Our analysis of fungal ABC proteins provides an insight into the diversity of this group of proteins within the main fungal lineages. It shows that ABC proteins are a highly dynamic group that has undergone a significant diversification after the divergence of fungal phyla (chytridiomycetes, 'zygomycetes', ascomycetes, and basidiomycetes). The process of gene duplication was apparently accompanied by gene loss events, and this resulted in a great variety of ABC proteins that we can observe today in the fungal genomes. Clearly, two evolutionary scenarios can be recognized. The number of members of the 'small' subfamilies (ABC-A, -D, -E, -F, half-size ABC-B proteins, and unclassified ABC proteins) remained low and quite constant in the analyzed species, with only few exceptions, like an amplification of the ABC-F subfamily in R. oryzae. On the other hand, there is a remarkable variation in the number of members of the 'large' subfamilies (ABC-B, -C, and -G) between the different species. These differences can be as high as 11-fold in the case of ABC-G proteins. The reasons for the massive proliferation of ABC-G proteins, most notably in species of the Pezizomycotina group, is currently not well understood. This is because of the very limited information available about the physiological functions of fungal ABC transporters in general except for S. cerevisiae and S. pombe.
Few ABC proteins are strictly required for cell viability. For example, in S. cerevisiae
there are only three essential ABC proteins, Yef3p, Arb1p, and Rli1p, none of which is involved in transport. The number of essential ABC proteins might be larger in filamentous fungi, especially with respect to the mitochondrial transporters. On the other hand, an extensive amplification of ABC transporters in fungal genomes may have resulted in their partial functional redundancy. Trying to define a 'minimal' set of ABC proteins in fungi, we focused on two species that contain the lowest numbers, namely E. cuniculi
and S. pombe
with 13 and 19 ABC proteins, respectively. E. cuniculi
is a highly specialized parasitic species with a very compact genome. Members of only four out of the 7 eukaryotic subfamilies of ABC proteins were found in this species (ABC-B, -E, -F, and-G), and ABC proteins are only distantly related to those of other fungi. So, this species can hardly serve as a good model for fungi in general. On the other hand, the set of S. pombe
ABC proteins may be close to the minimal set needed for a free-living organism, as it is among the smallest of the sequenced eukaryotic genomes according to the TransportDB database [106
]. It lacks ABC-A proteins and even more remarkably it is the only free-living species in our analysis that lacks peroxisomal ABC-D transporters, although peroxisomes are present in this organism. At the same time, there are no counterparts of two S. pombe
transporters, Pmd1 and Hmt1, in the genomes of Saccharomycetales
, indicating that even a further reduction of the number of ABC transporters might be possible.
Three species, S. punctatus, B. dendrobatidis and R. oryzae, were of special interest as they represent basal lineages that received only little attention as compared to asco- and basidiomycetes. Some of ABC proteins from these species could be assigned to the well-defined groups of orthologous proteins (like Atm1-, Mdl1-, or Hmt1-related transporters) that are highly conserved throughout the fungal kingdom. However, there are also a lot of lineage-specific proteins that form separated clusters in the phylogenetic trees. Especially remarkable is the coexistence of full-length and half-size ABC-A transporters in the genomes of chytrid fungi, which is unique among the species included in our analysis.
Sets of ABC proteins in the genomes of basidiomycetes and ascomycetes (in particular members of the subphylum Pezizomycotina
) have a lot in common. The number of members of the particular subfamilies in the genomes of basidiomycetes, however, tends to be lower than in those of ascomycetes, and P. graminis
has the lowest number of ABC proteins per 1 Mb of genome among analyzed species (Additional file 2
). Within the phylum Ascomycota
, there is a trend towards an increase of the number of ABC proteins. This is especially evident within the subphylum Pezizomycotina
(especially prominent in Aspergillus
species and in G. zeae
), while S. pombe
and members of the order Saccharomycetales
contain a significantly reduced set of ABC proteins, as several of the groups of ABC-proteins present in other ascomycetes are missing from their genomes. Some distinct features of the S. pombe
transportome were already discussed above. Members of Saccharomycetales
also lack ABC-A proteins, with a notable exception of Y. lipolytica
indicating that these systems were most likely lost after the divergence of the lineage leading to this species from the rest of the group. The full-length ABC-B transporters in Saccharomycetales
are represented by a single protein, the mating pheromone transporter Ste6p/Hst6 (again, Y. lipolytica
is an exception from this rule, as it has 3 additional full-length ABC proteins). Finally, Saccharomycetales
species (once again, except for Y. lipolytica
) are characterized by the duplication of the gene encoding the mitochondrial half-size transporters Mdl1. Higher ascomycetes belonging to the subphylum Pezizomycotina
contain the most diverse sets of ABC proteins, with several groups of proteins specific for this subphylum. Unfortunately, the information about their physiological functions is still scarce and mainly restricted to multidrug resistance.
The expansion of ABC proteins must have occurred frequently and independently in different lineages of the fungal kingdom. The difficulty in establishing groups of orthologous proteins poses problems for the nomenclature. So far, the only fungal species with names assigned to all ABC proteins are S. cerevisiae
and S. pombe
. However, those gene names can hardly be used to classify the diversity of fungal ABC proteins simply because the two model species lack many of the ABC proteins found in filamentous fungi. Therefore, we suggest to adopt a nomenclature system recently proposed for plant ABC proteins [12
]. According to this system, the name of a given fungal ABC transporter should contain a species identifier based on a Latin binomial (e.g., Sc for S. cerevisae
), the subfamily abbreviation (e.g. ABCB) and a number for each gene family member (e.g. ABCB1, ABCB2 and so forth). Use of such nomenclature should help to cope with an increasing amount of data about fungal ABC proteins produced by numerous genome sequencing projects.
Another problem is the lack of functional data on fungal ABC transporters. Most of the available information was obtained from studies on S. cerevisiae and S. pombe. Both species have significantly reduced set of ABC proteins and cannot serve as a good model for other fungi. Only a small fraction of ABC proteins found in the remaining species have been characterized so far, but for the majority the function is unknown. In fact, most of the papers published on fungal ABC transporters in the last decade deal with the role of these transporters in the multidrug resistance, leaving other aspects of their biology unnoticed. This view is, however, slowly changing as it has become increasingly clear that the physiological roles of the proteins previously described as multidrug transporters is much broader. Our analysis contributes to the functional characterization of the fungal ABC proteins in several ways. First, it identified orthologues of the well-characterized ABC proteins thus providing a first clue about their function. It also highlights the areas of special interest and that have only been marginally studied thus far. One of those is a role of ABC-A proteins in fungi. This group appears to be much more abundant within the fungal kingdom than previously realized. Its function(s), however, remains less understood, in part because of the absence of members from the genomes of both S. cerevisiae and S. pombe. Another largely unexplored area concerns the role of fungal ABC proteins in secondary metabolism. It is well known that ABC transporters are often found within prokaryotic secondary metabolism clusters where they contribute to the excretion of final products. Our analysis shows that some of the transporters associated with secondary metabolism clusters are highly conserved within fungi. Further experiments are needed to uncover their role within such clusters.
Although our analysis does not cover the whole set of ABC proteins present in the databases, it provides an insight into their astonishing diversity. The obtained results can be used as a starting point for the development of an universal classification system of fungal ABC proteins and for a further in-depth characterization of members of this highly important group.