1 Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
2 Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.
3 R&D Department, Novozymes Latin America, Araucária, Paraná, Brazil.
4 Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands.
5 US Department of Energy Joint Genome Institute, Walnut Creek, California.
6 Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea.
7 Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
8 Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University, Marseille, France.
9 Institut National de la Recherche Agronomique, USC 1408 AFMB, Marseille, France.
10 Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
11 Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
12 Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.

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

Mol Ecol. 2018 12;27(23):4808-4819

Authors: Grum-Grzhimaylo AA, Falkoski DL, van den Heuvel J, Valero-Jiménez CA, Min B, Choi IG, Lipzen A, Daum CG, Aanen DK, Tsang A, Henrissat B, Bilanenko EN, de Vries RP, van Kan JAL, Grigoriev IV, Debets AJM

Abstract

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.

PMID: 30368956 [PubMed - in process]