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Lima ST, Ampolini BG, Underwood EB, Graf TN, Earp CE, Khedi IC, Pasquale MA, Chekan JR. A Widely Distributed Biosynthetic Cassette Is Responsible for Diverse Plant Side Chain Cross-Linked Cyclopeptides. Angew Chem Int Ed Engl 2023; 62:e202218082. [PMID: 36529706 PMCID: PMC10107690 DOI: 10.1002/anie.202218082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Cyclopeptide alkaloids are an abundant class of plant cyclopeptides with over 200 analogs described and bioactivities ranging from analgesic to antiviral. While these natural products have been known for decades, their biosynthetic basis remains unclear. Using a transcriptome-mining approach, we link the cyclopeptide alkaloids from Ceanothus americanus to dedicated RiPP precursor peptides and identify new, widely distributed split BURP peptide cyclase containing gene clusters. Guided by our bioinformatic analysis, we identify and isolate new cyclopeptides from Coffea arabica, which we named arabipeptins. Reconstitution of the enzyme activity for the BURP found in the biosynthesis of arabipeptin A validates the activity of the newly discovered split BURP peptide cyclases. These results expand our understanding of the biosynthetic pathways responsible for diverse cyclic plant peptides and suggest that these side chain cross-link modifications are widely distributed in eudicots.
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Affiliation(s)
- Stella T Lima
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Brigitte G Ampolini
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Ethan B Underwood
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Tyler N Graf
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Cody E Earp
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Imani C Khedi
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Michael A Pasquale
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
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Albornos L, Casado-Del-Castillo V, Martín I, Díaz-Mínguez JM, Labrador E, Dopico B. Specific tissue proteins 1 and 6 are involved in root biology during normal development and under symbiotic and pathogenic interactions in Medicago truncatula. PLANTA 2021; 253:7. [PMID: 33387090 DOI: 10.1007/s00425-020-03538-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
ST1 and ST6 are possibly involved in primary and lateral root and symbiotic nodule development, but only ST6 participates in the interaction with hemibiotrophic fungi. Specific tissue (ST) proteins have been shown to be involved in several processes related to plant nutritional status, development, and responses to biotic agents. In particular, ST1 and ST6 are mainly expressed in roots throughout plant development. Here, we analyze where and how the expression of the genes encoding both proteins are modulated in the legume model plant Medicago truncatula in response to the plant developmental program, nodulation induced by a beneficial nitrogen-fixing bacterium (Sinorhizobium meliloti) and the defense response triggered by a pathogenic hemibiotrophic fungus (Fusarium oxysporum). Gene expression results show that ST1 and ST6 participate in the vasculature development of both primary and lateral roots, although only ST6 is related to meristem activity. ST1 and ST6 clearly display different roles in the biotic interactions analyzed, where ST1 is activated in response to a N2-fixing bacterium and ST6 is up-regulated after inoculation with F. oxysporum. The role of ST1 and ST6 in the nodulation process may be related to nodule organogenesis rather than to the establishment of the interaction itself, and an increase in ST6 correlates with the activation of the salicylic acid signaling pathway during the infection and colonization processes. These results further support the role of ST6 in response to hemibiotrophic fungi. This research contributes to the understanding of the complex network that controls root biology and strengthens the idea that ST proteins are involved in several processes such as primary and lateral root development, nodule organogenesis, and the plant-microbe interaction.
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Affiliation(s)
- Lucía Albornos
- Departamento de Botánica y Fisiología Vegetal, Universidad de Salamanca, C/ Licenciado Méndez Nieto s/n, Campus Miguel de Unamuno, 37007, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Campus de Villamayor, C/ Río Duero 12, Villamayor, 37185, Salamanca, Spain
| | - Virginia Casado-Del-Castillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Edificio departamental, 37007, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Campus de Villamayor, C/ Río Duero 12, Villamayor, 37185, Salamanca, Spain
| | - Ignacio Martín
- Departamento de Botánica y Fisiología Vegetal, Universidad de Salamanca, C/ Licenciado Méndez Nieto s/n, Campus Miguel de Unamuno, 37007, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Campus de Villamayor, C/ Río Duero 12, Villamayor, 37185, Salamanca, Spain
| | - José M Díaz-Mínguez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Edificio departamental, 37007, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Campus de Villamayor, C/ Río Duero 12, Villamayor, 37185, Salamanca, Spain
| | - Emilia Labrador
- Departamento de Botánica y Fisiología Vegetal, Universidad de Salamanca, C/ Licenciado Méndez Nieto s/n, Campus Miguel de Unamuno, 37007, Salamanca, Spain
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Campus de Villamayor, C/ Río Duero 12, Villamayor, 37185, Salamanca, Spain
| | - Berta Dopico
- Departamento de Botánica y Fisiología Vegetal, Universidad de Salamanca, C/ Licenciado Méndez Nieto s/n, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Campus de Villamayor, C/ Río Duero 12, Villamayor, 37185, Salamanca, Spain.
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Silvestri A, Fiorilli V, Miozzi L, Accotto GP, Turina M, Lanfranco L. In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant. BMC Genomics 2019; 20:169. [PMID: 30832582 PMCID: PMC6399891 DOI: 10.1186/s12864-019-5561-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/22/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are short non-coding RNA molecules (20-30 nt) that regulate gene expression at transcriptional or post-transcriptional levels in many eukaryotic organisms, through a mechanism known as RNA interference (RNAi). Recent studies have highlighted that they are also involved in cross-kingdom communication: sRNAs can move across the contact surfaces from "donor" to "receiver" organisms and, once in the host cells of the receiver, they can target specific mRNAs, leading to a modulation of host metabolic pathways and defense responses. Very little is known about RNAi mechanism and sRNAs occurrence in Arbuscular Mycorrhizal Fungi (AMF), an important component of the plant root microbiota that provide several benefits to host plants, such as improved mineral uptake and tolerance to biotic and abiotic stress. RESULTS Taking advantage of the available genomic resources for the AMF Rhizophagus irregularis we described its putative RNAi machinery, which is characterized by a single Dicer-like (DCL) gene and an unusual expansion of Argonaute-like (AGO-like) and RNA-dependent RNA polymerase (RdRp) gene families. In silico investigations of previously published transcriptomic data and experimental assays carried out in this work provided evidence of gene expression for most of the identified sequences. Focusing on the symbiosis between R. irregularis and the model plant Medicago truncatula, we characterized the fungal sRNA population, highlighting the occurrence of an active sRNA-generating pathway and the presence of microRNA-like sequences. In silico analyses, supported by host plant degradome data, revealed that several fungal sRNAs have the potential to target M. truncatula transcripts, including some specific mRNA already shown to be modulated in roots upon AMF colonization. CONCLUSIONS The identification of RNAi-related genes, together with the characterization of the sRNAs population, suggest that R. irregularis is equipped with a functional sRNA-generating pathway. Moreover, the in silico analysis predicted 237 plant transcripts as putative targets of specific fungal sRNAs suggesting that cross-kingdom post-transcriptional gene silencing may occur during AMF colonization.
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Affiliation(s)
- Alessandro Silvestri
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
| | - Laura Miozzi
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 73, 10131 Torino, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 73, 10131 Torino, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 73, 10131 Torino, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
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