Limits...
Cell-type-specific transcriptional profiles of the dimorphic pathogen Penicillium marneffei reflect distinct reproductive, morphological, and environmental demands.

Pasricha S, Payne M, Canovas D, Pase L, Ngaosuwankul N, Beard S, Oshlack A, Smyth GK, Chaiyaroj SC, Boyce KJ, Andrianopoulos A - G3 (Bethesda) (2013)

Bottom Line: Deletion of ergM resulted in severe growth defects with increased sensitivity to azole-type antifungal agents but not amphotericin B.The data defined gene classes based on spatio-temporal expression such as those expressed early in the dimorphic switch but not in the terminal cell types and those expressed late.Such classifications have been helpful in linking a given gene of interest to its expression pattern throughout the P. marneffei dimorphic life cycle and its likely role in pathogenicity.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Melbourne, Victoria 3010, Australia.

ABSTRACT
Penicillium marneffei is an opportunistic human pathogen endemic to Southeast Asia. At 25° P. marneffei grows in a filamentous hyphal form and can undergo asexual development (conidiation) to produce spores (conidia), the infectious agent. At 37° P. marneffei grows in the pathogenic yeast cell form that replicates by fission. Switching between these growth forms, known as dimorphic switching, is dependent on temperature. To understand the process of dimorphic switching and the physiological capacity of the different cell types, two microarray-based profiling experiments covering approximately 42% of the genome were performed. The first experiment compared cells from the hyphal, yeast, and conidiation phases to identify "phase or cell-state-specific" gene expression. The second experiment examined gene expression during the dimorphic switch from one morphological state to another. The data identified a variety of differentially expressed genes that have been organized into metabolic clusters based on predicted function and expression patterns. In particular, C-14 sterol reductase-encoding gene ergM of the ergosterol biosynthesis pathway showed high-level expression throughout yeast morphogenesis compared to hyphal. Deletion of ergM resulted in severe growth defects with increased sensitivity to azole-type antifungal agents but not amphotericin B. The data defined gene classes based on spatio-temporal expression such as those expressed early in the dimorphic switch but not in the terminal cell types and those expressed late. Such classifications have been helpful in linking a given gene of interest to its expression pattern throughout the P. marneffei dimorphic life cycle and its likely role in pathogenicity.

Show MeSH

Related in: MedlinePlus

Gene expression clustering pattern in P. marneffei cell states. Clustering analysis was performed using the top 400 unique genes differentially expressed in hyphal, yeast, or conidiation conditions with MeV Six clusters were created using k-means clustering with Pearson correlation. The median of gene expression under each condition is represented as a continuous black line. The dark shaded region in each graph represents the differential expression values that lie within the first and third quartiles of the cluster. The lighter shading extends the spread of data from zero to the fourth quartile. (A) Genes upregulated in hyphal cells. (B) Genes upregulated in hyphal cells, followed by conidiation, and genes downregulated in yeast cells. (C) Genes upregulated during conidiation. (D) Genes upregulated in both hyphal and yeast cells with respect to conidiation. (E) Genes upregulated in hyphae and during conidiation, with respect to yeast cells. (F) Genes upregulated in yeast cells.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3815061&req=5

fig2: Gene expression clustering pattern in P. marneffei cell states. Clustering analysis was performed using the top 400 unique genes differentially expressed in hyphal, yeast, or conidiation conditions with MeV Six clusters were created using k-means clustering with Pearson correlation. The median of gene expression under each condition is represented as a continuous black line. The dark shaded region in each graph represents the differential expression values that lie within the first and third quartiles of the cluster. The lighter shading extends the spread of data from zero to the fourth quartile. (A) Genes upregulated in hyphal cells. (B) Genes upregulated in hyphal cells, followed by conidiation, and genes downregulated in yeast cells. (C) Genes upregulated during conidiation. (D) Genes upregulated in both hyphal and yeast cells with respect to conidiation. (E) Genes upregulated in hyphae and during conidiation, with respect to yeast cells. (F) Genes upregulated in yeast cells.

Mentions: Trends in gene expression were examined by k-means clustering using MeV (Saeed et al. 2006). The data were clustered into six general expression profiles using Pearson correlation (Figure 2). Gene clusters reflect genes that are exclusively expressed or upregulated in one state, as well as those coregulated in two states (represented as percentages of total expression). Because both hyphal growth and conidiation occur at 25°, and because conidiation begins only after a period of hyphal growth, the presence of genes commonly upregulated in both states is expected. Genes that showed increased expression in hyphal and yeast cells relative to conidiation are likely to represent general cellular processes required for vegetative growth as opposed to those specific for the differentiation processes involved in conidiation. Interestingly, there is an underrepresentation of genes downregulated in hyphal cells and upregulated during both conidiation and in yeast cells. This may be indicative of the difference in specificity involved in reproduction by fission in yeast cells and differentiation during conidiation. Binary fission involves the segregation of replicated genetic material to the poles of a cell that then splits into two identical cells. However, asexual reproduction during conidiation is performed in a budding fashion with the specialized differentiation of uninucleate cells (Borneman et al. 2000; Clutterbuck 1969). Genes that have opposing expression in these cell states may provide information regarding what gene groups govern these differences in cell division. As a way of addressing what categories of genes are within each cluster and whether any of these are enriched for a particular state, GO terms were assigned to each gene represented by the microarray probes, and these were curated further by a qualitative literature-based approach. These GO assignments were then used to examine significant gene relationships within each cluster (p-value < 0.05) (http://go.princeton.edu/) (Figure S2), and they highlighted, in particular, the enrichment of gene groups during conidiation (Table 2).


Cell-type-specific transcriptional profiles of the dimorphic pathogen Penicillium marneffei reflect distinct reproductive, morphological, and environmental demands.

Pasricha S, Payne M, Canovas D, Pase L, Ngaosuwankul N, Beard S, Oshlack A, Smyth GK, Chaiyaroj SC, Boyce KJ, Andrianopoulos A - G3 (Bethesda) (2013)

Gene expression clustering pattern in P. marneffei cell states. Clustering analysis was performed using the top 400 unique genes differentially expressed in hyphal, yeast, or conidiation conditions with MeV Six clusters were created using k-means clustering with Pearson correlation. The median of gene expression under each condition is represented as a continuous black line. The dark shaded region in each graph represents the differential expression values that lie within the first and third quartiles of the cluster. The lighter shading extends the spread of data from zero to the fourth quartile. (A) Genes upregulated in hyphal cells. (B) Genes upregulated in hyphal cells, followed by conidiation, and genes downregulated in yeast cells. (C) Genes upregulated during conidiation. (D) Genes upregulated in both hyphal and yeast cells with respect to conidiation. (E) Genes upregulated in hyphae and during conidiation, with respect to yeast cells. (F) Genes upregulated in yeast cells.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815061&req=5

fig2: Gene expression clustering pattern in P. marneffei cell states. Clustering analysis was performed using the top 400 unique genes differentially expressed in hyphal, yeast, or conidiation conditions with MeV Six clusters were created using k-means clustering with Pearson correlation. The median of gene expression under each condition is represented as a continuous black line. The dark shaded region in each graph represents the differential expression values that lie within the first and third quartiles of the cluster. The lighter shading extends the spread of data from zero to the fourth quartile. (A) Genes upregulated in hyphal cells. (B) Genes upregulated in hyphal cells, followed by conidiation, and genes downregulated in yeast cells. (C) Genes upregulated during conidiation. (D) Genes upregulated in both hyphal and yeast cells with respect to conidiation. (E) Genes upregulated in hyphae and during conidiation, with respect to yeast cells. (F) Genes upregulated in yeast cells.
Mentions: Trends in gene expression were examined by k-means clustering using MeV (Saeed et al. 2006). The data were clustered into six general expression profiles using Pearson correlation (Figure 2). Gene clusters reflect genes that are exclusively expressed or upregulated in one state, as well as those coregulated in two states (represented as percentages of total expression). Because both hyphal growth and conidiation occur at 25°, and because conidiation begins only after a period of hyphal growth, the presence of genes commonly upregulated in both states is expected. Genes that showed increased expression in hyphal and yeast cells relative to conidiation are likely to represent general cellular processes required for vegetative growth as opposed to those specific for the differentiation processes involved in conidiation. Interestingly, there is an underrepresentation of genes downregulated in hyphal cells and upregulated during both conidiation and in yeast cells. This may be indicative of the difference in specificity involved in reproduction by fission in yeast cells and differentiation during conidiation. Binary fission involves the segregation of replicated genetic material to the poles of a cell that then splits into two identical cells. However, asexual reproduction during conidiation is performed in a budding fashion with the specialized differentiation of uninucleate cells (Borneman et al. 2000; Clutterbuck 1969). Genes that have opposing expression in these cell states may provide information regarding what gene groups govern these differences in cell division. As a way of addressing what categories of genes are within each cluster and whether any of these are enriched for a particular state, GO terms were assigned to each gene represented by the microarray probes, and these were curated further by a qualitative literature-based approach. These GO assignments were then used to examine significant gene relationships within each cluster (p-value < 0.05) (http://go.princeton.edu/) (Figure S2), and they highlighted, in particular, the enrichment of gene groups during conidiation (Table 2).

Bottom Line: Deletion of ergM resulted in severe growth defects with increased sensitivity to azole-type antifungal agents but not amphotericin B.The data defined gene classes based on spatio-temporal expression such as those expressed early in the dimorphic switch but not in the terminal cell types and those expressed late.Such classifications have been helpful in linking a given gene of interest to its expression pattern throughout the P. marneffei dimorphic life cycle and its likely role in pathogenicity.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, University of Melbourne, Victoria 3010, Australia.

ABSTRACT
Penicillium marneffei is an opportunistic human pathogen endemic to Southeast Asia. At 25° P. marneffei grows in a filamentous hyphal form and can undergo asexual development (conidiation) to produce spores (conidia), the infectious agent. At 37° P. marneffei grows in the pathogenic yeast cell form that replicates by fission. Switching between these growth forms, known as dimorphic switching, is dependent on temperature. To understand the process of dimorphic switching and the physiological capacity of the different cell types, two microarray-based profiling experiments covering approximately 42% of the genome were performed. The first experiment compared cells from the hyphal, yeast, and conidiation phases to identify "phase or cell-state-specific" gene expression. The second experiment examined gene expression during the dimorphic switch from one morphological state to another. The data identified a variety of differentially expressed genes that have been organized into metabolic clusters based on predicted function and expression patterns. In particular, C-14 sterol reductase-encoding gene ergM of the ergosterol biosynthesis pathway showed high-level expression throughout yeast morphogenesis compared to hyphal. Deletion of ergM resulted in severe growth defects with increased sensitivity to azole-type antifungal agents but not amphotericin B. The data defined gene classes based on spatio-temporal expression such as those expressed early in the dimorphic switch but not in the terminal cell types and those expressed late. Such classifications have been helpful in linking a given gene of interest to its expression pattern throughout the P. marneffei dimorphic life cycle and its likely role in pathogenicity.

Show MeSH
Related in: MedlinePlus