Table 1.
Overview of characteristics of grass pollen allergens [8–19].
Fig 1.
Protein domain architecture of representative allergen proteins from each group.
The protein domains in pollen allergen groups are identified by SDAP (Structural Database of Allergenic Proteins) database and verified using the SMART (http://smart.embl-heidelberg.de) and PFAM (http://pfam.sanger.ac.uk/). Lol p 1 (P14946) for group 1, Lol p 2 (P14947) for group 2/3, Lol p 4 (Q5TIW3) for group 4, Lol p 5 (Q40240) for group 5, Phl p 7 (O82040) for group 7, Lol p 11 (Q7M1X5) for group 11, Phl p 12 (P35079) for group 12 and Phl p 13 (CAB42886) for group 13 were chosen as representative members respectively.
Fig 2.
Phylogenetic analysis of pollen allergen protein families in B. distachyon and representative member of each group from Ryegrass and Timothy grass.
The protein sequences were aligned by Clustal X2.0 and unrooted phylogenetic tree was constructed by neighbour-joining method with 100 bootstrap replicates. Branches with less than 50% bootstrap support were collapsed. The tree was divided into eight phylogenetic clusters. The members were distinctly coloured to represent respective protein family. Lol p 1 (P14946) for group 1, Lol p 2 (P14947) for group 2/3, Lol p 4 (Q5TIW3) for group 4, Lol p 5a (Q40240) for group 5, Phl p 7 (O82040) for group 7, Lol p 11 (Q7M1X5) for group 11, Phl p 12 (P35079) for group 12 and Phl p 13 (CAB42886) for group 13 were chosen as representative members respectively.
Fig 3.
Phylogenetic tree and domain architecture of pollen allergens.
Neighbour-Joining phylogenetic tree is constructed based on protein alignments of putative allergen-encoding proteins of B. distachyon and known pollen allergens from other grasses using ClustalX2. Bootstrap values greater than 50% are shown at the nodes. The schematic diagrams show the domain organization of these proteins as obtained from SMART and PFAM searches. Different domains are indicated by the use of different colours as shown at the bottom of the figure. The accession numbers for the sequences used in the alignment are also listed in the figure.
Fig 4.
Expression profile and evolutionary pattern of pollen allergens.
The heat map shows the relative abundances of putative allergen-encoding genes identified in B. distachyon. The level of expression for a gene across different samples are represented as percentage of the maximum expression level in colour code from 0% (white) to 100% (black). Heat map was plotted against the phylogenetic tree constructed using B. distachyon protein sequences. The diagram also shows relative expression values in anther tissue of B. distachyon based on RNA-Seq data analysis obtained from nine developmental stages. Inflo1 is for pre-emergence flowers stage, Inflo2 is for post-emergence flowers stage, Seed1 is for whole seed at 5days after pollination, Seed2 is for whole seed at 10 days after pollination and Endosp is for endosperm respectively.
Fig 5.
Distribution of 24 putative allergen-encoding genes onto five B. distachyon chromosomes.
The chromosomal position of each gene was mapped according to the B. distachyon genome. The chromosome number is indicated at the top of each chromosome. The scale is 5 Mb. Genes are marked on the left and right hand side of each chromosome based on their orientation. Genes belonging to different groups of pollen allergens are indicated by the use of different colours as shown at the bottom of the figure.
Fig 6.
Predicted structures of putative pollen allergen proteins in B. distachyon.
The structure of 24 putative allergen-encoding proteins with >90% confidence level were shown.
Fig 7.
Duplication frequency of 14 most abundant cis-regulatory elements (CREs) in putative allergen-encoding genes in B. distachyon.