title: PacC and pH-dependent transcriptome of the mycotrophic fungus Trichoderma virens.
abstract: BACKGROUND
  In fungi, environmental pH is an important signal for development, and successful host colonization depends on homeostasis. Surprisingly, little is known regarding the role of pH in fungal-fungal interactions. Species of Trichoderma grow as soil saprobes but many are primarily mycotrophic, using other fungi as hosts. Therefore, Trichoderma spp. are studied for their potential in biocontrol of plant diseases. Particularly in alkaline soil, pH is a critical limiting factor for these biofungicides, whose optimal growth pH is 4-6. Gaining an understanding of pH adaptability is an important step in broadening the activity spectrum of these economically important fungi.
  
  
  RESULTS
  We studied the pH-responsive transcription factor PacC by gene knockout and by introduction of a constitutively active allele (pacCc). ΔpacC mutants exhibited reduced growth at alkaline pH, while pacCc strains grew poorly at acidic pH. In plate confrontation assays ΔpacC mutants showed decreased ability to compete with the plant pathogens Rhizoctonia solani and Sclerotium rolfsii. The pacCc strain exhibited an overgrowth of R. solani that was comparable to the wild type, but was unable to overgrow S. rolfsii. To identify genes whose expression is dependent on pH and pacC, we designed oligonucleotide microarrays from the transcript models of the T. virens genome, and compared the transcriptomes of wild type and mutant cultures exposed to high or low pH. Transcript levels from several functional classes were dependent on pacC, on pH, or on both. Furthermore, the expression of a set of pacC-dependent genes was increased in the constitutively-active pacCc strain, and was pH-independent in some, but not all cases.
  
  
  CONCLUSIONS
  PacC is important for biocontrol-related antagonism of other fungi by T. virens. As much as 5% of the transcriptome is pH-dependent, and of these genes, some 25% depend on pacC. Secondary metabolite biosynthesis and ion transport are among the relevant gene classes. We suggest that ΔpacC mutants may have lost their full biocontrol potential due to their inability to adapt to alkaline pH, to perceive ambient pH, or both. The results raise the novel possibility of genetically manipulating Trichoderma in order to improve adaptability and biocontrol at alkaline pH.
authors: Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
authors: Naomi
authors: N
authors: Trushina
authors: Michal
authors: M
authors: Levin
authors: Prasun K
authors: PK
authors: Mukherjee
authors: Benjamin A
authors: BA
authors: Horwitz
mesh_terms: D000483:Alleles; D001483:Base Sequence; D001487:Basidiomycota / Q000254:growth & development; D001665:Binding Sites; D016000:Cluster Analysis; D004247:DNA / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics* / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D055786:Gene Knockout Techniques; D005800:Genes, Fungal; D006863:Hydrogen-Ion Concentration; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D010935:Plant Diseases / Q000382:microbiology; D012232:Rhizoctonia / Q000254:growth & development; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D014242:Trichoderma / Q000235:genetics* / Q000254:growth & development
chemical_list: D005656:Fungal Proteins; D014157:Transcription Factors; D004247:DNA