The Mushrom Kinome

The kinome analysis of the mushroom provides the first detailed kinome of a multicellular fungus, and a distant relative of Saccharomyces. Major findings include several highly-expanded unusual kinase families, direct orthologs of many fungal-specific S. cerevisiae kinases, and the presence of several kinase classes found in animals and/or Dictyostelium and secondarily lost from yeast.
Coprinopsis flowering body on PNAS cover
Genome evolution in mushrooms: insights from the assembled chromosomes of the basidiomycete Coprinopsis cinerea (Coprinus cinereus).
Stajich, JE, Wilke, SK, Ahrén, D, Au, TCH, Birren, BW, Borodovsky, M, Burns, C, Canback, B, Casselton, LA, Cheng, BCK, Deng, J, Dietrich, FS, Fargo, DC, Farman, M, Gathman, AC, Goldberg, J, Guigo, R, Hoegger, P, Hooker, JB, Huggins, A, James, TY, Kamada, T, Kilaru, S, Kodira, C, Kues, U, Kwan, H-S, Li, W, Lilly, WL, Ma, L-J, Mackey, AJ, Manning, G, Martin, F, Muraguchi, H, Palmerini, H, Ramesh, M, Rehmeyer, C, Shenoy, N, Stanke, M, Tunlid, A, Velagapudi, R, Vision, TJ, Zeng, Q, Zolan, ME, Pukkila, PJ. PNAS 107:11889-94 (Medline, PDF)

Highlights of the Coprinopsis Kinome

A second fungal kinome
As only the second highly annotated fungal kinome, Coprinopsis provides a good comparison to Saccharomyces cerevisiae. In particular, many yeast kinases could not be classified into shared subfamilies (and so stayed in "X-Unclassified" subfamilies). Coprinopsis has several clear orthologs of these genes, allowing us (soon!) to create new fungal-specific subfamilies. In contrast, other genes now more clearly are seen as duplicates from the recent history of Saccharomyces, and other kinases again are found in Coprinopsis and animals but not yeast, showing secondary loss in the lineage leading to Saccharomyces.

The crazy FunK1 family
The FunK1 family encodes very divergent kinases, and is found only in multicellular fungi, both in the Ascomycetes and Basidiomycetes. There is a huge expansion of the family in Coprinopsis, to 133 members, with considerable diversity within the family. Many of them map to duplicated regions, inculding 59 to a short region near the end of chromosome 9.

More Odd Kinases
Coprinopsis also has several other PKL fold kinases that may or may not be protein kinases, and further extend the sequence range of this class. These have been classified under the group 'PKL' in KinBase.


All Coprinopsis sequences and classification are now available through our KinBase database, where domain structures and alignments can also be generated (pending release, July 2010). Genome wide information is available from the Broad Institute Coprinopsis database.


The kinome analsis was carried out in co-operation with Jonathan Goldberg of the Broad Institute, and Jason Stajich from UC Riverside who also managed the overall genome project.