Abstract
Secondary metabolite clusters (SMCs) encode the machinery for fungal toxin production. However, understanding their function and analyzing their products requires investigation of the developmental and environmental conditions in which they are expressed. Gene expression is often restricted to specific and unexamined stages of the life cycle. Therefore, we applied comparative genomics analyses to identify SMCs in Neurospora crassa and analyzed extensive transcriptomic data spanning nine independent experiments from diverse developmental and environmental conditions to reveal their life cycle-specific gene expression patterns. We reported 20 SMCs comprising 177 genes—a manageable set for investigation of the roles of SMCs across the life cycle of the fungal model N. crassa—as well as gene sets coordinately expressed in 18 predicted SMCs during asexual and sexual growth under three nutritional and two temperature conditions. Divergent activity of SMCs between asexual and sexual development was reported. Of 126 SMC genes that we examined for knockout phenotypes, al-2 and al-3 exhibited phenotypes in asexual growth and conidiation, whereas os-5, poi-2, and pmd-1 exhibited phenotypes in sexual development. SMCs with annotated function in mating and crossing were actively regulated during the switch between asexual and sexual growth. Our discoveries call for attention to roles that SMCs may play in the regulatory switches controlling mode of development, as well as the ecological associations of those developmental stages that may influence expression of SMCs.
| Original language | American English |
|---|---|
| Journal | mSystems |
| Volume | 7 |
| Issue number | 3 |
| DOIs | |
| State | Published - Jun 2022 |
Bibliographical note
Funding Information:This study was supported by funding to J.P.T. from the National Institutes of Health R01 grant AI146584, the National Science Foundation grant IOS 1457044 to J.P.T., the National Science Foundation grant IOS 1456482 to F.T., and DEB-1638999 to J.S. O.Y., Z.W., and J.P.T. were supported by funding from the Binational Israel-U.S. Science Foundation grant number 2018712. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Funding Information:
We thank the Broad Institute, JGI, and FungiDB for making Neurospora crassa genomic and phenotype data available and Rudy Diaz for a helpful edit of the manuscript. We declare that no competing interests exist. This study was supported by funding to J.P.T. from the National Institutes of Health R01 grant AI146584, the National Science Foundation grant IOS 1457044 to J.P.T., the National Science Foundation grant IOS 1456482 to F.T., and DEB-1638999 to J.S. O.Y., Z.W., and J.P.T. were supported by funding from the Binational Israel-U.S. Science Foundation grant number 2018712. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Publisher Copyright:
© 2022 Wang et al.
Keywords
- Neurospora crassa
- asexual development
- environmental microbiology
- filamentous fungi
- gene cluster
- secondary metabolism
- sexual development
- transcriptomics