This work provides an important stepping stone in understanding and eventually controlling this pathogen which is devastating cacao plantations. An associated review describes what we have and can learn about Witches’ broom disease.

See related:

• Will you always be able to satisfy that chocolate craving?
• Theobroma cacao to be sequenced, Oompa Loompa genome to follow.

Jorge MC Mondego, Marcelo F Carazzolle, Gustavo GL Costa, Eduardo F Formighieri, Lucas P Parizzi, Johana Rincones, Carolina Cotomacci, Dirce M Carraro, Anderson F Cunha, Helaine Carrer, Ramon O Vidal, Raissa C Estrela, Odalys Garcia, Daniela PT Thomazella, Bruno V de Oliveira, Acassia BL Pires, Maria Carolina S Rio, Marcos Renato R Araujo, Marcos H de Moraes, Luis AB Castro, Karina P Gramacho, Marilda S Goncalves, Jose P Moura Neto, Aristoteles Goes Neto, Luciana V Barbosa, Mark J Guiltinan, Bryan A Bailey, Lyndel W Meinhardt, Julio CM Cascardo, Goncalo AG Pereira (2008). A genome survey of Moniliophthora perniciosa gives new insights into Witches’ Broom Disease of cacao BMC Genomics, 9 (1) DOI: 10.1186/1471-2164-9-548

I find the current nomenclature for this family of genes confusing but it has been I am sure a difficult job and wrangled to a large part by David Nelson (who also has a new paper on the CYPome of Aspergillus nidulans). I have found it difficult to follow the logic for naming these members, as it didn’t seem to be particularly phylogenetic at first, although I think that has improved. However, a stable and solid reference database is needed to for naming these gene members and for mapping new members in through straightforward analyses is an essential resource. Park et al have made great inroads to that end and it may indeed meet needs (I am cautious to say it is solved without more exploration or some sense of whether it is intended or will be taken up as just that sort of reference by the P450 community).  It has seemed to me that a proper phylogenetic (or really, a phylogenomic) approach is essential for naming the P450 member genes as orthologous or paralogous members across multiple species. The group has defined their classes as clusters of homologs (e.g. Mg004 is Magnaporthe grisea gene in Cluster 9.1) and linked these also to the Nelson nomeclature (CYP68E1).  By defining orthologous family members we can make more interpretations about how to transfer functional annotation in a truly phylogenomic context. 

The overall family is so large and diverse (they report 4538 fungal P450s into 141 clusters/sub-families from 68 species) across many different species. The fungi tend to have very large families in some clades (e.g. some filamentous fungi) so I think this type of systematic and searchable system that will have stable identities for clusters is an essential resource. I know I’m going to try and give it a whirl. We have a couple of cool findings about changes in the P450 families in Basidiomycete Coprinopsis and related species comparisons that I hope we’ll be able to better interpret with this additional phylogenomic naming of gene family members.

Jongsun Park, Seungmin Lee, Jaeyoung Choi, Kyohun Ahn, Bongsoo Park, Jaejin Park, Seogchan Kang, Yong-Hwan Lee (2008). Fungal cytochrome P450 database BMC Genomics, 9 (1) DOI: 10.1186/1471-2164-9-402

Then authors cloning and combining the domains from a cDNA template of pksA [accession AY371490]  (from Aspergillus parasiticus) into various combinations and then evaluated the synthesized products via HPLC.  This deconstruction of a complicated protein and its domains is a great example of functionally mapping the role of each part of the enzyme and integrating with the biochemistry of the synthesized products.  The findings of this research also mapped a role for the PT product template domain which could suggest where modifications could be made to tweak the synthesized products by these enzymes.

Crawford, J.M., Thomas, P.M., Scheerer, J.R., Vagstad, A.L., Kelleher, N.L., Townsend, C.A. (2008). Deconstruction of Iterative Multidomain Polyketide Synthase Function. Science, 320(5873), 243-246. DOI: 10.1126/science.1154711

They infer from phylogenies we’ve published (Fitzpatrick et al, James et al) that plant pathogenic capabilities have arisen at least 5 times in the fungi and at least 7 times in the eukaryotes. In addition they use data on gene duplication and loss in the ascomycete fungi (Wapinski et al) to infer there large numbers of losses and gains of genes have occurred in fungal lineages.

The findings of large numbers of GPCR in many filamentous ascomycete fungi including as many as 61 in the Magnaporthe grisea (Dean et al) and 84 in the Fusarium graminearum (Cuomo et al) genomes also suggest phytopathogenic fungi have an expanded repertoire for detecting and responding to biotic and abiotic cues. What is still missing is detailed analyses pinpointing the exact timing of this family diversification, and whether it is actually a significant expansion or can be equally explained by drift. Analysis of the gene trees for these families can better identify the young and old copies of the genes to see if there are a class that may represent recent adaptation to a plant host.

The authors go on to talk about the numbers of secreted proteins in these genomes. It seems to me like we have yet to connect the predictions from the genome to actual observed molecules beyond some general trends. However, they highlight some of the interesting examples such as the the large fraction of secreted proteins in Ustilago maydis arranged in 12 clusters (Kamper et al) but most with no known function. Analyses of effector proteins in Oomycetes found large class of these in both the sudden oak death (P. ramorum) and soybean rust (P. sojae) but little overlap in these effectors genes with genes found in fungi.

The authors also discuss secondary metabolites enzymes (PKS, NRPS, P450) and the broad range of toxin and other metabolites biosynthesis capabilities in filamentous fungi. Fungi use these different metabolites to manipulate the plant host: from calcium signaling to growth regulators, to various biotoxins. The expansion and diversification of these happened at different points in fungal evolution, although I am not convinced that the initial expansion directly lead to pathogenic capabilities, but rather was part of expanding saprobe lifestyles to try and establish territory.

I’m excited about the syntheses we are able to achieve now with available functional and evolutionary data. With our ongoing work looking at the genomes of early branches of the fungal tree including the Chytrids we should have additional resolution to map numbers and types changes in gene families that have lead to lifestyle changes for saprobes, phytopathogens, animal pathogens, and rise of multicellular and developmental lifestages.

Soanes, D.M., Richards, T.A., Talbot, N.J. (2007). Insights from Sequencing Fungal and Oomycete Genomes: What Can We Learn about Plant Disease and the Evolution of Pathogenicity?. THE PLANT CELL ONLINE, 19(11), 3318-3326. DOI: 10.1105/tpc.107.056663

We hypothesize that gene modules that are contiguous in one species and noncontiguous in others are the result of rearrangements in an ancestral species. 

This sort of rearrangement of a cluster to bring together genes has been seen such as the DAL cluster in Saccharomyces.I don’t know how much further research has been done to identify other putative clusters through comparative analyses. Certainly this was looked at in recent comparative genome paper but I don’t recall any major identification of new biosynthesis clusters based on unexpected synteny or clustering of PKS or NRPS genes.