Effector proteins of Rhizophagus proliferus: conserved protein domains may play a role in host-specific interaction with different plant species

Abstract

Arbuscular mycorrhizal (AM) fungi show high promiscuity in terms of host. Effector proteins expressed by AM fungi are found important in establishing interaction with host. However, the mechanistic underlying host-specific interactions of the fungi remain unknown. The present study aimed (i) to identify effectors encoded by Rhizophagus proliferus and (ii) to understand molecular specificity encoded in effectors for interaction with specific plant species. The effectors predicted from the whole genome sequence were annotated by homology search in NCBI non-redundant protein, Interproscan, and pathogen-host interaction (PHI) databases. In total, 416 small secreted peptides (SSPs) were predicted, which were effector peptides with presence of nuclear localization signal, small cysteine-rich, and repeat-containing proteins domains. Similar to the functionally validated SP7 effectors in Rhizophagus irregularis, two proteins (RP8598 and RP23081) were identified in R. proliferus. To understand whether interaction between SP7 and the plant target protein, ERF19, is specific in nature, we examined protein-peptide interaction using in silico molecular docking. Pairwise interaction of RP8598 and RP23081 with the ethylene-responsive factors (ERF19) coded by five different plant species (Lotus japonicus, Solanum lycopersicum, Ocimum tenuiflorum, Medicago truncatula, Diospyros kaki) was investigated. Prediction of high-quality interaction of SP7 effector with ERF19 protein expressed only by specific plant species was observed in in silico molecular docking, which may reiterate the role of effectors in host specificity. The outcomes from our study indicated that sequence precision encoded in the effector peptides of AM fungi and immunomodulatory proteins of host may regulate host specificity in these fungi.

Keywords: AM-plant interaction; Arbuscular mycorrhizal fungi (AM fungi); ERF19; Effector proteins; Protein-peptide molecular docking; SP7.

Fig. 1

R. proliferus effectors sharing homology with five proteins that belong to the set of 22 AMF protein tribe in R. irregularis. RP indicates effectors of R. proliferus and Rir indicates effectors of R. irregularis

Fig. 2

Homologous effector proteins among R. proliferus, R. irregularis, and R. clarus. Venn diagram shows homologs for effectors identified in R. proliferus among R. irregularis (marked in blue) and R. clarus (marked in yellow) and region marked in gray indicates common effectors among all the three species

Fig. 3

Functions of the 15 functionally conserved effectors

Fig. 4

Multiple sequence alignment of SP7 proteins coded by R. proliferus and R. irregularis genomes. RP23081 and RP8598: R. proliferus-coded SP7 proteins; AEK82120.1, AEK82121.1, and AEK8212.1: R. irregularis-coded SP7 proteins; green color represents a conserved region, red boxes indicate Kex2 cleavage sites, and residues in yellow color indicate the presence of tandem repeats

Fig. 5

In silico molecular docking analysis. (i) Interaction between SP7 (a RP8598; b RP23081) and ERF19 of L. japonicus; (ii) interaction between SP7 (a RP8598; b RP23081) and ERF19 of S. lycopersicum; (iii) interaction between SP7 (RP8598) and D. kaki. Amino acids of the SP7 (p14) present at the binding site are marked in black color and the interacting amino acids of the AP2 domain of ERF19 are marked in green color

Fig. 5

In silico molecular docking analysis. (i) Interaction between SP7 (a RP8598; b RP23081) and ERF19 of L. japonicus; (ii) interaction between SP7 (a RP8598; b RP23081) and ERF19 of S. lycopersicum; (iii) interaction between SP7 (RP8598) and D. kaki. Amino acids of the SP7 (p14) present at the binding site are marked in black color and the interacting amino acids of the AP2 domain of ERF19 are marked in green color

Fig. 5

In silico molecular docking analysis. (i) Interaction between SP7 (a RP8598; b RP23081) and ERF19 of L. japonicus; (ii) interaction between SP7 (a RP8598; b RP23081) and ERF19 of S. lycopersicum; (iii) interaction between SP7 (RP8598) and D. kaki. Amino acids of the SP7 (p14) present at the binding site are marked in black color and the interacting amino acids of the AP2 domain of ERF19 are marked in green color