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Pérez G, Pangilinan J, Pisabarro AG, Ramírez L. Telomere organization in the ligninolytic basidiomycete Pleurotus ostreatus. Appl Environ Microbiol 2009; 75:1427-36. [PMID: 19114509 PMCID: PMC2648151 DOI: 10.1128/aem.01889-08] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 12/21/2008] [Indexed: 01/19/2023] Open
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.
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Affiliation(s)
- Gúmer Pérez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
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Hane JK, Oliver RP. RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences. BMC Bioinformatics 2008; 9:478. [PMID: 19014496 PMCID: PMC2621366 DOI: 10.1186/1471-2105-9-478] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 11/12/2008] [Indexed: 11/13/2022] Open
Abstract
Background Repeat-induced point mutation (RIP) is a fungal-specific genome defence mechanism that alters the sequences of repetitive DNA, thereby inactivating coding genes. Repeated DNA sequences align between mating and meiosis and both sequences undergo C:G to T:A transitions. In most fungi these transitions preferentially affect CpA di-nucleotides thus altering the frequency of certain di-nucleotides in the affected sequences. The majority of previously published in silico analyses were limited to the comparison of ratios of pre- and post-RIP di-nucleotides in putatively RIP-affected sequences – so-called RIP indices. The analysis of RIP is significantly more informative when comparing sequence alignments of repeated sequences. There is, however, a dearth of bioinformatics tools available to the fungal research community for alignment-based RIP analysis of repeat families. Results We present RIPCAL , a software tool for the automated analysis of RIP in fungal genomic DNA repeats, which performs both RIP index and alignment-based analyses. We demonstrate the ability of RIPCAL to detect RIP within known RIP-affected sequences of Neurospora crassa and other fungi. We also predict and delineate the presence of RIP in the genome of Stagonospora nodorum – a Dothideomycete pathogen of wheat. We show that RIP has affected different members of the S. nodorum rDNA tandem repeat to different extents depending on their genomic contexts. Conclusion The RIPCAL alignment-based method has considerable advantages over RIP indices for the analysis of whole genomes. We demonstrate its application to the recently published genome assembly of S. nodorum.
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Affiliation(s)
- James K Hane
- Australian Centre for Necrotrophic Fungal Pathogens, Faculty of Health Sciences, Murdoch University, Murdoch, Australia.
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McDonagh A, Fedorova ND, Crabtree J, Yu Y, Kim S, Chen D, Loss O, Cairns T, Goldman G, Armstrong-James D, Haynes K, Haas H, Schrettl M, May G, Nierman WC, Bignell E. Sub-telomere directed gene expression during initiation of invasive aspergillosis. PLoS Pathog 2008; 4:e1000154. [PMID: 18787699 PMCID: PMC2526178 DOI: 10.1371/journal.ppat.1000154] [Citation(s) in RCA: 205] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Accepted: 08/14/2008] [Indexed: 11/23/2022] Open
Abstract
Aspergillus fumigatus is a common mould whose spores are a
component of the normal airborne flora. Immune dysfunction permits developmental
growth of inhaled spores in the human lung causing aspergillosis, a significant
threat to human health in the form of allergic, and life-threatening invasive
infections. The success of A. fumigatus as a pathogen is unique
among close phylogenetic relatives and is poorly characterised at the molecular
level. Recent genome sequencing of several Aspergillus species
provides an exceptional opportunity to analyse fungal virulence attributes
within a genomic and evolutionary context. To identify genes preferentially
expressed during adaptation to the mammalian host niche, we generated multiple
gene expression profiles from minute samplings of A. fumigatus
germlings during initiation of murine infection. They reveal a highly
co-ordinated A. fumigatus gene expression programme, governing
metabolic and physiological adaptation, which allows the organism to prosper
within the mammalian niche. As functions of phylogenetic conservation and
genetic locus, 28% and 30%, respectively, of the
A. fumigatus subtelomeric and lineage-specific gene
repertoires are induced relative to laboratory culture, and physically clustered
genes including loci directing pseurotin, gliotoxin and siderophore biosyntheses
are a prominent feature. Locationally biased A. fumigatus gene
expression is not prompted by in vitro iron limitation, acid,
alkaline, anaerobic or oxidative stress. However, subtelomeric gene expression
is favoured following ex vivo neutrophil exposure and in
comparative analyses of richly and poorly nourished laboratory cultured
germlings. We found remarkable concordance between the A.
fumigatus host-adaptation transcriptome and those resulting from
in vitro iron depletion, alkaline shift, nitrogen
starvation and loss of the methyltransferase LaeA. This first transcriptional
snapshot of a fungal genome during initiation of mammalian infection provides
the global perspective required to direct much-needed diagnostic and therapeutic
strategies and reveals genome organisation and subtelomeric diversity as
potential driving forces in the evolution of pathogenicity in the genus
Aspergillus. Airborne spores of the fungus Aspergillus fumigatus are present
in significant quantities worldwide and are responsible for a range of illnesses
from allergy to deadly invasive lung infection. A number of fungal properties
are likely required for germination and growth of the fungus in the host, and
now that the genome sequence of A. fumigatus is available it is
possible to address which genes become important during initiation of infection.
Understanding this might lead to new therapeutics and diagnostic tools. We have
compared A. fumigatus gene activation during infection in a
murine model to that in a laboratory culture to identify fungal attributes
preferentially employed during disease. Our analysis entailed measurement of
activity from most of the >9000 A. fumigatus genes,
identifying iron limitation, alkaline stress, and nitrogen starvation as
prominent stresses imposed by the host environment. We also found that genes
preferentially employed for infection occur in clusters and are more likely to
reside near the end of chromosomes, otherwise known as telomeres.
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Affiliation(s)
- Andrew McDonagh
- Department of Microbiology, Imperial College London, London, United
Kingdom
| | - Natalie D. Fedorova
- The J. Craig Venter Institute, Rockville, Maryland, United States of
America
| | - Jonathan Crabtree
- Department of Microbiology, Imperial College London, London, United
Kingdom
| | - Yan Yu
- The J. Craig Venter Institute, Rockville, Maryland, United States of
America
| | - Stanley Kim
- Korea University, College of Medicine, Department of Medicine, Anam-Dong,
Seongbuk-Gu, Seoul, Korea
| | - Dan Chen
- The J. Craig Venter Institute, Rockville, Maryland, United States of
America
| | - Omar Loss
- Department of Microbiology, Imperial College London, London, United
Kingdom
| | - Timothy Cairns
- Department of Microbiology, Imperial College London, London, United
Kingdom
| | - Gustavo Goldman
- Faculdade de Ciências Farmacêuticas de
Ribeirão Preto, Universidade de São Paulo,
Brazil
| | | | - Ken Haynes
- Department of Microbiology, Imperial College London, London, United
Kingdom
| | - Hubertus Haas
- Biocenter-Divison of Molecular Biology, Innsbruck Medical University,
Innsbruck, Austria
| | - Markus Schrettl
- Biocenter-Divison of Molecular Biology, Innsbruck Medical University,
Innsbruck, Austria
| | - Gregory May
- Microbiology and Molecular Genetics, UT-Houston Medical School, Houston,
Texas, United States of America
| | - William C. Nierman
- The J. Craig Venter Institute, Rockville, Maryland, United States of
America
- The George Washington University School of Medicine, Department of
Biochemistry and Molecular Biology, Washington D.C., United States of
America
| | - Elaine Bignell
- Department of Microbiology, Imperial College London, London, United
Kingdom
- * E-mail:
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