We focus on three eukaryotic kingdoms, fungi, animals (Animalia) and plants (Plantae). Gene family whose member containing N-glycosylation domain name was named after the domain name ID. conserved across taxa. Genes arising by duplication-divergence is usually attributable enormously to domain name duplication and divergence, and gene births constantly give rise to new domains7. Likewise, gene fusion essentially occurs through recombination of conserved domains, namely domain shuffling, that are found to be present in different instances8,9. In this article, we investigate how genes responsible for protein were collected (Table 1, Fig. 1, Supplementary Table S1). Of the 24 genes, all encode glycosyltranseferases, except for two mannosidases (MNS1 and GMII). 23 Pfam domains were identified in the peptide sequences of the 24 genes. Among them, combination of domains were identified in Och1, Van1, 1,4-FucT, and GnTV, respectively, while several domains were shared by multiple (2C3) enzymes (Table 1). Table 1 Known enzymes and identified domains responsible for PNG reactions. which is close to the base of the flowering herb lineage. Hence, in total, we used 153 genomes for identification of PNG domain-containing genes (Supplementary Table S2). Based on the identified domains in reference genes of PNG enzymes, we used HMMER, a domain-centric method to compare profile hidden Markov models (HMMs) of PfamA to peptide datasets, to identify homologous sequences, by which 4491 sequences were obtained in total25,26. BLAST searches were performed too, which did not generate any sequences beyond HMMER search results. 6 domains or domain name combinations as contained in PNG sequences are confined in a specific Rabbit Polyclonal to ATPG eukaryotic lineage; this distribution is usually consistent with that of genes made up of these domains related to PNG (Fig. 2, Supplementary Physique S1). For example, Mnn9, Van1 and Anp1, which are involved in protein and Basidiomycota representing basal fungi clades, no homologs were identified. The phylogeny of this family resolved multiple distinctive clades, which indicated that this members have evolved into different biological/enzymatic roles. Mnn10 and Mnn11 represented the only 2 members of PF05637 in genes contain domain name PF11051. Among them, MNN2 (YBR015C) and MNN5 (YJL186W) are specifically involved in genes are in the other AM211 group (Clade II) (Supplementary Physique S4). An Arabidopsis gene was identified, which was grouped in the clade II, whose biological function has not been reported yet, to our knowledge (Supplementary Physique S4). Och1 (YGL038C) initiates genes encoding GnTI were in an impartial clade (Supplementary Physique S7, Clade AM211 III)56,57. The Clade IV, as shown in Supplementary Physique S7, comprising Chordata genes, contains a human gene encoding protein and genes, while genes in Group III consist of genes from species spanning from lower to higher land plants (Supplementary Physique S14). In this group, although no genes were definitely identified enzymatically, AT3G10320 was exhibited as a putative xylosyltransferase which was recently characterized as MUCI21, while the genes AT3G18170 and AT3G18180 are expressed highly in a heteroxylan made up of mucilaginous tissues, which indicated that this genes in this group are related to mucilage production in terrestrial plants94,95. 1,3-fucose transferase (1,3-FucT) and 1,4-fucose transferase (1,4-FucT) add fucose residue to the basal and terminal part of the glycan core, respectively. In Arabidopsis, the genes encoding these enzymes were identified (AT3G19280 and AT1G49710 for 1,3-FucT, and AT1G71990 for 1,4-FucT)96,97. The Arabidopsis genes encoding both the enzymes conferred domain name PF00852. Genes made up of this domain name were identified in both plants and animals, but not in other eukaryotic species. Copy numbers in animals are slightly more than those in plants. Phylogenetic analysis results showed that this herb sequences were clustered into two groups, and each contained one of Arabidopsis fucose transferases, respectively, indicating that the genes in these two groups represent AM211 genes encoding 1,3-FucT and 1,4-FucT, respectively, which play roles in plant-specific in animal lineage. Although less acknowledged, domain name shuffling is an important way of new genes arising. In this study, 1,3-GalT is an example of domain name shuffling, which takes an essential role in plant-specific Lea formation. Peptide sequence of 1 1,3-GalT contains two domains, PF00337 and PF01762. Genes made up of PF01762 were identified in fungi and animals too, and PF00337 was also present in animals. In animals, the two domains were in separated genes, and only in plants the two domains were identified to be fused, probably through domain shuffling. Overall, this is an example that shows component novelty,.
Categories