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Genome-Wide Identification and Characterization of Effector Candidates with Conserved Motif in Falciphora oryzae
Mengdi Dai1,2, Zhenzhu Su3, Xueming Zhu1
1State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
Abstract:
Microbes employ effectors to disrupt immune responses and promote host colonization. Conserved motifs including RXLR, LFLAK-HVLVxxP (CRN), Y/F/WxC, CFEM, LysM, Chitin-bind, DPBB_1 (PNPi), and Cutinase have been discovered to play crucial roles in the functioning of effectors in filamentous fungi. Nevertheless, little is known about effectors with conserved motifs in endophytes. This research aims to discover the effector genes with conserved motifs in the genome of rice endophyte Falciphora oryzae. SignalP identified a total of 622 secreted proteins, out of which 227 were predicted as effector candidates by EffectorP. By utilizing HMM features, we discovered a total of 169 effector candidates with conserved motifs and three novel motifs. Effector candidates containing LysM, CFEM, DPBB_1, Cutinase, and Chitin_bind domains were conserved across species. In the transient expression assay, it was observed that one CFEM and one LysM activated cell death in tobacco leaves. Moreover, two CFEM and one Chitin_bind inhibited cell death induced by Bax protein. At various points during the infection, the genes' expression levels were increased. These results will help to identify functional effector proteins involving omics methods using new bioinformatics tools, thus providing a basis for the study of symbiosis mechanisms.
Insights
Researchers identified novel effector genes with conserved motifs in the rice endophyte Falciphora oryzae, revealing their roles in host interactions and providing insights into fungal symbiosis mechanisms.
Area of Science:
- Plant-microbe interactions
- Fungal genomics
- Bioinformatics
Background:
- Microbial effectors are key to host immune evasion and colonization.
- Conserved motifs in fungal effectors are well-studied, but less is known about endophytes.
- Falciphora oryzae is a rice endophyte with uncharacterized effector proteins.
Purpose of the Study:
- To discover effector genes with conserved motifs in the rice endophyte Falciphora oryzae.
- To identify novel conserved motifs in fungal effectors.
- To investigate the functional roles of these effectors in host interactions.
Main Methods:
- Bioinformatic analysis using SignalP and EffectorP for secreted protein and effector prediction.
- Hidden Markov Model (HMM) features utilized to identify conserved motifs.
- Transient expression assays in tobacco to assess effector function (cell death activation/inhibition).
- Gene expression analysis during host infection.
Main Results:
- Identified 622 secreted proteins, with 227 predicted as effector candidates.
- Discovered 169 effector candidates with conserved motifs, including three novel motifs.
- Found conserved domains (LysM, CFEM, DPBB_1, Cutinase, Chitin_bind) across species.
- Observed effector-mediated modulation of cell death in tobacco assays.
- Detected increased gene expression during host infection stages.
Conclusions:
- The study successfully identified and characterized effector genes with conserved motifs in Falciphora oryzae.
- These findings provide a foundation for functional omics studies using bioinformatics tools.
- The results contribute to understanding the symbiotic mechanisms between rice and its endophyte.
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