The obligate alkalophilic soda‐lake fungus Sodiomyces alkalinus has shifted to a protein diet

• Published in: Molecular ecology Vol. 27; no. 23; pp. 4808 - 4819
• Main Authors: Grum‐Grzhimaylo, Alexey A., Falkoski, Daniel L., Heuvel, Joost, Valero‐Jiménez, Claudio A., Min, Byoungnam, Choi, In‐Geol, Lipzen, Anna, Daum, Chris G., Aanen, Duur K., Tsang, Adrian, Henrissat, Bernard, Bilanenko, Elena N., Vries, Ronald P., Kan, Jan A. L., Grigoriev, Igor V., Debets, Alfons J. M.
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.12.2018; Wiley; Wiley-Blackwell
• Subjects: alkalophilic fungus; BASIC BIOLOGICAL SCIENCES; brine shrimps; Cell walls; Crustaceans; Diet; Enzymes; EPS; Food; Food availability; Food plants; Food sources; Fungi; Gene transfer; Genomes; Hemicellulases; HGT; Laboratorium voor Erfelijkheidsleer; Laboratorium voor Fytopathologie; Laboratorium voor Phytopathologie; Laboratory of Genetics; Laboratory of Phytopathology; Lakes; Life Sciences; PE&RC; pH effects; Plant biomass; Prokaryotes; Proteins; Proteolysis; Proteomes; Quantitative Methods; Sodiomyces alkalinus; Substrates; enzymes; prokaryotes; Sodiomyces alkalinus; HGT; alkalophilic fungus; brine shrimps
• ISSN: 0962-1083; 1365-294X
• DOI: 10.1111/mec.14912

Sodiomyces alkalinus is one of the very few alkalophilic fungi, adapted to grow optimally at high pH. It is widely distributed at the plant‐deprived edges of extremely alkaline lakes and locally abundant. We sequenced the genome of S. alkalinus and reconstructed evolution of catabolic enzymes, using a phylogenomic comparison. We found that the genome of S. alkalinus is larger, but its predicted proteome is smaller and heavily depleted of both plant‐degrading enzymes and proteinases, when compared to its closest plant‐pathogenic relatives. Interestingly, despite overall losses, S. alkalinus has retained many proteinases families and acquired bacterial cell wall‐degrading enzymes, some of them via horizontal gene transfer from bacteria. This fungus has very potent proteolytic activity at high pH values, but slowly induced low activity of cellulases and hemicellulases. Our experimental and in silico data suggest that plant biomass, a common food source for most fungi, is not a preferred substrate for S. alkalinus in its natural environment. We conclude that the fungus has abandoned the ancestral plant‐based diet and has become specialized in a more protein‐rich food, abundantly available in soda lakes in the form of prokaryotes and small crustaceans.