosome ends. Data about basidiomycete telomeres are available for U. maydis (Sanchez-Alonso & Guzman, 1998), M. anisopliae (Inglis et al, 2005) and P. ostreatus (Perez et al, 2009). In the three cases, the conserved telomere repetitive unit is TTAGGG, and the number of tandem repetitions varies among species: 37 times in U. maydis, from 18 to 26 in M. anisopliae, and from 25 to 150 in P. ostreatus.…”

“…The particular sequence organization of telomere makes difficult its genetic mapping and sequencing due to they are cloning recalcitrant and underrepresented in mapping and final assembled genomes. Consequently, their cloning and characterization must be made by dedicated molecular and bioinformatics strategies (Perez et al, 2009;Sanchez-Alonso & Guzman, 2008). …”