Omics Approaches for Understanding Biogenesis, Composition and Functions of Fungal Extracellular Vesicles

This is the final version. Available on open access from Frontiers Media via the DOI in this recordExtracellular vesicles (EVs) are lipid bilayer structures released by organisms from all kingdoms of life. The diverse biogenesis pathways of EVs result in a wide variety of physical properties and functions across different organisms. Fungal EVs were first described in 2007 and different omics approaches have been fundamental to understand their composition, biogenesis, and function. In this review, we discuss the role of omics in elucidating fungal EVs biology. Transcriptomics, proteomics, metabolomics, and lipidomics have each enabled the molecular characterization of fungal EVs, providing evidence that these structures serve a wide array of functions, ranging from key carriers of cell wall biosynthetic machinery to virulence factors. Omics in combination with genetic approaches have been instrumental in determining both biogenesis and cargo loading into EVs. We also discuss how omics technologies are being employed to elucidate the role of EVs in antifungal resistance, disease biomarkers, and their potential use as vaccines. Finally, we review recent advances in analytical technology and multi-omic integration tools, which will help to address key knowledge gaps in EVs biology and translate basic research information into urgently needed clinical applications such as diagnostics, and immuno- and chemotherapies to fungal infections.NIHPacific Northwest National Laboratory (PNNL)CNPq/Science Without Borders Science Program, BrazilJohns Hopkins Malaria Research InstituteFAPESPCAPESCNPqMedical Research Council (MRC

Regulation of yeast-to-hyphae transition in Yarrowia lipolytica

© 2018 Pomraning et al. The yeast Yarrowia lipolytica undergoes a morphological transition from yeast-to-hyphal growth in response to environmental conditions. A forward genetic screen was used to identify mutants that reliably remain in the yeast phase, which were then assessed by whole-genome sequencing. All the smooth mutants identified, so named because of their colony morphology, exhibit independent loss of DNA at a repetitive locus made up of interspersed ribosomal DNA and short 10- to 40-mer telomere-like repeats. The loss of repetitive DNA is associated with downregulation of genes with stress response elements (5'-CCCCT-3') and upregulation of genes with cell cycle box (5'-ACGCG-3') motifs in their promoter region. The stress response element is bound by the transcription factor Msn2p in Saccharomyces cerevisiae. We confirmed that the Y. lipolytica msn2 (Ylmsn2) ortholog is required for hyphal growth and found that overexpression of Ylmsn2 enables hyphal growth in smooth strains. The cell cycle box is bound by the Mbp1p/Swi6p complex in S. cerevisiae to regulate G1-to-S phase progression. We found that overexpression of either the Ylmbp1 or Ylswi6 homologs decreased hyphal growth and that deletion of either Ylmbp1 or Ylswi6 promotes hyphal growth in smooth strains. A second forward genetic screen for reversion to hyphal growth was performed with the smooth-33 mutant to identify additional genetic factors regulating hyphal growth in Y. lipolytica. Thirteen of the mutants sequenced from this screen had coding mutations in five kinases, including the histidine kinases Ylchk1 and Ylnik1 and kinases of the high-osmolarity glycerol response (HOG) mitogen-activated protein (MAP) kinase cascade Ylssk2, Ylpbs2, and Ylhog1. Together, these results demonstrate that Y. lipolytica transitions to hyphal growth in response to stress through multiple signaling pathways

Microbial oils as nutraceuticals and animal feeds

45 p.-5 fig.-3 tab.Lipids and oils are produced by all single-cell organisms for essential structural and functional roles; however, the term single cell oils (SCOs) is mainly restricted to describe the lipids produced by a limited number of oleaginous microorganisms (archaea, bacteria, yeast, fungi, and microalgae) with oil contents higher than 20% of biomass weigh. SCOs have different fatty acid compositions from those of plant seed or fish oils and are nowadays considered as new sources of nutraceuticals and animal feeds. In spite of the current commercial success of some SCOs, the development of more efficient microbial fermentation processes and the possibility of manipulating by systems metabolic engineering the lipid composition of cells require new biotechnological strategies to obtain high yields of the desired SCOs. Understanding the synthesis and regulatory mechanisms involved in the production of SCOs is fundamental to eliminate the metabolic bottlenecks that impair achieving high oil yields.This chapter is supported by grants from the Community of Madrid and the Structural Funds of the European Union (Ref: S2013/ABI2783 (INSPIRA1-CM)), the Ministry of Economy, the Industry and Competitiveness (Ref: RTC-2016-4860-2; Ref: BFU2014-55534-C2-1-P), and the Intramural Program of the CSIC (Ref: 201420E086) and the H2020 FET-OPEN program (LIAR: Ref 686585).Peer reviewe