Comparison of gpd genes and their protein products in basidiomycetes

Abstract

We compared promoters, coding sequences, introns and terminators of glyceraldehyde 3-phosphate dehydrogenase genes (gpd) from various basidiomycetes. Coding regions of these housekeeping genes are highly conserved (between 60 to 99% DNA identity) whilst non-coding regions have DNA identities of around 40%. Amongst all homobasidiomycete promoters, the TATA region and a CT-rich region with the potential transcription start sites are highest conserved. Surprisingly, there are no other conserved motifs common to all promoters. Up to five introns are clustered at the far 5 ́ ends of the genes, hinting to a potential function in efficient gene expression. Creative Commons License This work is licensed under a Creative Commons Attribution-Share Alike 4.0 License. This regular paper is available in Fungal Genetics Reports: http://newprairiepress.org/fgr/vol52/iss1/6 18 Fungal Genetics Newsletter Comparison of gpd genes and their protein products in basidiomycetes Sreedhar Kilaru and Ursula Kües Molecular Wood Biotechnology, Institute of Forest Botany, Georg-August-University Göttingen, 37077 Göttingen, Germany Fungal Genetics Newsletter 52:18-23 We compared promoters, coding sequences, introns and terminators of glyceraldehyde 3-phosphate dehydrogenase genes (gpd) from various basidiomycetes. Coding regions of these housekeeping genes are highly conserved (between 60 to 99% DNA identity) whilst non-coding regions have DNA identities of around 40%. Amongst all homobasidiomycete promoters, the TATA region and a CT-rich region with the potential transcription start sites are highest conserved. Surprisingly, there are no other conserved motifs common to all promoters. Up to five introns are clustered at the far 5 ́ ends of the genes, hinting to a potential function in efficient gene expression. Little is known about promoters in higher basidiomycetes. Constitutive promoter activities have been described for some homologous and heterologous promoters in Coprinopsis cinerea with the Agaricus bisporus gpdII (glyceraldehyde 3-phosphate dehydrogenase gene 2) promoter being highest in activity (Kilaru et al., 2005). Use of gpd promoters from A. bisporus, Flammulina velutipes, Lentinula edodes, Phanerochaete chrysosporium, Schizophyllum commune and Trametes versicolor has by now been made in different species either for laccase and peroxidase production or for expression of gfp (green fluorescent protein gene) or the bacterial hygromycin resistance gene hph (for references see Kilaru et al., 2005). Surprisingly, homology among these promoter sequences is relatively low (Kilaru et al., 2005). In contrast, the two known gpd genes from A. bisporus (termed gpdI and gpdII), the single gpd gene from P. chrysosporium and an isolated gpd gene from S. commune have been described as highly conserved in intron positions as well as in sequence of their products (Harmsen et al., 1992). Analysis of all gpd genes from basidiomycetes currently present in the NCBI database and of two putative gpd genes of C. cinerea deduced from the published genomic sequence (http://www.broad.mit.edu/annotation/fungi/coprinus_cinereus/) and submitted to the genome annotation database at Duke (http://genome.semo.edu/cgi-bin/gbrowse/coprinus) confirmed this in most other instances (Table 1). Table 1. Comparisons of sequences from homobasidiomycetous gpd genes Sequences analyzed Sequence identity/similarity in percentage a Lowest Highest Mean ± standard deviation Promoter 34 85 41.4 ± 5.8 b Gene (from start to stop codon) 48 78 59.3 ± 4.8 Coding sequence 60 (60) 88 (99 ) 72.0 ± 5.2 (72.9 ± 5.2) c g Intron 1 25 57 41.0 ± 7.5 d Intron 2 23 56 40.0 ± 6.1 d Intron 3 22 57 42.0 ± 7.3 d,e Intron 4 25 60 40.8 ± 7.2 d Intron 5 20 54 36.5 ± 7.8 d Intron 6 24 57 40.1 ± 6.8 d Intron 7 30 52 41.0 ± 5.2 d Intron 8 21 61 38.5 ± 7.5 d Intron 9 32 54 41.6 ± 5.7 d Terminator 33 96 40.2 ± 9.9 f Protein product 63/77 c (63/77) 88/93 (99/99 ) g 74.5 ± 4.5/84.8 ± 3.2 (75.3 ± 4.2/85.0 ± 3.1) For source of sequences see Fig. 1, GenBank accession numbers AY842301 and AB075243 for promoters of V. volvacea and a T. versicolor and Harmsen et al. (1992) for promoters and introns of A. bisporus, P. chrysosporium and S. commune, respectively. 280-300 bp promoter sequence upstream to the startcodon was used except for A. bisporus gpdI, and T. cucumeris where only b 264, respectively 200 bp were available. Values in brackets include sequences from heterobasidiomycetes. c The number refers to intron positions in the two A. bisporus genes gpdI and gpdII (Fig. 2). d Only a conserved 58 bp region was considered from the 121 bp long intron in O. olearius. e 300 bp sequence downstream to the stopcodon was used except for F. velutipes (113 bp), O. olearius (212 bp) and the unknown f basidiomycete (127 bp). The high value of 99% from the combination X. dendrorhous and P. rhodozyma has not been included in calculating mean values. g Published by New Prairie Press, 2017