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Comparative Study
. 2013 May 16:13:108.
doi: 10.1186/1471-2180-13-108.

Comparative analysis of the repertoire of G protein-coupled receptors of three species of the fungal genus Trichoderma

Sabine Gruber  1 , Markus Omann, Susanne Zeilinger
Affiliations
Comparative Study

Comparative analysis of the repertoire of G protein-coupled receptors of three species of the fungal genus Trichoderma

Sabine Gruber et al. BMC Microbiol. .

Abstract

Background: Eukaryotic organisms employ cell surface receptors such as the seven-transmembrane G protein-coupled receptors (GPCRs) as sensors to connect to the environment. GPCRs react to a variety of extracellular cues and are considered to play central roles in the signal transduction in fungi. Several species of the filamentous ascomycete Trichoderma are potent mycoparasites, i.e. can attack and parasitize other fungi, which turns them into successful bio-fungicides for the protection of plants against fungal phytopathogens. The identification and characterization of GPCRs will provide insights into how Trichoderma communicates with its environment and senses the presence of host fungi.

Results: We mined the recently published genomes of the two mycoparasitic biocontrol agents Trichoderma atroviride and Trichoderma virens and compared the identified GPCR-like proteins to those of the saprophyte Trichoderma reesei. Phylogenetic analyses resulted in 14 classes and revealed differences not only among the three Trichoderma species but also between Trichoderma and other fungi. The class comprising proteins of the PAQR family was significantly expanded both in Trichoderma compared to other fungi as well as in the two mycoparasites compared to T. reesei. Expression analysis of the PAQR-encoding genes of the three Trichoderma species revealed that all except one were actually transcribed. Furthermore, the class of receptors with a DUF300 domain was expanded in T. atroviride, and T. virens showed an expansion of PTH11-like receptors compared to T. atroviride and T. reesei.

Conclusions: Comparative genome analyses of three Trichoderma species revealed a great diversity of putative GPCRs with genus- and species- specific differences. The expansion of certain classes in the mycoparasites T. atroviride and T. virens is likely to reflect the capability of these fungi to establish various ecological niches and interactions with other organisms such as fungi and plants. These GPCRs consequently represent interesting candidates for future research on the mechanisms underlying mycoparasitism and biocontrol.

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Figures

Figure 1
Figure 1
Phylogenetic analysis of predicted GPCRs(except PTH11-like proteins)identified in the genomes of the two mycoparasitesT.atrovirideandT.virens,and the saprophyteT.reesei. The 7TM regions were aligned and the tree was constructed using neighbor-joining methods resulting in a grouping into 13 classes (I-XIII). Classes were numbered according to former classification schemes [12,36]. Nodes supported with bootstrap values above 70% (1000 repetitions) are indicated with a black dot, nodes with bootstrap values between 50 -70% are indicated with a grey dot, bootstrap values less than 50% were removed.
Figure 2
Figure 2
Phylogenetic analysis of PAQR family(class VIII)members. PAQR members identified in the genomes of the three Trichoderma species and those present in N. crassa (NCU03238, NCU04987), A. nidulans (AnGprP, AnGprO), F. graminearum (FG04051, FG01064), M. grisea (MG0901, MG05072, MG04679), S. cerevisiae (Izh1p, Izh2p, Izh3p, Izh4p), and the human mPR (mPR-alpha, -beta, -gamma) and adiponectin-receptors (adipor1, adipor2) were aligned using ClustalX. The alignment was then processed using the Gblocks server [56] and the tree was constructed using neighbor-joining methods. Nodes supported with bootstrap values above 70% (1000 repetitions) are indicated with a black dot, nodes with bootstrap values between 50 -70% are indicated with a grey dot, bootstrap values less than 50% were removed.
Figure 3
Figure 3
Relative transcription ratios of PAQR family(class VIII)members. mRNA levels of the respective genes of T. atroviride (A), T. virens (B) and T. reesei (C) upon direct contact with the host fungus R. solani (black bars) were assessed by RT-qPCR and compared to a control where the respective Trichoderma species was grown alone (white bars). Samples of the gene with highest expression in the control condition were arbitrarily assigned the factor 1. sar1 was used as reference gene.
Figure 4
Figure 4
Schematic drawing of theT.atroviridegenomic locus with the PAQR(class VIII)-encoding genes Triat142946, Triat142943, and Triat46847 and the loci with their orthologues inT.virensandT.reesei. Scaffolds and position numbers are given as specified in the respective genome databases [57-59]. PAQR-encoding genes are indicated by white arrows; other genes are given in grey (1: Triat47305/Trive123162, putative subtilisin-like peptidase; 2: Triat178339/Trive160495, putative ankyrin repeat domain protein; 3: Triat255480, putative ankyrin repeat domain protein; 4: Triat215171/Trive160757, hypothetical NACHT and ankyrin domain protein; 5: Triat305654, predicted small secreted cystein-rich protein; 6: Triat290393, hypothetical protein; 7: Trive66658, hypothetical protein).
Figure 5
Figure 5
Neighbor-joining tree of PTH11-related proteins identified in the genomes of the threeTrichodermaspecies. The clade containing proteins with a CFEM domain is marked with a black line. Nodes supported with bootstrap values above 70% (1000 repetitions) are indicated with a black dot, nodes with bootstrap values between 50 -70% are indicated with a grey dot, bootstrap values less than 50% were removed.
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