Genome-enabled Investigations of the Role of Secreted Proteins and Reactive Metabolites in Carbon Degradation by Pure and Mixed Ascomycete Fungal Communities
EMSL Project ID
48100
Abstract
The Eumycete fungi (primarily Basidiomycota and Ascomycota) are key organisms in the degradation of wood, plant and animal material. While ascomycetes are less capable of rapid wood decay than basidiomycetes, they are considered more important lignocellulose degraders in compromised environmental systems. As our biogeochemical landscape continues to change, for instance through increasing soil temperatures, it can be assumed then that the relative role of ascomycetes in carbon processing will increase. Yet, the rates, mechanisms, and regulation of lignocelluose degradation by ascomycetes have undergone only minimal investigation and remain poorly understood. Fungi secrete a plethora of oxidative and hydrolytic enzymes for carbon degradation. In many cases, soluble small molecules are required for activation of the enzyme or to directly oxidize the carbon units. For instance, lignocellulose can be degraded via reaction with the extremely strong oxidants Mn(III) and hydroxyl radical, produced as a consequence of manganese peroxidase and laccase activity. Fungal-derived organic metabolites (e.g., oxalate) and electron transfer mediators (e.g., quinones) have also been implicated in stabilization of these soluble oxidants and production of radical species that degrade carbon. Ascomycete fungi are known to produce these soluble and insoluble oxidants, including various reactive oxygen species (ROS), quinone radicals, soluble Mn(III) and Mn oxides. In fact, we have 12 hyphal fungi isolated from contaminated sediments and coal mine drainage treatment systems that have the demonstrated ability to degrade cellulose, oxidize Mn(II) to Mn(III), precipitate highly reactive Mn oxide minerals and produce copious amounts of ROS. Production of oxidized Mn and ROS occurs in the fungal secretomes, whose reactivity varies with fungal species and as a function of growth stage. We have also recently observed that species-dependent interactions either enhances or inhibits ROS production and Mn(II) oxidation, further implicating secreted proteins and small molecules in ROS production, Mn(II) oxidation and possibly species recognition. We therefore predict that carbon degradation by these organisms involves a complex web of direct enzymatic activity, ROS and Mn(III) production, and small molecule synthesis (e.g., quinones).
The specific objective of this research is to identify the pathways for carbon degradation in a diverse group of ascomycete fungi, with particular attention to the role of secreted proteins and small molecules. Our proposed research approach involves three integrated tasks that increase in spatial and temporal resolution to progress to a molecular-level understanding of ascomycete carbon oxidation processes. The research proposed herein can only be accomplished by taking a multi-disciplinary approach using a complementary suite of spectroscopic, microscopic and genome enabled omics analysis, including EPR, NMR-based metabolomics, and both global and spatially resolved (e.g., IMS) proteomics. There are no sequenced genomes for most of the proposed fungi and very few closely related relatives, and thus EMSL-based metabolomic and proteomic analysis is reliant upon sequencing of the target fungi by JGI. By providing a molecular-level framework upon which to predict fungal induced carbon cycling, this research supports BER’s mission to understand the geochemical and biological determinants of environmental sustainability and stewardship, particularly through the use of genome-enabled discovery.
Project Details
Project type
FICUS Research
Start Date
2013-10-01
End Date
2015-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Co-Investigator(s)
Team Members
Related Publications
Zeiner CA, Purvine SO, Zink EM, Pasa-Tolic L, Chaput DL, et al. (2016) Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi. PLoS ONE 11(7): e0157844. doi: 10.1371/journal.pone.0157844
Zeiner CA, SO Purvine, EM Zink, L Pasa Tolic, DL Chaput, S Wu, CM Santelli, and CM Hansel. 2017. "Quantitative iTRAQ-based secretome analysis reveals species-specific and temporal shifts in carbon utilization strategies among manganese(II)-oxidizing Ascomycete fungi." Fungal Genetics and Biology : FG & B 106:61-75. doi:10.1016/j.fgb.2017.06.004