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

  • Bacterial and Fungal Pathogenesis - Research Paper
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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.

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Acknowledgments

The authors thank Ms. Deepti Varshney and Mr. Aditya Gaur, TERI Deakin Nanobiotechnology Centre, Gwal Pahari, Haryana, India, for software support on high-performance computing cluster required in this study. The authors also thank Ms. Sadhana Shukla and Dr. Reena Singh for maintaining and providing monosporal culture of R. proliferus. Sequencing was performed at Agrigenome Labs, Kochi, and Kerala, India.

Funding

This work was financially supported by the grant-in-aid for research by the Department of Science and Technology (DST), India, under the grant number “EMR/2017/000657”.

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Authors and Affiliations

  1. TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gwal Pahari, Gurgaon Faridabad Road, Gurugram, Haryana, 122001, India

    Pushplata Prasad Singh, Divya Srivastava, Akanksha Jaiswar & Alok Adholeya

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  1. Pushplata Prasad Singh
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  2. Divya Srivastava
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  3. Akanksha Jaiswar
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Contributions

All authors have read and approved the final manuscript. PPS was involved in conceptualization of the project, study design, data analyses, data compilation, manuscript writing, critical inputs, and finalization of the manuscript. DS and AJ were involved in genomics data analysis, data compilation, and manuscript writing. AA gave critical comments and reviewed the work.

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Correspondence to Pushplata Prasad Singh.

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Electronic supplementary material

Figure S1

RiLySM and RiSIS1 proteins coded by R. proliferus and their homologs identified in R. irregularis (PNG 85 kb)

High Resolution Image (TIF 142 kb)

Table S1

Effector proteins identified in R. proliferus (DOCX 47 kb)

Table S2

Homologous effector proteins among R. proliferus, R. irregularis and R. clarus (DOCX 46 kb)

Table S3

Functions of the 15 functionally conserved effectors in all three species of Rhizophagus and had a homolog in PHI db (DOCX 33 kb)

Table S4

Annotation of effector proteins unique to R. proliferus (DOCX 65 kb)

Table S5

Molecular docking interaction between SP7 and ERF19 proteins (DOCX 37 kb)

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Prasad Singh, P., Srivastava, D., Jaiswar, A. et al. Effector proteins of Rhizophagus proliferus: conserved protein domains may play a role in host-specific interaction with different plant species. Braz J Microbiol 50, 593–601 (2019). https://doi.org/10.1007/s42770-019-00099-x

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