Biocontrol strategies are a promising alternative to achieve food safety and food security. The aim of this study was to decipher the molecular interactions involving the biocontrol agent (BCA) yeast Papiliotrema terrestris strain LS28, the postharvest pathogen Penicillium expansum, and Malus domestica. RNAseq analysis was performed during both their dual and tritrophic interactions to identify the differentially expressed genes of BCA, pathogen, and host. Analysis of transcriptome changes in the BCA revealed overexpression of genes involved in nitrogen catabolite repression and oxidative stress response, regardless of the presence of the pathogen, suggesting that these pathways are crucial for the BCA to rapidly colonize the ecological niche (fruit wounds) and outcompete the pathogen. In the absence of P. expansum, BCA genes involved in metabolism and transport of carbohydrates and branched-chain amino acids were highly represented, suggesting a different nutritional requirement of P. terrestris when it does not compete with the pathogen. To confirm transcriptomic data at phenotypic level, targeted mutants of the BCA were generated for several overexpressed genes. The in vitro phenotypic characterization and biocontrol assay revealed a crucial role of a putative amino acid transporter in the biocontrol activity of P. terrestris against P. expansum. The transcriptomic analysis of P. expansum revealed that genes involved in transcription, oxido-reductive processes, transmembrane transport, and amine and peptide metabolism were the most represented GO categories, regardless of the presence of the BCA. Whereas in the absence of the BCA there was only enrichment of oxido-reductive processes-related transcripts, in its presence transcripts involved in metabolic processes of polysaccharides, aminoglycan and glucosamine-containing compounds were strongly enriched, suggesting a substantial nutritional rewiring of the pathogen to directly outcompete the BCA. Analysis of the transcriptomic changes of the host M. domestica revealed overexpression of genes involved in host defense signaling pathways in the presence of both the BCA and the pathogen, and a prevalence of pathogen triggered immunity (PTI) and effector trigger immunity (ETI) host genes overexpressed only during interaction with P. expansum. This comprehensive analysis contributed to advance the knowledge on the molecular mechanisms that underlie biocontrol activity and the tritrophic interaction of the BCA with the pathogen and the host.
L’utilizzo dei mezzi di lotta biologica al fine di contenere lo sviluppo dei patogeni fungini e ridurre le perdite di derrate alimentari consente anche di sostituire progressivamente l’impiego di fungicidi di sintesi riducendo l’impatto che questi ultimi hanno sull’ambente e sulla nostra salute. La presente attività di ricerca è stata incentrata sull’analisi dei dati di un esperimento di RNA-sequencing che coinvolge tre organismi in una stretta interazione reciproca (interazione tritrofica). Oggetto di studio sono l’agente di biocontrollo Papiliotrema terrestris ceppo LS28, l’agente patogeno Penicillium expansum ceppo 7015 entrambi inoculati in ferita di mela (Malus domestica). L’obiettivo di tale studio è l’approfondimento riguardo la comprensione dei meccanismi di azione che sono alla base del biocontrollo, ossia dell’attività antagonistica del ceppo LS28 nel contrastare lo sviluppo dell’agente patogeno Penicillium expansum in ferita di mela. A tal fine, sulla base dell’interpretazione dei dati ottenuti dallo studio di espressione genica sul ceppo LS28, è stata stilata una lista di geni che sono stati mutati mediante l’applicazione della target mutagenesi (mutagenesi sito-specifica). Attraverso la delezione del gene prescelto (sulla base dei dati ottenuti dallo studio di trascrittomica), ne è stata caratterizzatala relativa perdita di funzione in vitro e in vivo. Inoltre sono stati valutati, interpretati e confrontati con studi simili i principali processi biologici coinvolti nell’espressione genica del patogeno (Penicillium expansum) durante la colonizzazione della mela con/senza il ceppo LS28, e nell’ospite (Malus domestica) durante l’interazione con entrambi (interazione tritrofica) e con ciascuno di essi.
Transcriptomic and functional approaches to unveil the interaction between a biocontrol yeast and a postharvest fungal pathogen on host fruit
BARONE, GIUSEPPE
2022-09-26
Abstract
Biocontrol strategies are a promising alternative to achieve food safety and food security. The aim of this study was to decipher the molecular interactions involving the biocontrol agent (BCA) yeast Papiliotrema terrestris strain LS28, the postharvest pathogen Penicillium expansum, and Malus domestica. RNAseq analysis was performed during both their dual and tritrophic interactions to identify the differentially expressed genes of BCA, pathogen, and host. Analysis of transcriptome changes in the BCA revealed overexpression of genes involved in nitrogen catabolite repression and oxidative stress response, regardless of the presence of the pathogen, suggesting that these pathways are crucial for the BCA to rapidly colonize the ecological niche (fruit wounds) and outcompete the pathogen. In the absence of P. expansum, BCA genes involved in metabolism and transport of carbohydrates and branched-chain amino acids were highly represented, suggesting a different nutritional requirement of P. terrestris when it does not compete with the pathogen. To confirm transcriptomic data at phenotypic level, targeted mutants of the BCA were generated for several overexpressed genes. The in vitro phenotypic characterization and biocontrol assay revealed a crucial role of a putative amino acid transporter in the biocontrol activity of P. terrestris against P. expansum. The transcriptomic analysis of P. expansum revealed that genes involved in transcription, oxido-reductive processes, transmembrane transport, and amine and peptide metabolism were the most represented GO categories, regardless of the presence of the BCA. Whereas in the absence of the BCA there was only enrichment of oxido-reductive processes-related transcripts, in its presence transcripts involved in metabolic processes of polysaccharides, aminoglycan and glucosamine-containing compounds were strongly enriched, suggesting a substantial nutritional rewiring of the pathogen to directly outcompete the BCA. Analysis of the transcriptomic changes of the host M. domestica revealed overexpression of genes involved in host defense signaling pathways in the presence of both the BCA and the pathogen, and a prevalence of pathogen triggered immunity (PTI) and effector trigger immunity (ETI) host genes overexpressed only during interaction with P. expansum. This comprehensive analysis contributed to advance the knowledge on the molecular mechanisms that underlie biocontrol activity and the tritrophic interaction of the BCA with the pathogen and the host.File | Dimensione | Formato | |
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