Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei

PLoS Genet. 2014 Oct 16;10(10):e1004662. doi: 10.1371/journal.pgen.1004662. eCollection 2014 Oct.

Abstract

Systemic dimorphic fungi cause more than one million new infections each year, ranking them among the significant public health challenges currently encountered. Penicillium marneffei is a systemic dimorphic fungus endemic to Southeast Asia. The temperature-dependent dimorphic phase transition between mycelium and yeast is considered crucial for the pathogenicity and transmission of P. marneffei, but the underlying mechanisms are still poorly understood. Here, we re-sequenced P. marneffei strain PM1 using multiple sequencing platforms and assembled the genome using hybrid genome assembly. We determined gene expression levels using RNA sequencing at the mycelial and yeast phases of P. marneffei, as well as during phase transition. We classified 2,718 genes with variable expression across conditions into 14 distinct groups, each marked by a signature expression pattern implicated at a certain stage in the dimorphic life cycle. Genes with the same expression patterns tend to be clustered together on the genome, suggesting orchestrated regulations of the transcriptional activities of neighboring genes. Using qRT-PCR, we validated expression levels of all genes in one of clusters highly expressed during the yeast-to-mycelium transition. These included madsA, a gene encoding MADS-box transcription factor whose gene family is exclusively expanded in P. marneffei. Over-expression of madsA drove P. marneffei to undergo mycelial growth at 37°C, a condition that restricts the wild-type in the yeast phase. Furthermore, analyses of signature expression patterns suggested diverse roles of secreted proteins at different developmental stages and the potential importance of non-coding RNAs in mycelium-to-yeast transition. We also showed that RNA structural transition in response to temperature changes may be related to the control of thermal dimorphism. Together, our findings have revealed multiple molecular mechanisms that may underlie the dimorphic transition in P. marneffei, providing a powerful foundation for identifying molecular targets for mechanism-based interventions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Fungal Proteins / genetics
  • Fungal Proteins / metabolism
  • Gene Expression Regulation, Fungal*
  • Genome, Fungal
  • MADS Domain Proteins / genetics
  • Multigene Family
  • Mycelium / genetics
  • Penicillium / genetics*
  • Penicillium / growth & development
  • Penicillium / pathogenicity
  • RNA, Fungal / chemistry
  • Temperature
  • Transcription Factors / genetics
  • Transcriptome

Substances

  • Fungal Proteins
  • MADS Domain Proteins
  • RNA, Fungal
  • Transcription Factors

Associated data

  • BioProject/PRJNA251717
  • BioProject/PRJNA251718

Grant support

EY is supported by TAMU-CVM Postdoctoral Trainee Research Grant, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University. KYY, PCYW and SKPL are supported by the commissioned grant of the Research Fund for the control of infectious disease, Food and Health Bureau of the Hong Kong Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.