A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction

Candice L Swift; Nikola G Malinov; Stephen J Mondo; Asaf Salamov; Igor V Grigoriev; Michelle A O'Malley

doi:10.3389/ffunb.2021.708358

A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction

Front Fungal Biol. 2021 Aug 9:2:708358. doi: 10.3389/ffunb.2021.708358. eCollection 2021.

Authors

Candice L Swift¹, Nikola G Malinov¹, Stephen J Mondo^{2

3}, Asaf Salamov², Igor V Grigoriev^{2

4

5}, Michelle A O'Malley^{1

6}

Affiliations

¹ Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States.
² U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
³ Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States.
⁴ Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States.
⁵ Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States.
⁶ Joint BioEnergy Institute, Emeryville, CA, United States.

Abstract

Anaerobic fungi are a potential biotechnology platform to produce biomass-degrading enzymes. Unlike model fungi such as yeasts, stress responses that are relevant during bioprocessing have not yet been established for anaerobic fungi. In this work, we characterize both the heat shock and unfolded protein responses of four strains of anaerobic fungi (Anaeromyces robustus, Caecomyces churrovis, Neocallimastix californiae, and Piromyces finnis). The inositol-requiring 1 (Ire1) stress sensor, which typically initiates the fungal UPR, was conserved in all four genomes. However, these genomes also encode putative transmembrane kinases with catalytic domains that are similar to the metazoan stress-sensing enzyme PKR-like endoplasmic reticulum kinase (PERK), although whether they function in the UPR of anaerobic fungi remains unclear. Furthermore, we characterized the global transcriptional responses of Anaeromyces robustus and Neocallimastix californiae to a transient heat shock. Both fungi exhibited the hallmarks of ER stress, including upregulation of genes with functions in protein folding, ER-associated degradation, and intracellular protein trafficking. Relative to other fungi, the genomes of Neocallimastigomycetes contained the greatest gene percentage of HSP20 and HSP70 chaperones, which may serve to stabilize their asparagine-rich genomes. Taken together, these results delineate the unique stress response of anaerobic fungi, which is an important step toward their development as a biotechnology platform to produce enzymes and valuable biomolecules.

Keywords: HSR; UPR; anaerobic fungi; chaperones; protein folding; stress response; transcriptomics.