Draft Genome Sequence of Penicillium marneffei Strain PM1

Woo, Patrick C. Y.; Lau, Susanna K. P.; Liu, Bin; Cai, James J.; Chong, Ken T. K.; Tse, Herman; Kao, Richard Yi Tsun; Chan, Che-Man; Chow, Wang Ngai; Yuen, Kwok‐Yung

doi:10.1128/ec.05255-11

Cited by 37 publications

(39 citation statements)

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“…The draft genome of P. marneffei PM1 was obtained using the whole-genome shotgun (WGS) approach (29). A total of 311,029 WGS reads of an average length of 690 bp were assembled into 2,780 contigs, which were subsequently ordered into 273 supercontigs ( Table 1).…”

Section: Resultsmentioning

confidence: 99%

“…In a previous publication (29), we briefly announced the sequencing of the genome of P. marneffei strain PM1, without providing in-depth genomic and transcriptomic analyses. In the present study, we use comparative genomic and transcriptomic approaches to systematically characterize P. marneffei genomic sequences and global gene expression.…”

Section: P Marneffei Blastomyces Dermatitidis Histoplasma Capsulatmentioning

confidence: 99%

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Unraveling the Molecular Basis of Temperature-Dependent Genetic Regulation in Penicillium marneffei

et al. 2013

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c Penicillium marneffei is an opportunistic fungal pathogen endemic in Southeast Asia, causing lethal systemic infections in immunocompromised patients. P. marneffei grows in a mycelial form at the ambient temperature of 25°C and transitions to a yeast form at 37°C. The ability to alternate between the mycelial and yeast forms at different temperatures, namely, thermal dimorphism, has long been considered critical for the pathogenicity of P. marneffei, yet the underlying genetic mechanisms remain elusive. Here we employed high-throughput sequencing to unravel global transcriptional profiles of P. marneffei PM1 grown at 25 and 37°C. Among ϳ11,000 protein-coding genes, 1,447 were overexpressed and 1,414 were underexpressed at 37°C. Counterintuitively, heat-responsive genes, predicted in P. marneffei through sequence comparison, did not tend to be overexpressed at 37°C. These results suggest that P. marneffei may take a distinct strategy of genetic regulation at the elevated temperature; the current knowledge concerning fungal heat response, based on studies of model fungal organisms, may not be applicable to P. marneffei. Our results further showed that the tandem repeat sequences (TRSs) are overrepresented in coding regions of P. marneffei genes, and TRS-containing genes tend to be overexpressed at 37°C. Furthermore, genomic sequences and expression data were integrated to characterize gene clusters, multigene families, and species-specific genes of P. marneffei. In sum, we present an integrated analysis and a comprehensive resource toward a better understanding of temperature-dependent genetic regulation in P. marneffei.

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Section: Resultsmentioning

confidence: 99%

Section: P Marneffei Blastomyces Dermatitidis Histoplasma Capsulatmentioning

confidence: 99%

Unraveling the Molecular Basis of Temperature-Dependent Genetic Regulation in Penicillium marneffei

et al. 2013

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“…Proteins were identified by PMF using the ms ‐ fit software (http://prospector.ucsf.edu) and an in‐house sequence database of P. marneffei PM1 proteins generated using available P. marneffei genome sequence data (Genbank accession no. AGCC00000000 and ABAR00000000) . At least three independent experiments for each growth condition were performed to ensure reproducibility of results.…”

Section: Methodsmentioning

confidence: 99%

Proteome profiling of the dimorphic fungusPenicillium marneffeiextracellular proteins and identification of glyceraldehyde-3-phosphate dehydrogenase as an important adhesion factor for conidial attachment

Lau

Tse

Chan

et al. 2013

FEBS J

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Despite being the most important thermal dimorphic fungus causing systemic mycosis in Southeast Asia, the pathogenic mechanisms of Penicillium marneffei remain largely unknown. By comparing the extracellular proteomes of P. marneffei in mycelial and yeast phases, we identified 12 differentially expressed proteins among which glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and heat shock protein 60 (HSP60) were found to be upregulated in mycelial and yeast phases respectively. Based on previous findings in other pathogens, we hypothesized that these two extracellular proteins may be involved in adherence during P. marneffei-host interaction. Using inhibition assays with recombinant GAPDH (rGAPDH) proteins and anti-rGAPDH sera, we demonstrated that adhesion of P. marneffei conidia to fibronectin and laminin was inhibited by rGAPDH or rabbit anti-rGAPDH serum in a dose-dependent manner. Similarly, a dose-dependent inhibition of conidial adherence to A549 pneumocytes by rGAPDH or rabbit anti-rGAPDH serum was observed, suggesting that P. marneffei GAPDH can mediate binding of conidia to human extracellular matrix proteins and pneumocytes. However, HSP60 did not exhibit similar inhibition on conidia adherence, and neither GAPDH norHSP60 exhibited inhibition on adherence to J774 or THP-1 macrophage cell lines. This report demonstrates GAPDH as an adherence factor in P. marneffei by mediating conidia adherence to host bronchoalveolar epithelium during the early establishment phase of infection.Abbreviations 2-DE, two-dimensional gel electrophoresis; DTT, dithiothreitol; ECM, extracellular matrix; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; HRP, horseradish peroxidase; HSP60, heat shock protein 60; pAb, polyclonal antibody; PGK, phosphoglycerate kinase; PMF, peptide mass fingerprinting; PMSF, phenylmethanesulfonyl fluoride; rGAPDH, recombinant glyceraldehyde-3-phosphate dehydrogenase; rHSP60, recombinant heat shock protein 60.

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“…In 2002, we started the P. marneffei genome project in an attempt to expedite the study of biology, epidemiology and virulence factors of this dimorphic fungus [34][35][36][37][38][39][40][41]. Based on the available genome sequence data, potential genes encoding proteins important for miRNA biogenesis can be identified in P. marneffei.…”

Section: Introductionmentioning

confidence: 99%

Identification of MicroRNA-Like RNAs in Mycelial and Yeast Phases of the Thermal Dimorphic Fungus Penicillium marneffei

et al. 2013

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Background Penicillium marneffei is the most important thermal dimorphic fungus causing systemic mycosis in China and Southeast Asia. While miRNAs are increasingly recognized for their roles in post-transcriptional regulation of gene expression in animals and plants, miRNAs in fungi were less well studied and their potential roles in fungal dimorphism were largely unknown. Based on P. marneffei genome sequence, we hypothesize that miRNA-like RNAs (milRNAs) may be expressed in the dimorphic fungus.Methodology/Principal FindingsWe attempted to identify milRNAs in P. marneffei in both mycelial and yeast phase using high-throughput sequencing technology. Small RNAs were more abundantly expressed in mycelial than yeast phase. Sequence analysis revealed 24 potential milRNA candidates, including 17 candidates in mycelial and seven in yeast phase. Two genes, dcl-1 and dcl-2, encoding putative Dicer-like proteins and the gene, qde-2, encoding Argonaute-like protein, were identified in P. marneffei. Phylogenetic analysis showed that dcl-2 of P. marneffei was more closely related to the homologues in other thermal dimorphic pathogenic fungi than to Penicillium chrysogenum and Aspergillus spp., suggesting the co-evolution of dcl-2 among the thermal dimorphic fungi. Moreover, dcl-2 demonstrated higher mRNA expression levels in mycelial than yeast phase by 7 folds (P<0.001). Northern blot analysis confirmed the expression of two milRNAs, PM-milR-M1 and PM-milR-M2, only in mycelial phase. Using dcl-1KO, dcl-2KO, dclDKO and qde-2KO deletion mutants, we showed that the biogenesis of both milRNAs were dependent on dcl-2 but not dcl-1 or qde-2. The mRNA expression levels of three predicted targets of PM-milR-M1 were upregulated in knockdown strain PM-milR-M1 KD, supporting regulatory function of milRNAs.Conclusions/SignificanceOur findings provided the first evidence for differential expression of milRNAs in different growth phases of thermal dimorphic fungi and shed light on the evolution of fungal proteins involved in milRNA biogenesis and possible role of post-transcriptional control in governing thermal dimorphism.

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Draft Genome Sequence of Penicillium marneffei Strain PM1

Cited by 37 publications

References 11 publications

Unraveling the Molecular Basis of Temperature-Dependent Genetic Regulation in Penicillium marneffei

Unraveling the Molecular Basis of Temperature-Dependent Genetic Regulation in Penicillium marneffei

Proteome profiling of the dimorphic fungusPenicillium marneffeiextracellular proteins and identification of glyceraldehyde-3-phosphate dehydrogenase as an important adhesion factor for conidial attachment

Identification of MicroRNA-Like RNAs in Mycelial and Yeast Phases of the Thermal Dimorphic Fungus Penicillium marneffei

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