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PLoS One. 2012; 7(1): e29817.
Published online Jan 4, 2012. doi:  10.1371/journal.pone.0029817
PMCID: PMC3251606

The Origin of GPCRs: Identification of Mammalian like Rhodopsin, Adhesion, Glutamate and Frizzled GPCRs in Fungi

Chaoyang Xue, Editor

Abstract

G protein-coupled receptors (GPCRs) in humans are classified into the five main families named Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin according to the GRAFS classification. Previous results show that these mammalian GRAFS families are well represented in the Metazoan lineages, but they have not been shown to be present in Fungi. Here, we systematically mined 79 fungal genomes and provide the first evidence that four of the five main mammalian families of GPCRs, namely Rhodopsin, Adhesion, Glutamate and Frizzled, are present in Fungi and found 142 novel sequences between them. Significantly, we provide strong evidence that the Rhodopsin family emerged from the cAMP receptor family in an event close to the split of Opisthokonts and not in Placozoa, as earlier assumed. The Rhodopsin family then expanded greatly in Metazoans while the cAMP receptor family is found in 3 invertebrate species and lost in the vertebrates. We estimate that the Adhesion and Frizzled families evolved before the split of Unikonts from a common ancestor of all major eukaryotic lineages. Also, the study highlights that the fungal Adhesion receptors do not have N-terminal domains whereas the fungal Glutamate receptors have a broad repertoire of mammalian-like N-terminal domains. Further, mining of the close unicellular relatives of the Metazoan lineage, Salpingoeca rosetta and Capsaspora owczarzaki, obtained a rich group of both the Adhesion and Glutamate families, which in particular provided insight to the early emergence of the N-terminal domains of the Adhesion family. We identified 619 Fungi specific GPCRs across 79 genomes and revealed that Blastocladiomycota and Chytridiomycota phylum have Metazoan-like GPCRs rather than the GPCRs specific for Fungi. Overall, this study provides the first evidence of the presence of four of the five main GRAFS families in Fungi and clarifies the early evolutionary history of the GPCR superfamily.

Introduction

G protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors with about 800 members in the human genome serving as targets for many drugs [1], [2]. Over the years, the repertoire of GPCRs has been analyzed in several species which are from the phyla Chordata, Echinodermata, Arthropoda, Nematoda, Cnidaria, Placozoa and Amoebozoa [3][8]. At first, in 1994, Attwood and Findlay categorized the superfamily into six classes (A–F) based on sequence homology and functional similarity [9]. Later, our comprehensive phylogenetic analysis of the human repertoire provided the GRAFS classification. This system grouped the mammalian GPCR repertoire into five main families; Glutamate (Class C), Rhodopsin (Class A), Adhesion (Class B), Frizzled (Class F), and Secretin (Class B) [10]. The Rhodopsin family is the largest with 683 members in humans [8], characterized by short N-termini and interactions with a broad variety of ligands. The Glutamate family is distinguished with long N-termini which act as the endogenous ligand binding region. The Adhesion receptors have long N-termini which contain a plethora of multiple domains while the Frizzled receptors have long cysteine-rich N-termini [1].

Mining of GPCRs has revealed that each of the five main mammalian families have long evolutionary histories. Recently, our group has shown the connections between the GPCR families and provided strong evidence that the Rhodopsin, Adhesion, Frizzled and Secretin share a common origin with the cAMP receptors (Class E) and dismissed relationship with families like the insect odorant receptors, insect gustatory receptors, trehalose receptors and DUF267, which in many publications were considered to be GPCRs [8]. Our previous study [8] also showed an early presence of Rhodopsin (7tm_1) family members in the phylum Placozoa (Trichoplax adhaerens), an invertebrate which forms the basal group of Metazoa [11], while Adhesion (7tm_2) and Frizzled family members were found in the phylum Amoebozoa (Dictyostelium discoideum), which is a basal group to both Fungi and Metazoa [12]. The Glutamate (7tm_3) family members were found in the phylum Heterokontophyta (Thalassiosira pseudonana), a diatom classified under the Chromalveolata kingdom [13] while the earliest occurrence of Secretin family members, which evolved from Adhesion receptor family [14], was found in the phylum Nematoda (Caenorhabditis elegans) [15]. Further, the cAMP receptor family, predicted to be the ancestor to the main families (Class A, B and F) is present only in invertebrates within the Metazoan lineage [8], [16].

Recently, a multi-taxon genome sequencing initiative endorsed by National Human Genome Research Institute (NHGRI) shed light on how multicellularity evolved. The study suggests that the two main eukaryotic kingdoms- Metazoa and Fungi along with unicellular relatives like Choanoflagellata and Filasterea share a common origin or group together under a eukaryotic supergroup known as Opisthokonta [17]. Over the years, GPCR repertoires have been particularly well studied in Metazoa as compared to Fungi. The five main GPCR families have previously not been found in Fungi, despite the presence of Adhesion, Frizzled and Glutamate family members in D. discoideum [8]. Literature reports that GPCR homologues already identified in Fungi can be classified into at least six classes or families that do not belong to the mammalian GRAFS families. The six classes include pheromone receptors sensing peptide pheromones (Ste2), pheromone receptors sensing lipid modified peptide pheromones (Ste3), nutrient sensors (Gpr1), Stm1-like nitrogen sensors (Stm1), microbial opsins (Nop-1 and Orp-1) and cAMP like receptors [18]. Until today, a few GPCR homologues have been identified in Saccharomyces cerevisiae, Aspergillus nidulans, Cryptococcus neoformans, Magnaporthe grisea and in Neurospora crassa, but they are categorized under the known six classes of fungal GPCRs and not among the GRAFS families [18][21].

GPCRs in Fungi were proposed to have a role in fungal-plant interactions. They are involved in recognizing various signal molecules or ligands from plant cells paving the way for the Fungi to destroy valuable crops [22]. Pathogenic Fungi are also responsible for causing diseases in humans like Histoplasmosis and severe Pneumonia in people with immune system problems [23], [24]. Recent advances in sequencing technologies led to a remarkable increase in the number of fully sequenced fungal genomes. The Fungal genome initiative (FGI) endorsed by Broad institute at MIT (http://www.broad.mit.edu/annotation/fgi) and DOE Joint Genome Institute (JGI; http://www.jgi.doe.gov/), sequenced several fungal genomes that are pathogenic to humans and plants.

In this study, we have mined for GPCRs in a complete proteome dataset of Fungi from UniProt and over 18 genomes of Fungi that are available at FGI (Broad institute). We have also investigated genomes belonging to eukaryotic lineages like Choanoflagellata (Salpingocea rosetta), Filasterea (Capsaspora owczarzaki), which share a common origin with Metazoa and from Alveolata (Paramecium tetraurelia and Tetrahymena thermophila). Overall, we systematically mined for GPCRs in 83 genomes to obtain a nearly complete set of GPCRs in Fungi and unicellular Metazoan relatives.

Results

Identification of novel homologues of the Rhodopsin, Adhesion, Glutamate and Frizzled like receptors in Fungi and major eukaryotic lineages

We searched for GPCRs in a comprehensive protein sequence dataset that comprise proteomes of several species representing the eukaryotic lineages like Fungi (79 species), Choanoflagellata (S. rosetta), Filasterea (C. owczarzaki), Alveolata (P. tetraurelia, T. thermophila) and from collection of proteins (3465 proteins) from several species that are from the phylum Porifera, which is one of the most basal Metazoan lineages. The complete dataset was searched using Hidden Markov Models (HMM) models for the 11912 families of the Pfam database (version 24), which revealed that the characteristic Metazoan GPCR families of the GRAFS classification are wide spread in the eukaryotic domain. This study identified 142 novel sequences distributed among the Rhodopsin, Adhesion, Glutamate and Frizzled families that have not previously been reported in the Fungi kingdom. In S. rosetta, 8 novel members of the Adhesion and 1 member of the Glutamate family were found. In C. owczarzaki, 7 novel sequences of the Adhesion and 20 for the Glutamate family were found.

Also, one sole representative was found for the Glutamate family in Porifera. In addition to the GRAFS families, our study identified 57 cAMP receptor family sequences in Fungi, 8 in Alveolata, and more surprisingly 1 cAMP receptor each in Branchiostoma floridae and Lottia gigantea. All identified novel sequences in individual species are listed with their accession numbers (Table S1); FASTA sequences are provided in Dataset S1 and the list of species investigated is given in Table S2.

The Rhodopsin and cAMP receptor family

The Rhodopsin family of GPCRs constitutes the largest family of GPCRs in vertebrates with 683 members in humans, classified into four main groups, termed α-, β-, γ-, and δ-group, and 13 major subfamilies [10]. The Rhodopsin family is very well represented in both vertebrates and in invertebrates with the ancient members (343 receptors) was found in T. adhaerens. On the other hand, the cAMP receptor family in D. discoideum is found in plants and in Alveolata [8]. Also, they are present in Fungi kingdom, but found in very few invertebrate species and subsequently lost in the vertebrates within the Metazoan lineages [8], [17].

Novel homologues

This study identified 12 novel sequences of the Rhodopsin family in Fungi. However, the sequences were only found in 3 species: Allomyces macrogynus (3 sequences) from Phylum Blastocladiomycota, Batrachochytrium dendrobatidis (1 sequence) and Spizellomyces punctatus (8 sequences) which belong to the phylum Chytridiomycota, known to be a basal fungal lineage and found to have split prior to the Dikarya subkingdom. Similar to the previous reports, our search did not identify Rhodopsin family members in Dikarya that includes the two major phyla Ascomycota and Basidiomycota of Fungi. Further, search for the Rhodopsin family members in Choanoflagellata, Filasterea, Alveolata and Porifera failed to find homologues.

Conserved features

The 12 novel Fungi members of the Rhodopsin family share many motifs characteristic for the Rhodopsin family in Metazoa, such as aspartate (D) in TM2, D/ERY in TM3, NP in TM7 and cysteine (C) in ELC1 and 2 (Figure 1). In addition, there are motifs that provide a link between the cAMP receptor family and the Rhodopsin family like: arginine (R)/lysine (K) in ICL1, aspartate (D) in TM2, tyrosine (Y) in TM3 & 5, cysteine (C) in ELC1 & 2. Further, we found 8 sequences which were initially identified as putative members of the Rhodopsin family in the Pfam search. They are distributed as 2 sequences in the phylum Alveolata, 4 in Ascomycota and 1 each in Basidiomycota and Chytridiomycota. These 8 sequences lack the D/ERY motif that is common for the Rhodopsin family but instead has motif NxY that are present among the cAMP receptor sequences (Figure 1).

Figure 1
Alignment showing shared and group specific motifs between Rhodopsin and cAMP like receptors in eukaryotes.

Phylogenetic analysis

The phylogenetic relationships for the Rhodopsin and cAMP receptor family were investigated using the Bayesian approach implemented in MrBayes 3.1.2. Two preliminary trees were constructed: the first tree included the novel Rhodopsin family members identified in Fungi (Chytridiomycota and Blastocladiomycota) with the representative sequences from 13 subgroups of the Rhodopsin family in humans (Figure S1): the second tree included Fungi (12 sequences) and the representative Rhodopsin family members from T. adhaerens, which belong to the most basal lineage of Metazoa and therefore containing the evolutionarily most distant members of the Rhodopsin family (Figure S2). Both these preliminary trees demonstrated that the Fungi Rhodopsin family members cluster together with more than 90% posterior probability (PP) and clearly separate the cluster from its homologues in humans and T. adhaerens, respectively. Further, the 8 sequences (identified as Rhodopsin family members in Pfam search) that do not have the D/ERY motif and instead have motifs corresponding to the cAMP receptor family, cluster (PP>95%, 367/500) separate from the Rhodopsin family members identified in Fungi. Based on this inference, a separate phylogeny was constructed that included all newly identified homologues of the cAMP receptor family and the Rhodopsin family with the representative sequences from previous repertoires of both the families (Figure 2). The unrooted tree demonstrated two clusters, one grouping the cAMP receptor family and the other grouping the Rhodopsin family.

Figure 2
Phylogenetic relationships between the cAMP and Rhodopsin families across eukaryotic lineages.

All newly identified cAMP receptor family sequences in Fungi, Alveolata, Metazoa, Choanoflagellata and the representative sequences in D. discoideum and homologues from plants cluster together with a posterior probability greater than 90% (466/500). Furthermore, the tree demonstrated that the ancient cAMP receptor family members identified from Alveolata (ciliates) cluster together (PP>80%) with the cAMP receptors from plants. The 8 sequences identified as Rhodopsin family in Pfam search cluster with the cAMP receptor family homologues. Of the 8 sequences, Q23WQ7_TETTS and XP_001447229.1 from ciliates were placed in the branch with the other cAMP receptor family members from ciliates (PP>90%) and D. discoideum (PP>70%), respectively (Figure 2). The rest of the sequences were from Fungi (BDEG_02994, FOXG_08466, FVEG_06210, FGSG_05239, B6HSY3_PENCW) and unambiguously clustered with the putative cAMP receptors from Fungi (>80%) with the exception of Q4P8Z0_USTMA, which was placed basal to the node clustering all cAMP receptor family sequences. Instead, we classified the sequence Q4P8Z0_USTMA as a member of the cAMP receptor family based on the characteristic NxY motif in TM3 (Figure 1). All the Rhodopsin family members in Fungi cluster (PP>90%) with the sequences in human. However, the sequences in Fungi form a separate cluster (PP>90%) that is distinct from the human sequences, which are representative for 13 Metazoan subgroups of the Rhodopsin family.

Scatter plot

The similarity between the Rhodopsin (PF00001) and the Dictyostelium cyclic AMP receptor: Dicty_CAR (PF05462) was tested using the HMM models downloaded from Pfam database. A scatter plot on a logarithmic scale was made using the e-value for each sequence (used in the phylogeny) aligned with both Rhodopsin and Dicty_CAR HMM models using HMMSEARCH (Figure 3). The plot demonstrates that there are uncertain sequences which receive very similar scores but were classified as Rhodopsin family based on a negligible difference in e-value which over scored the Dicty_CAR HMM model. However, based on the strong support from phylogeny and sequence motifs, we classified these sequences as cAMP receptor homologues.

Figure 3
Scatter plot distinguishing cAMP and the Rhodopsin like sequences.

The Adhesion receptor family

The Adhesion family of GPCRs is the second largest according to the GRAFS GPCR classification with 33 members in humans [3]. The family is characterized with long N-termini containing multiple functional domains and having numerous sites for glycosylation events [1]. Comprehensive phylogenetic analysis on the TM regions of human Adhesion receptors classified the family into 8 main groups (I–VIII). The phylogenetic classification was also supported by the composition of the functional domains in the N-termini which differs between the subgroups.

Novel homologues

This study identified 32 novel Adhesion family members in Fungi. They are distributed as 30 sequences within 22 species of the phylum Ascomycota and 2 sequences in A. macrogynus from the phylum Blastocladiomycota. Also, 8 sequences in S. rosetta, 7 in C. owczarzaki and 1 in P. tetraurelia were found. Interestingly, the Adhesion family members were not found in the phylum Basidiomycota despite being grouped with the phylum Ascomycota, which has 30 members of the Adhesion family.

Conserved features

The 48 novel Adhesion family members found in major eukaryotic lineages shared motifs of the Adhesion family common to known Metazoan sequences. The common motifs/conserved residues were adapted from our previous study on the overall relationship between the GPCR families [8]. Residues cysteine (C) in ECL 1 & 2, tryptophan (W) in TM3, proline (P) in TM4 & 5 and glycine (G) in TM7 were found to be >90% conserved between all eukaryotic lineages in which the Adhesion family receptors were identified.

Phylogenetic analysis

A phylogenetic tree of the Adhesion family was built with the novel members of the family identified from Fungi, Choanoflagellata, Filasterea and Alveolata with the formerly classified sequences from human (Group I–VIII and VLGR1) and representative sequences from C. intestinalis, B. floridae, N. vectensis and T. adhaerens, which have key evolutionary position within the Metazoan lineages (Figure S3). The phylogenetic analysis revealed that the Adhesion family sequences from Fungi (Ascomycota and Chytridiomycota) clustered separately (PP 99%, 443/500) indicating that were not orthologous to any of the Metazoan receptors, though they have diverged from a common ancestor to all Metazoan and Fungi genes of the Adhesion family. Within the largest cluster of Fungi Adhesion family members, the sequences from the phylum Ascomycota split into two groups. Furthermore, the sequences from the phylum Blastocladiomycota (AMAG_09540, AMAG_13158 from A. macrogynus) clustered with the group of Ascomycota. Interestingly, the lone representative (XP_001450983) of the Adhesion family from T. thermophila (Alveolata) clustered with the Adhesion family members in Fungi with a posterior probability of >95% (272/500). The novel putative members of the Adhesion family from S. rosetta and C. owczarzaki clustered with the representative sequences of the Adhesion family from the Metazoan lineage, as they all share a common origin. VLGR1 from human and its orthologue in N. vectensis (NV_242264) were placed basal to the node that clustered the Metazoan sequences.

N-terminal domain architecture

The N-terminal domains of all newly identified Adhesion family members were searched and presented together with abbreviations in Figure 4. The N-terminal domain architecture for the representative sequences from group I–VIII in human and for two sequences MB_7962 and MB_10341 from M. brevicollis are thoroughly described in our previous report [14].

Figure 4
Conserved features and structural motifs within the Adhesion receptor family in eukaryotes.

Adhesion family members identified in S. rosetta and C. owczarzaki have long N-termini ranging from 312–4202 amino acid residues, comparative to the N-termini of the Adhesion family receptors in human, which range from 430–5906 residues. The sequences in S. rosetta and C. owczarzaki have a GPS domain characteristic for the Adhesion family members, which is not found in any other GPCR family. One exception is SALP_EGD83019.1 which lacks the GPS domain but has 4 EGF_CA domains, which are present in the sequence of EMR1 (Group II) and CELSR1 (Group III) in human. The same sequence also has one Tsp1 domain, which is found in sequence BAI1 (Group VII) and LamG domain found in sequences CELSR1 (Group III) and GPR144 (Group V). Furthermore, CASP_EFW45600.1 in C. owczarzaki has five Calx_beta domains, which are a signature for VLGR1 (the very long G protein-coupled receptors) in Metazoa. This may suggest that CASP_EFW45600.1 is a putative orthologue to VLGR1 in human. Several domains were identified that have not been reported previously in the Adhesion family like the TIG domain in the sequences SALP_EGD77907.1, SALP_EGD77908.1; the TLD domain in sequence SALP_EGD78309.1 from S. rosetta and the RLD domain in sequences CASP_EFW40287.1 and CASP_EFW39861.1 from C. owczarzaki. Interestingly, the 30 putative Adhesion family members in phylum Ascomycota of Fungi and 1 member in Alveolata have short N-termini ranging from 2–66 residues with no functional domains. But the Adhesion receptors (AMAG_09540 and AMAG_13158) identified in A. macrogynus, belonging to the basal fungal lineage Blastocladiomycota, has an N-termini length of 251 and 254, respectively.

The Glutamate receptor family

The Glutamate family consists of 22 members in human. Most of these receptors have long N-termini that serve as an endogenous ligand binding region. Furthermore, the N-terminal region of the majority of receptors in human is also characterized with the presence of a cysteine rich domain (has 9 conserved cysteine residues) known as CRD or NCD3G. The ancient member of this family is present in species T. pseudonana.

Novel homologues

Significantly, 118 novel members of the Glutamate family were found, of which 96 receptors are found in Fungi, 1 in Geodia cydonium (Porifera), and 1 each in M. brevicollis and S. rosetta and 20 in C. owczarzaki. Surprisingly, 96 putative Glutamate receptors in Fungi are from only 4 species, with a remarkable number of 78 members in A. macrogynus from phylum Blastocladiomycota (the most found in any species including human), 14 in S. punctatus and 3 in B. dendrobatidis from phylum Chytridiomycota (which also have Rhodopsin and Adhesion receptor homologues) and 1 in Rhizopus oryzae from phylum Zygomycota. Similar to the previous reports, we did not find any Glutamate receptors in the Fungi phyla Ascomycota and Basidiomycota.

Conserved features

In the multiple sequence alignments there were partially or completely conserved residues across the 7TM region between the identified novel Glutamate family members and the characterized members of the Glutamate family in human (Figure S4). It is noteworthy that the 78 putative members of the Glutamate receptor family in A. macrogynus share about 27.4% identity in the 7TM regions and full length identity of just about 14.5%. This relatively low value suggests that even if these genes are a possible outcome of duplication, or local expansion, within the species, they seem to have diverged considerably.

Phylogenetic analysis

Phylogenetic analysis was performed including the novel members of the Glutamate family identified in Fungi, Choanoflagellata, Filasterea and Porifera with the known Glutamate receptors in human, D. discoideum and T. pseudonana (Figure S5). The analysis revealed that the putative Glutamate receptors identified in Fungi clustered (PP>80%) separately from the homologues of the Glutamate family in Metazoa. The sequences found in C. owczarzaki forms a distinct cluster with a posterior probability >70%. Further, the tree demonstrates that the sequence GB_CAA76688.1 in species G. cydonium from phylum Porifera cluster (PP 100%) with GABBR1 (gamma amino butyric acid B receptor) in human, which suggests a close relationship with each other.

N-terminal domain architecture

The N-termini of almost all identified members of the Glutamate family in Fungi and other eukaryotic lineages, was very similar in both length and the nature of the functional domains present in the Glutamate family receptors in human (Figure 5). The length of the N-termini of the novel sequences range from 57–1667 (average of 497) residues, which was similar to humans, which range from 31–621 (average of 446) residues. The functional domains included the ANF_receptor (PF01094), which is one of the members of clan Periplasmic binding protein like (CL0144; Periplas_BP) and is part of the N-terminal region for CASR, GABBR1 &2, GRMs and TAS1Rs receptors in human. Curiously, the ANF_receptor domain was also present in most of the Glutamate family members identified in Fungi, 3 sequences in C. owczarzaki and also in sequence DD231976 identified in D. discoideum. It is noteworthy that GB_CAA76688.1 from the phylum Porifera, which clusters with GABBR1 in the phylogenetic tree, lacks the ANF_receptor domain. Further, additional domains were found that belong to the same Pfam clan CL0144; Periplas_BP. This includes BMP (PF02608) domain in 13 members of the Glutamate family identified in D. discoideum and in two sequences AMAG_08984, AMAG_12053 from A. macrogynus. In addition, we found other periplasmic binding protein domains that are (grouped in a separate Pfam clan, PBP: CL0177) not found in human Glutamate receptors, but found in putative Glutamate receptors identified in Fungi. They are LysR_substrate (PF03466) domain (in AMAG_01751, 04246, SPPG_00031), PBP_like_2 (PF12849) domain (in SPPG_06488), OpuAC (PF04069) domain (in AMAG_01750, 04252, 14324, 14326, 15836 and 17562) and SBP_bac_1 (PF01547) domain in 8 sequences in A. macrogynus. But the NCD3G (PF07562) domain found in CASR, GRMs, TAS1Rs in human is absent in all identified novel non-Metazoan members.

Figure 5
Schematic presentations of N-terminal domains of the Glutamate receptor family across the eukaryotic tree.

Further, domains were found that have not been reported previously in the Glutamate family like Pentaxin (PF00354) domain in CASP_EFW47134.1, 5_nucleotid_C (PF02872) domain in CASP_EFW44378.1, TIG (PF01833) domain in CASP_EFW40850.1 from C. owczarzaki and Cache_1 (PF02743) domain in TP_7830 in T. pseudonana from Alveolata. It is noteworthy that the Pentaxin domain is found in the Adhesion family receptors GPR144 and GPR126 in humans and TIG domain in the Adhesion receptors from S. rosetta.

The Frizzled receptor family

The Frizzled family of GPCRs consists of 10 receptors (FZD1–10) in human [10]. They are mostly known as receptors for Wnt proteins and play key role in tissue polarity and cell signaling [1]. The family members are characterized by the CRD_FZ domain or FZ domain which has 10 conserved cysteine residues. The ancient member or origin of this family can be traced back to D. discoideum [8].

Novel homologues

Our analysis identified 6 new Frizzled receptor sequences, distributed as 2 in Fungi (S. punctatus) and 4 in sponges (3 sequences in species Amphimedon queenslandica, 1 in Suberites domuncula), which belong to phylum Porifera. However, we did not find any Frizzled receptors in Choanoflagellata, Filasterea, Fungi phyla Ascomycota and Basidiomycota and in Alveolata.

Conserved features

Multiple sequence alignment of the known Frizzled receptors in human and 6 novel sequences in Fungi and Porifera revealed that they are conserved with an identity of about 40%. Multiple cysteine residues along the sequence of the frizzled receptors were found to be completely conserved in most, and partially in a few cases (Figure S6).

Phylogenetic analysis

Phylogenetic analysis of the Frizzled family was performed using the sequences from human, N. vectensis, T. adhaerens and D. discoideum and compared to the novel homologues from Fungi and Porifera (Figure S7). The tree is rooted with the node clustering the ancient members of the family in D. discoideum. The analysis revealed that the two sequences SPPG_01720 and SPPG_06172 in S. punctatus of Fungi cluster together (PP 100%) and placed basal to the node which cluster (PP 100%, 492/500) the Metazoan homologues of the Frizzled family. Furthermore, the tree demonstrates that the two sequences ADO16580.1 and ADO16569.1 from phylum Porifera (sponges), the closest relatives or sister group to the Metazoans do not show orthologous relationship with Metazoan receptors. In contrast, the other two sequences ADO16570.1 and CAD97575.1 identified in Porifera, cluster (PP 98%) together along with the sequences FZD4, FZD9 and FZD10 from humans, TA_31674 from T. adhaerens, NV_168924 and NV_139208 from N. vectensis.

Fungi specific GPCRs

In this study, we also searched for the previously known Fungi kingdom specific GPCRs that involve in pheromone sensing (Ste2, Ste3), sensors for glucose (Git3), and nitrogen sensors (stm1) among others. We identified 619 fungal specific GPCRs across the 79 species analyzed in this study (Table S3). Surprisingly, we could not find reliable homologues for Ste2, Ste3 and Git3 in Phylum Chytridiomycota that instead has homologues for mammalian like GRAFS families. Similarly, Zygomycetes R. oryzae has no homologues except for the nutrient sensing receptors. This observation is in line with the previous report on R. oryzae [18]. It is noteworthy that a widespread representation of these unique Fungi specific GPCRs was found only in Ascomycota and Basidiomycota that thoroughly lack the mammalian like GRAFS families.

Discussion

Here we provide the first evidence that four of the five main mammalian families of GPCRs, namely Rhodopsin, Adhesion, Glutamate and Frizzled, are present in Fungi. The evidence is convincing for all the families and we were able to create alignments of the human and fungal members for each of the families. The results are further supported by a number of motifs that seem remarkably conserved and these are likely to be crucial for the function of the family specific properties of these receptors. Also, we identified GPCRs in T. pseudonana and P. tetraurelia, which belong to the eukaryotic kingdom known as Chromalveolata. Based on this comprehensive study covering 83 species, we establish that the origin of the Rhodopsin family could be traced back to the ancestor of Opisthokonts (~1100 MYA), the Adhesion and the Frizzled family to Unikonts (~1275 MYA) and the Glutamate and the cAMP receptor family to the common ancestor of Alveolates and Unikonts, early in eukaryotic evolution (>1400 MYA) (Figure 6). We provide higher resolution and deduced precise timeframe of the origin and diversification of the GRAFS families than previous reports [8]. We establish that the Frizzled and the Adhesion family evolved from the cAMP receptor family before the split of Unikonts from the common ancestor of eukaryotes. The Rhodopsin family evolved from the cAMP receptor family in the common ancestor of Opisthokonts, after the divergence of D. discoideum. It is interesting to note the similarities between the cAMP and Rhodopsin families, suggesting that the Rhodopsin family is an expansion of the more ancient cAMP branch perhaps taking over its functions in more complex organisms while cAMP receptors then become redundant. Later, the Secretin family evolved from the Adhesion family in an event that happened between the split of Cnidaria (N. vectensis) and the split of Nematoda (C. elegans) in the Metazoan lineage, as we previously reported [14]. Also, we have traced the lineage and species specific losses of these families across the eukaryotic tree (Figure 6). This study also highlights the importance of an ancient role of the N-terminal functional domains of the Adhesion and the Glutamate families across the diverse eukaryotic lineages. Intriguingly, the widespread distribution of these classical membrane receptors across the eukaryotic domain demonstrates that evolutionary divergent eukaryotes like the unicellular Alveolates and the complex multicellular organisms of Metazoan lineage share a basal signal transduction system that was present already in early eukaryotic evolution.

Figure 6
Schematic presentation of the origin, evolution and lineage-specific losses of the five main GRAFS families, cAMP receptor family and the Fungi kingdom specific GPCRs.

Rhodopsin and cAMP receptor family

We provide convincing evidence that the split of the large Rhodopsin family from the cAMP receptor family can be placed at the emergence of the common ancestor of Opisthokonts (Fungi and Metazoa) and not in Placozoa (basal lineage of Metazoa) as earlier assumed [8]. Interestingly, we found that the newly identified sequences of the Rhodopsin and the cAMP receptor family in the basal eukaryotic genomes share conserved motifs between them. This includes the important DRY and NPXXY motifs of the Rhodopsin family that are crucial to the functional integrity of these receptors [25], [26]. These motifs are present as ERY and NPXXX in the 12 novel Rhodopsin family sequences in Fungi and N(S)XY and NS(A)XXY in the cAMP receptors from Fungi and Alveolata, respectively (Figure 1). This conservation within the 7TM region strongly links these families. In addition, the phylogenetic tree clearly clusters (PP>90%, 466/500) all the novel sequences from the Rhodopsin family and cAMP receptor family into two separate groups and suggest a common origin between these two families (Figure 2). Also, the scatter plot (Figure 3) clearly demonstrates the similarity between the Pfam HMM models of the Rhodopsin and the cAMP receptor family. This is in good agreement with our earlier report that the Rhodopsin family and the cAMP receptor family share an HHsearch (HMM-HMM search) homology probability of 99.4% [8]. Also, we noticed insensitivity of the Pfam HMM models to distinguish between the two families prevails right at the point where the split of the Rhodopsin family from cAMP receptor family have occurred. Further, the cAMP receptor family is present in plants, Alveolata, Amoebozoa and Fungi but subsequently become redundant in the Metazoan lineage as it is found in 3 invertebrate species and lost in the vertebrates (Figure 6). Taken all these findings together, it is evident that the cAMP receptor family gave rise to the Rhodopsin family in an event close to the common ancestor of Opisthokonts and then persisted and evolved as a large Rhodopsin family in the Metazoan lineage.

Adhesion receptor family

We have traced the origin of the Adhesion family to the ancestor of Unikonts (Figure 6). Here we provide the first evidence for the presence of Adhesion receptors in Filasterea (C. owczarzaki), Choanoflagellata (S. rosetta) and in two of the four major phyla of the Fungi kingdom. Also, our search emphasize that Adhesions are not found in eukaryotic lineages before the split of D. discoideum. The sole representative of Adhesions from Alveolata is a possible horizontal gene transfer from Fungi, since it cluster with the Adhesion receptors found in Ascomycota of Fungi (PP 99%) (Figure S3). This is also supported by a pair wise identity of about 50% in the 7TM region (Figure S8), which is relatively high for lineages that are as distant as Fungi and Alveolata. Considering these findings together with our earlier report showing an HHsearch homology probability of 99.8% with the cAMP receptor family [8], we validate that the Adhesions evolved from the ancient cAMP receptor family in an event close to the split of Unikonts from the common ancestor of eukaryotes.

Intriguingly, the complexity of the Adhesion receptors with long N-termini containing multiple functional domains observed in the Metazoan lineage is absent in receptors from Fungi, Amoebozoa and Alveolata, whereas the 7TM region is conserved in species ranging from unicellular Alveolates to human (Figure 4). These results may suggest that ligand binding and signaling mechanisms of the Adhesion receptors in Fungi and other basal eukaryotes could be confined within the 7TM region. However, the conservation of these motifs in the Metazoan lineage suggests that they are important for the signaling mechanisms along with the long N-termini with multiple functional domains. The complex multi-domain N-termini that emerged close to the radiation and diverged within the Metazoan lineage might reflect the need for a broader signal transduction system in the intricate cell to cell communication that is characteristic for Metazoan multicellularity. Prime examples are the emergence of the characteristic Adhesion family domains, GPS and Calx-beta domain in Filasterea and EGF-CA domain in Choanoflagellata, which prevailed in the multicellular Metazoan species (Figure 6). In addition, we extended the knowledge of the N-terminal region of the Adhesions by adding at least three novel domains TIG, TLD and RLD to the known 31 unique domains [14].

Glutamate receptor family

Our results suggest that the origin of the ancient Glutamate receptor lies in the common ancestor of eukaryotes, since we found them in Chromalveolata, Unikonts and Opisthokonts. For the first time, we have found 120 novel Glutamate receptors in the basal Opisthokont lineages which include Fungi and the close relatives of animals- Choanoflagellata, Filasterea and Porifera. We have also shown that they are also present in D. discoideum and T. pseudonana, which diverged before the Opisthokont lineage [8]. We found that the ancient Glutamate family is present in almost all eukaryotic lineages except in plants and in the Fungi subkingdom Dikarya, which include Ascomycota and Basidiomycota (see Figure 6).

Interestingly, the conserved length and the nature of the functional domains within the N-termini across all eukaryotic lineages in which the Glutamate receptors were found suggest that the endogenous ligand binding or so called Venus flytrap mechanism (VFTM) and the subsequent signal transduction mechanism emerged early in the eukaryotic life (Figure 5). This is in contrast with the Adhesion receptor family where the N-termini complexity is absent in the basal eukaryotes. Further, we found that >90% of the functional domains in the N-termini of the Glutamate receptors in diverse eukaryotic lineages, belong to the periplasmic binding protein superfamily. This includes the domain ANF Receptor and the four novel domains, BMP, LysR_Substrate, SBP_bac_1 and OpuAC that have not previously been identified in the Glutamate receptors. Taken together, it suggests a conserved fundamental role and remarkable adaptability of these periplasmic binding protein superfamily domains in regulating the signaling mechanisms of the Glutamate receptors from unicellular organisms to human.

Frizzled receptor family

We establish that the Frizzled family evolved from the cAMP receptor family before the divergence of Unikonts from a common ancestor of eukaryotes. This is supported by our extensive search in genomes that diverged before the eukaryotic supergroup Unikonts, which showed that they are absent in plant kingdom and Alveolata. Our earlier report showed that the Frizzled share an HHsearch homology probability of 99.4% with the cAMP receptor family [8]. However, we cannot trace which of the Adhesion and the Frizzled family diverged first; as they evolved within the same timeframe from the cAMP receptor family (see Figure 6). In addition, here we provided the first identification of 6 novel Frizzled family receptors in Fungi and Porifera. Interestingly, they are present only in the basal fungal lineage Chytridiomycota, which also have Rhodopsin, Adhesion and Glutamate families that all together account to 112 novel receptors. This suggests that Chytridiomycota phylum have remarkable necessity for a broader signaling system than the other 3 major phyla of Fungi that resembles the Metazoan GPCR repertoire.

Fungi specific GPCRs

Our results suggest that the pheromone sensing receptors (Ste2, Ste3) that are mainly involved in exchanging mating signals across the individuals of the same species, emerged after the split of Dikarya subkingdom. Interestingly, the Chytridiomycota has only Metazoan GPCRs (except the presence of Fungi nutrient sensing GPCRs) while Dikarya, which evolved later, has only fungal specific GPCRs. This could suggest that the basal fungal lineages that had the Metazoan like GPCR signaling system could have evolved later to become fungal specific GPCRs in Ascomycota and Basidiomycota. This observation finds support from our previous report which suggests that these pheromone sensing GPCRs were closely related to cAMP receptors with an HHsearch homology probability of 96.1% [8]. Considering the fact that the Dictyostelium cAMP receptors are involved in sexual chemotaxis and development [27], [28], it is thus tempting to speculate that Dictyostelium cAMP like receptors in Chytridiomycota may perform similar roles in finding mates and that these functions could be analogous to the function of pheromone receptors in Dikarya.

Novel mammalian like GPCRs: a possible antifungal drug targets and candidates for deorphanization?

GPCRs mediated signaling is known to be involved in fungal pathogenic morphogenesis and mycotoxin production in filamentous Fungi [22], [29]. Despite the role of GPCRs in fungal pathogenesis, there is no current development of potential antifungal drugs that target GPCRs. There are several recent reports of infectious diseases caused by Fungi that affect humans and wild life [30], [31]. To highlight a few, Cryptococcus gattii (Basidiomycota) causes infectious diseases in immunocompromised individuals in United States and B. dendrobatidis that belong to the group Rhizophydiales under the phylum Chytridiomycota is a major cause for the decline of amphibians [32], [33]. As novel fungal pathogens are emerging, there is an increasing need to develop novel drugs in this field. One of the possible reasons for the lack of development of the drugs is there are only few fungal GPCRs known and these are not strongly related to the well characterized mammalian like GPCR families that are major drug targets [1], [34]. Here, we have identified the first mammalian like GPCRs in the basal fungal phyla Chytridiomycota and Blastocladiomycota, creating an opportunity to delineate potential antifungal targets and aid deorphanization of these receptors by comparison with the well studied mammalian counterparts that serve as targets for 36% of the available drugs.

Materials and Methods

Genomes and proteomes

Complete proteome and genome dataset for 79 fungal species were downloaded. The dataset consists of proteomes for 61 species from UniProt (http://www.uniprot.org), which are distributed in phylum Ascomycota (48 species), Basidiomycota (9 species), Microsporidia (4 species). Other 18 Fungi proteomes were downloaded from FGI endorsed by Broad institute at MIT (http://www.broad.mit.edu/annotation/fgi), which are distributed in Ascomycota (13 species), Basidiomycota (1 species), Zygomycota (1 species) and in Chytridiomycota (3 species). In addition to the fungal proteome dataset, the study investigated proteomes for unicellular species with key evolutionary positions within the eukaryotic tree: S. rosetta [35], C. owczarzaki [36], P. tetraurelia [37] from NCBI (http://www.ncbi.nlm.nih.gov/), and T. thermophila [38] from UniProt. Furthermore, a collection of proteins (3465 proteins from several species) were obtained from NCBI that represents the phylum Porifera, a basal group of animals [39].

Sequence retrieval, mining and removal

A) GRAFS families: Full-length Rhodopsin, Adhesion, Glutamate and Frizzled family sequences for representative Metazoan genomes and the cAMP receptor family sequences from D. discoideum and C. intestinalis were retrieved from previously published GPCR repertoires to compare the common motifs of individual families and to perform phylogenetic analysis [3][8]. GPCRs in 79 fungal and the remaining genomes from other eukaryotic lineages were mined using HMM searches performed using the recent version of profile HMM software HMMER3 (http://hmmer.janelia.org/) with the Pfam_scan.pl script available at the Pfam homepage [40]. The Pfam_scan.pl script aligns sequences with the HMMs corresponding to the Pfam domains and only keeps the best aligned Pfam domain for each region. The putative dataset was aligned to the complete Pfam database version 24, which has 11912 families with sensitive HMM models built using HMMER3 software [41]. For the search against the complete Pfam database, the standard settings were utilized as provided by Pfam_scan.pl. We retrieved only the sequences which received the Pfam domains 7tm_1 (PF00001), 7tm_2 (PF00002) 7tm_3 (PF00003), Frizzled (PF01534) and Dicty_CAR (PF05462) from each proteome and classified them into GPCR families based on the Pfam result. The sequences with a 7TM domain predicted to have fewer than six or more than nine transmembrane segments in Phobius [42] were excluded from further analysis in order to reduce the number of incomplete sequences. Furthermore, the program CD-HIT [43] was run within the sequences of each genome separately with 90% cutoff to reduce the size of the dataset.

B) Fungi specific GPCRs: Similar to the methodology mentioned above, we retrieved the sequences that received the Pfam domains STE2 (PF02116), STE3 (PF02076), Git3 (PF11710)/Git3_c (PF11970). For nutrient receptors, we constructed an HMM profile from the sequences retrieved from [18]. The HMM profile for the nutrient receptors was then used as a query for the HMMSEARCH program (with strict e-value cutoff of 1e−25) to search against our complete proteome dataset analyzed in this study. We identified 619 Fungi specific GPCRs from the 79 fungal genomes analyzed in this study. The accession numbers for all the identified sequences were given in Table S3.

Alignments and phylogenetic analysis

The selected GPCR candidates were aligned using MAFFT version 6 (MAFFT, (http://mafft.cbrc.jp/alignment/server/) using the E-INS_I version (optimal for sequences with conserved motifs and carrying multiple domains) with default parameters [44]. All the alignments and the phylogenetic analyses were constructed based only on the seven transmembrane spanning regions and, for the phylogenetic analysis, unaligned regions were removed. Consensus sequences for each of the subgroups reported in Figure 1 were generated from all available human GPCR sequences for each of the subfamilies. The sequences were obtained from our human GPCR repertoire [4]. Similarly, a consensus sequence for the cAMP receptor family homologues in Fungi (Figure 1) were generated from the identified sequences in this study. First, the sequences that belong to each of the subgroups were aligned and separate HMM profiles were built from those alignments. Each HMM profiles that are respective to the groups serves as an input for the HMMEMIT program and a consensus sequence were obtained using option “-C” as implemented in the HMMER3 package. The consensus sequence is formed using a plurality rule that selects the maximum probability residue at each match state from the HMM profiles. The alignments were inspected and edited using Jalview. The phylogenetic analysis was performed using a Bayesian approach as implemented in MrBayes version 3.1.2 [45]. Markov Chain Monte Carlo (MCMC) analysis was used to approximate the posterior probabilities of the trees. Analysis was run using a gamma shaped model for the variation of evolutionary rates across sites (rates = gamma) and the mixed option (aamodelpr = mixed) was used to estimate the best amino acid substitution model. Each analysis was set to run for 3000000 generations and every hundredth tree was sampled. A stop rule was applied to determine when to terminate the MCMC generations as recommended in the MrBayes manual (standard deviation of split frequencies <0.01). If the MCMC analysis doesn't hit the stop value within the default number of generations, additional generations were run for it to reach the minimum. The first 25% of the sampled trees were discarded (burnin = 0.25) to reassure a good sample from the posterior probability distribution. A consensus tree was built from the remaining 75% of the sampled trees with the MrBayes sumt command using the 50% majority rule method. The sump command was used to control so that an adequate sample of the posterior probability distribution was reached during the MCMC procedure. The topology of all the phylogenetic trees supported by the posterior probability (PP) of the Bayesian approach was cross verified with bootstrap analysis (500 replicates) using maximum likelihood (ML) approach as implemented in PhyML (version 3.0) program [46]. Bootstrap values were indicated for the nodes that received good support in ML approach. The phylogenetic tree was drawn in FigTree 1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/).

Domain search

The N-terminal domains for the identified Adhesion and Glutamate family members were identified with Pfam search and also verified using RPS-blast with a cutoff e-value of 0.01 against the Conserved Domain Database (CDD) version 2.29 position-specific scoring matrixes (PSSMs).

Supporting Information

Dataset S1

Amino acid sequences of all novel sequences identified in this study in standard FASTA format.

(TXT)

Table S1

Accession numbers of novel sequences identified in this study.

(XLS)

Table S2

List of species investigated.

(DOC)

Table S3

Accession numbers of all Fungi specific GPCRs identified in this study.

(XLS)

Figure S1

Phylogenetic relationship between the Rhodopsin family sequences in Fungi and human.

(TIF)

Figure S2

Phylogenetic relationship between the Rhodopsin family sequences in Fungi and T. adhaerens.

(TIF)

Figure S3

Phylogenetic relationship between the novel Adhesion family sequences in Fungi, Filasterea, Choanoflagellata and Alveolata with the representatives from Metazoa. The tree is rooted with D. discoideum. The node that is highlighted in red clustered the Adhesion receptor from Alveolata with the fungal members (PP>90%). They share about 50% identity within the 7TM regions (see Figure S8).

(TIF)

Figure S4

Alignment of the Glutamate family sequences in diverse eukaryotic lineages. The alignment shows the conserved regions within the 7TM region between the novel sequences in diverse eukaryotic lineages and human. The consensus sequence for each species was obtained from separate alignments. The number of sequences aligned to emit the consensus sequences for each species is given in the parenthesis. Regions which show >50% conservation are highlighted.

(TIF)

Figure S5

Phylogenetic relationship between the Glutamate family sequences in Fungi, Choanoflagellata, Porifera and Alveolata with human.

(TIF)

Figure S6

Alignment of the novel Frizzled receptor sequences in Fungi and Porifera with the representative consensus sequences of the Frizzled receptors from human, N. vectensis (NV), T. adhaerens (TA) and D. discoideum (dicty). Regions which show >50% conservation are highlighted. Multiple cysteine residues that are characteristic for the Frizzled family are mostly conserved in the novel sequences.

(TIF)

Figure S7

Phylogenetic relationship between the Frizzled family sequences in Fungi and sponges (Porifera) with the representatives from Metazoa.

(TIF)

Figure S8

Alignment showing the conservation in the 7TM region between the Adhesion receptor sequences in Fungi and Alveolata. Regions which show more than 50% conservation are highlighted.

(TIF)

Acknowledgments

We thank Dr. Michael Williams, Uppsala University for valuable comments on the manuscript.

Footnotes

Competing Interests: The authors have declared that no competing interests exist.

Funding: The study was supported by the Swedish Research Council, The Novo Nordisk Foundation, Swedish Royal Academy of Sciences, and Magnus Bergvall Foundation. RF was supported by the Swedish Research Council. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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