Figure 1.
Mating-type structure across the fungal kingdom.
α1, genes encoding transcription factors with an α1 domain; PPF, genes encoding proteins with a domain characterized by highly conserved proline and phenylalanine residues [41]; HMG, genes encoding transcription factors with an HMG domain; HD, genes encoding transcription factors with an homeodomain; OTHER, genes encoding proteins not relevant to this study. The standardized nomenclature [7] currently used for Pezizomycotina is indicated below the corresponding domains. +, gene present; +/−, gene present in some species from a group. Mating-type structures were compiled for the following species and corresponding references: Saccharomyces cerevisiae, Kluyveromyces lactis, Candida albicans and Yarrowia lipolytica [49], [65], Schizosaccharomyces pombe [8], Ustilago maydis [66], Phycomyces blakesleeanus [17] and Encephalitozoon cuniculi [46]. The Pc gene from S. pombe was placed in the HMG class in agreement with the current classification of Pc protein (P10841) in Swissprot. Mating-type genes from U. maydis, P. blakesleeanus and E. cuniculi were placed arbitrarily in mating type 1 or 2.
Figure 2.
Conserved sequence of α1 and HMG domains.
(A). WebLogo [19] representation of conserved sequences in α1, MATA-HMG, SOX and HMGB domains respectively. The x-axis represents amino acid position from the N to C terminal. The amino acid labeled as ‘1’ is located at position 11-48 and 1-2 in the α1 and HMG domains, respectively (NCBI Conserved Domain Database accession numbers: pfam04769 and cd00084). Logos represent an ∼40 amino acid core sequence of the DNA binding domain from 300 α1 domains, and 257 MATA_HMG, 3054 SOX_HMG and 2162 HMGB_UBF_HMG-box domains. (B) Consensus core sequences produced from conserved amino acids in A. α1 protein domains divided into those of Pleosporales (α1-a) and Pezizomycotina without Pleosporales (α1-b). α1-a and α1-b are considered as one for identity scoring. Three or more identical amino acids among sequences are coloured blue while two or more identical or similar amino acids are coloured grey. Conservation among the five sequences is shown; a letter is used to represent three or more identical amino acids and an asterisk (*) for two identical or similar amino acids. (C) Ancestral core region for α1 and MATA_HMG. Core regions from 300 α1 domains and 257 MATA_HMG sequences were used.
Figure 3.
Unrooted phylogram for the HMG superfamily and the α1 domain core amino acid sequences.
Clustering of core amino acid sequences using maximum-likelihood and model LG+G [67]. Labelling is as follows: α1 (A, green), MATA_HMG (B, yellow), SOX (C, orange), HMGB (D, blue), MAT1-1-3 subgroup of MATA_HMG (E, white), Microsporidia MAT sex locus HMG (F, white), Phycomyces blakesleeanus (Zygomycota) sexM (Phybl8) and sexP (Phybl9) are circled in purple. LR-ELW values above 70% are shown. Abbreviations: Ailme, Ailuropoda melanoleuca; Ajeca, Ajellomyces capsulatus; Altal, Alternaria alternata; Altbr, Alternaria brassicicola; Anoga, Anopheles gambiae; Antlo, Antonospora locustae; Arath, Arabidopsis thaliana; Aspfu, Aspergillus fumigatus; Aspni, Aspergillus nidulans; Bipsa, Bipolaris sacchari; Botfu, Botryotinia fuckeliana; Caee, Caenorhabditis elegans; Canal, Candida albicans; Cerel, Cervus elaphus yarkandensis; Ciosa, Ciona savignyi; Coche, Cochliobolus heterostrophus; Crypa, Cryphonectria parasitica; Culqu, Culex quinquefasciatus; Danre, Danio rerio; Dotpi, Dothistroma pini; Drome, Drosophila melanogaster; Enccu, Encephalitozoon cuniculi; Entbi, Enterocytozoon bieneusi; Fusac, Fusarium acaciae-mearnsii; Gibfu, Gibberella fujikuroi; Gibze, Gibberella zeae; Homsa, Homo sapiens; Lacth, Lachancea thermotolerans; Magor, Magnaporthe oryzae; Musmu, Mus musculus; Mycgr, Mycosphaerella graminicola; Neucr, Neurospora crassa; Penma, Penicillium marneffei; Pneca, Pneumocystis carinii; Podan, Podospora anserina; Pyrbr, Pyrenopeziza brassicae; Pyrte, Pyrenophora teres; Rhyse, Rhynchosporium secalis; Sacce, Saccharomyces cerevisiae; Schja, Schizosaccharomyces japonicus; Schpo, Schizosaccharomyces pombe; Sorma, Sordaria macrospora; Stesa, Stemphylium sarciniforme; Strpu, Strongylocentrotus purpuratus; Takru, Takifugu rubripes; Ustma, Ustilago maydis; Verda, Verticillium dahliae; Xenla, Xenopus laevis; Zygro, Zygosaccharomyces rouxii. Numbers after species names indicate α1 proteins (1), MATA_HMG (2), MAT1-1-3 (3), SOX (4), HMGB (5) and other HMG domains (6–9). When more than one domain is present for the same species, the suffix a, b or c was added. Accession numbers of species grouped by evolutionary affinity are in Table S1. Units indicate number of amino acid changes per position.
Figure 4.
Secondary structure of MATA_HMG and α1 domains from proteins of representative species of Pezizomycotina.
The alignment was obtained with ClustalW2 [63] and coloured according to the Clustal X colour scheme provided by Jalview [64]. This colour scheme is displayed in Table S3. The prediction of secondary structures was performed with Jpred3 [27]. All diplayed helices have a JNETCONF score of at least 7, except for helix 2 from S. pombe which has a JNETCONF score of 0 for all helix 2 positions. The secondary structure presented in the mSOX2_Xray line is from [28] and served to validate accuracy of Jpred3. Full species names and accession numbers are in Table S4.
Table 1.
Structure prediction with Phyre of HMG and α1 domains from representative species from major groups of Ascomycota.
Figure 5.
3D-structure of the α1 domain from MAT1-1-1/mat A-1 of N. crassa.
Schematic ribbon presentation of the superposition of the α1 domain (magenta) onto the structure of the Sox2 HMG domain (cyan) as observed in the tertiary DNA/Sox2/Oct1(POU domain) complex. DNA is represented as gold ribbons (polyphosphate) and blue sticks (bases). Amino acid residues important for DNA recognition and bending are represented as sticks. Residues (methionine M51, phenylalanine F53 and arginine R54) putatively important for function are labelled. Numbering is from the N-terminus methionine. Alpha helices are labelled h1, h2 and h3. Accession number: AAC37478, 3D structure established from residue 44 to 97.
Figure 6.
Alignment of the conserved region downstream of the MATα_HMG region of representative species from major groups of Pezizomycotina.
The alignment was obtained with ClustalW2 [63] and coloured according to the Clustal X colour scheme provided by Jalview [64]. This colour scheme is displayed in Table S3. The Y-[LMIF]-x3-G-[WL] motif is highlighted in pink in the consensus line. Accession numbers for MAT1-1-1 proteins: Podospora anserina (CAA45519), Neurospora crassa (AAC37478), Sordaria macrospora (CAA71623), Magnaporthe oryzae (strain 70-6) (BAC65087), Cryphonectria parasitica (AAK83346), Diaporthe spG (BAE93756), Diaporthe spW (BAE93750), Gibberella fujikuroi (AAC71055), Fusarium oxysporum (BAA75910), Gibberella zeae (AAG42809), Hypocrea jecorina (ACR78244), Isaria tenuipes (BAC67541), Pyrenopeziza brassicae (CAA06844), Coccidioides immitis (ABS19618), Histoplasma capsulatum (AB087596), Aspergillus nidulans (EAA63189), Aspergillus fumigatus (AAX83122), Aspergillus oryzae (Q2U537), Aspergillus niger (XP_001394976), Neosartorya fischeri (ABQ28692), Penicillium chrysogenum (CAP17332), Penicillium marneffei (ABC68484), Alternaria alternata (BAA75907), Cochliobolus heterostrophus (CAA48465), Cochliobolus homomorphus (AAD33441), Cochliobolus kusanoi (AAD33443), Cochliobolus luttrellii (AAD33439), Cochliobolus sativus (AAF87723), Pleospora eturmiuna (AAR00973), Phaeosphaeria nodorum (AAO31740), Leptosphaeria maculans (AAO37757), Stemphylium loti (AAR04470), Mycosphaerella graminicola (AAL30838), Cercospora zaea-maydis (ABB83705).
Figure 7.
Mating-type loci and DNA lyase gene position in representative species of Ascomycota.
The DNA lyase orthologs are indicated only when confirmed by sequencing. The physical linkage of the MAT locus and the DNA lyase gene may be relaxed, as exemplified by Cochliobolus heterostrophus, where the two genes are separated by 181 kb. Orthology of DNA lyase genes was determined by FUNGIpath [52]. Mating-type structures were compiled for the following species and corresponding references: C. heterostrophus [68], Leptosphaeria maculans [69], Mycosphaerella graminicola [70], Aspergillus fumigatus [71], Coccidioides immitis [72], Neurospora crassa [49], [50], Podospora anserina [43], Magnaporthe oryzae [43], Gibberella fujikuroi [73], Gibberella zeae [50], Cordyceps takaomontana [74], Yarrowia lipolytica [49], Encephalitozoon cuniculi [46]. Circled figures on the left: 1: Dothideomycetes; 2: Eurotiomycetes; 3: Sordariomycetes; 4: Saccharomycetales; 5: Microsporidia. Linkage of C. heterostrophus MAT1-1-1 to DNA lyase gene (ESTEXT_GENEWISE1PLUS.C_40361) was determined from the sequence data produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/. Linkage of G. fujikuroi (Fusarium verticillioides) MAT1-1-1 to DNA lyase gene (FVEG_02488) was determined from the version 1 sequence data produced by the Broad Institute http://www.broadinstitute.org/annotation/genome/fusarium_group/MultiHome.html.