A novel rubber tree PR-10 protein involved in host-defense response against the white root rot fungus Rigidoporus microporus

Background White root rot disease in rubber trees, caused by the pathogenic fungi Rigidoporus microporus, is currently considered a major problem in rubber tree plantations worldwide. Only a few reports have mentioned the response of rubber trees occurring at the non-infection sites, which is crucial for the disease understanding and protecting the yield losses. Results Through a comparative proteomic study using the two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) technique, the present study reveals some distal-responsive proteins in rubber tree leaves during the plant-fungal pathogen interaction. From a total of 12 selected differentially expressed protein spots, several defense-related proteins such as molecular chaperones and ROS-detoxifying enzymes were identified. The expression of 6 candidate proteins was investigated at the transcript level by Reverse Transcription Quantitative PCR (RT-qPCR). In silico, a highly-expressed uncharacterized protein LOC110648447 found in rubber trees was predicted to be a protein in the pathogenesis-related protein 10 (PR-10) class. In silico promoter analysis and structural-related characterization of this novel PR-10 protein suggest that it plays a potential role in defending rubber trees against R. microporus infection. The promoter contains WRKY-, MYB-, and other defense-related cis-acting elements. The structural model of the novel PR-10 protein predicted by I-TASSER showed a topology of the Bet v 1 protein family, including a conserved active site and a ligand-binding hydrophobic cavity. Conclusions A novel protein in the PR-10 group increased sharply in rubber tree leaves during interaction with the white root rot pathogen, potentially contributing to host defense. The results of this study provide information useful for white root rot disease management of rubber trees in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-023-04149-3.


Supplementary Figure 9:
The predicted normalized B-factor of predicted secondary structure of Uncharacterized protein LOC110648447 isoforms using I-TASSER server B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence.

Supplementary Tables
Supplementary Table 1:  The top 10 alignments reported above (in order of their ranking) are from the following threading programs: 1: MUSTER, 2: FFAS-3D, 3: SPARKS-X, 4: HHSEARCH2, 5: HHSEARCH, I 6: Neff-PPAS, 7: HHSEARCH, 8: pGenTHREADER, 9: wdPPAS, 10: PROSPECT2. Rank of templates represents the top ten threading templates used by I-TASSER. Ident1 is the percentage sequence identity of the templates in the threading aligned region with the query sequence. Ident2 is the percentage sequence identity of the whole template chains with query sequence. Coverage represents the coverage of the threading alignment and is equal to the number of aligned residues divided by the length of qu ery protein.

ID
Normalized Z-score is the normalized Z-score of the threading alignments. Alignment with a Normalized Z-score >1 mean a good alignment and vice versa. Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library. RMSDa is the RMSD between residues that are structurally aligned by TM-align. IDENa is the percentage sequence identity in the structurally aligned region. Cov represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Supplementary Table 7:
The predicted functions of Uncharacterized protein LOC110648447 isoforms by COFACTOR and COACH through I-TASSER server This section reports biological annotations of the target protein by COFACTOR and COACH based on the I-TASSER structure prediction. While COFACTOR deduces protein functions (ligand-binding sites, EC and GO) using structure comparison and protein-protein networks, COACH is a meta-server approach that combines multiple function annotation results (on ligand-binding sites) from the COFACTOR, TM-SITE and S-SITE programs. Crystal structure of major birch pollen allergen Bet v 1 a in ternary complex with 8anilonapthalene-1-sulfonate (ANS) and deoxycholic acid 2AN 8-anilo-1-napthalene sulfonate (ANS) 10,12,25,79,97,110,112,128,131,132,135,136 Note: C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction. Cluster size is the total number of templates in a cluster. Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster Cscore EC is the confidence score for the EC number prediction. Cscore EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction. TM-score is a measure of global structural similarity between query and template protein.

Supplementary
RMSDa is the RMSD between residues that are structurally aligned by TM-align. IDENa is the percentage sequence identity in the structurally aligned region.