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Mauceri A, Puccio G, Faddetta T, Abbate L, Polito G, Caldiero C, Renzone G, Lo Pinto M, Alibrandi P, Vaccaro E, Abenavoli MR, Scaloni A, Sunseri F, Cavalieri V, Palumbo Piccionello A, Gallo G, Mercati F. Integrated omics approach reveals the molecular pathways activated in tomato by Kocuria rhizophila, a soil plant growth-promoting bacterium. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108609. [PMID: 38615442 DOI: 10.1016/j.plaphy.2024.108609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024]
Abstract
Plant microbial biostimulants application has become a promising and eco-friendly agricultural strategy to improve crop yields, reducing chemical inputs for more sustainable cropping systems. The soil dwelling bacterium Kocuria rhizophila was previously characterized as Plant Growth Promoting Bacteria (PGPB) for its multiple PGP traits, such as indole-3-acetic acid production, phosphate solubilization capability and salt and drought stress tolerance. Here, we evaluated by a multi-omics approach, the PGP activity of K. rhizophila on tomato, revealing the molecular pathways by which it promotes plant growth. Transcriptomic analysis showed several up-regulated genes mainly related to amino acid metabolism, cell wall organization, lipid and secondary metabolism, together with a modulation in the DNA methylation profile, after PGPB inoculation. In agreement, proteins involved in photosynthesis, cell division, and plant growth were highly accumulated by K. rhizophila. Furthermore, "amino acid and peptides", "monosaccharides", and "TCA" classes of metabolites resulted the most affected by PGPB treatment, as well as dopamine, a catecholamine neurotransmitter mediating plant growth through S-adenosylmethionine decarboxylase (SAMDC), a gene enhancing the vegetative growth, up-regulated in tomato by K. rhizophila treatment. Interestingly, eight gene modules well correlated with differentially accumulated proteins (DAPs) and metabolites (DAMs), among which two modules showed the highest correlation with nine proteins, including a nucleoside diphosphate kinase, and cytosolic ascorbate peroxidase, as well as with several amino acids and metabolites involved in TCA cycle. Overall, our findings highlighted that sugars and amino acids, energy regulators, involved in tomato plant growth, were strongly modulated by the K. rhizophila-plant interaction.
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Affiliation(s)
- Antonio Mauceri
- University Mediterranea of Reggio Calabria, AGRARIA Department, Località Feo di Vito, 89122, Reggio Calabria, Italy
| | - Guglielmo Puccio
- National Research Council, Institute of Biosciences and Bioresources (IBBR), Via Ugo La Malfa 153, 90146, Palermo, Italy; University of Palermo, SAAF Department, Viale Delle Scienze, 90128, Palermo, Italy
| | - Teresa Faddetta
- University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy
| | - Loredana Abbate
- National Research Council, Institute of Biosciences and Bioresources (IBBR), Via Ugo La Malfa 153, 90146, Palermo, Italy
| | - Giulia Polito
- University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy
| | - Ciro Caldiero
- University Mediterranea of Reggio Calabria, AGRARIA Department, Località Feo di Vito, 89122, Reggio Calabria, Italy
| | - Giovanni Renzone
- National Research Council, Proteomics, Metabolomics and Mass Spectrometry Laboratory (ISPAAM), Piazzale E. Fermi 1, 80055, Portici, (Napoli), Italy
| | - Margot Lo Pinto
- University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy
| | - Pasquale Alibrandi
- Mugavero Teresa S.A.S., Corso Umberto e Margherita 1B, 90018, Termini Imerese, (Palermo), Italy
| | - Edoardo Vaccaro
- Mugavero Teresa S.A.S., Corso Umberto e Margherita 1B, 90018, Termini Imerese, (Palermo), Italy
| | - Maria Rosa Abenavoli
- University Mediterranea of Reggio Calabria, AGRARIA Department, Località Feo di Vito, 89122, Reggio Calabria, Italy
| | - Andrea Scaloni
- National Research Council, Proteomics, Metabolomics and Mass Spectrometry Laboratory (ISPAAM), Piazzale E. Fermi 1, 80055, Portici, (Napoli), Italy
| | - Francesco Sunseri
- University Mediterranea of Reggio Calabria, AGRARIA Department, Località Feo di Vito, 89122, Reggio Calabria, Italy
| | - Vincenzo Cavalieri
- University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy
| | | | - Giuseppe Gallo
- University of Palermo, STEBICEF Department, Viale Delle Scienze, 90128, Palermo, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy
| | - Francesco Mercati
- National Research Council, Institute of Biosciences and Bioresources (IBBR), Via Ugo La Malfa 153, 90146, Palermo, Italy.
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Dutt M, Mahmoud LM, Chamusco K, Stanton D, Chase CD, Nielsen E, Quirico M, Yu Q, Gmitter FG, Grosser JW. Utilization of somatic fusion techniques for the development of HLB tolerant breeding resources employing the Australian finger lime (Citrus australasica). PLoS One 2021; 16:e0255842. [PMID: 34375348 PMCID: PMC8354479 DOI: 10.1371/journal.pone.0255842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/23/2021] [Indexed: 11/18/2022] Open
Abstract
The Australian finger lime is a unique citrus species that has gained importance due to its unique fruit characteristics and perceived tolerance to Huanglongbing (HLB), an often-fatal disease of citrus trees. In this study, we developed allotetraploid finger lime hybrids and cybrids by utilizing somatic cell fusion techniques to fuse diploid ‘OLL8’ sweet orange or ‘Page’ tangelo callus-derived protoplasts with finger lime (FL) mesophyll-derived protoplasts. Six somatic fusions were regenerated from the ‘OLL8’ + FL fusion, while three putative cybrids were regenerated from the ‘Page’ + FL fusion. Ploidy levels and nuclear-expressed sequence tag derived simple sequence repeat (EST-SSR) markers confirmed the somatic hybrid production, and mitochondrial DNA primer sets confirmed the cybrid nature. Several trees produced by the somatic fusion remained HLB negative even after 6 years of growth in an HLB-endemic environment. Pathogenesis related (PR) and other genes that are often upregulated in HLB-tolerant trees were also upregulated in our somatic fusions. These newly developed somatic fusions and cybrids could potentially be used as breeding parents to develop the next generation of improved HLB-tolerant rootstocks and scions.
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Affiliation(s)
- Manjul Dutt
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
- * E-mail:
| | - Lamiaa M. Mahmoud
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
- Faculty of Agriculture, Pomology Department, Mansoura University, Mansoura, Egypt
| | - Karen Chamusco
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States of America
| | - Daniel Stanton
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Christine D. Chase
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States of America
| | - Ethan Nielsen
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Maria Quirico
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Qibin Yu
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Frederick G. Gmitter
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Jude W. Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
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Catalano C, Di Guardo M, Distefano G, Caruso M, Nicolosi E, Deng Z, Gentile A, La Malfa SG. Biotechnological Approaches for Genetic Improvement of Lemon ( Citrus limon (L.) Burm. f.) against Mal Secco Disease. PLANTS 2021; 10:plants10051002. [PMID: 34067841 PMCID: PMC8157051 DOI: 10.3390/plants10051002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022]
Abstract
Among Citrus species, lemon is one of the most susceptible to mal secco disease, a tracheomycosis caused by the mitosporic fungus Plenodomus tracheiphilus, which induces chlorosis followed by leaf drop and progressive desiccation of twigs and branches. Severe infection can cause the death of the plant. Since no effective control strategies are available to efficiently control the pathogen spread, host tolerance is the most desirable goal in the struggle against mal secco disease. To date, both traditional breeding programs and biotechnological techniques were not efficient in developing novel varieties coupling tolerance to mal secco with optimal fruit quality. Furthermore, the genetic basis of host resistance has not been fully deciphered yet, hampering the set-up of marker-assisted selection (MAS) schemes. This paper provides an overview of the biotechnological approaches adopted so far for the selection of mal secco tolerant lemon varieties and emphasizes the promising contribution of marker-trait association analysis techniques for both unraveling the genetic determinism of the resistance to mal secco and detecting molecular markers that can be readily used for MAS. Such an approach has already proved its efficiency in several crops and could represent a valuable tool to select novel lemon varieties coupling superior fruit quality traits and resistance to mal secco.
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Affiliation(s)
- Chiara Catalano
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Mario Di Guardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Gaetano Distefano
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Marco Caruso
- CREA, Research Centre for Olive, Fruit and Citrus Crops, Corso Savoia 190, 95024 Acireale, Italy;
| | - Elisabetta Nicolosi
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
| | - Ziniu Deng
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, China;
| | - Alessandra Gentile
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, China;
- Correspondence:
| | - Stefano Giovanni La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123 Catania, Italy; (C.C.); (M.D.G.); (G.D.); (E.N.); (S.G.L.M.)
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Systems level profiling of arginine starvation reveals MYC and ERK adaptive metabolic reprogramming. Cell Death Dis 2020; 11:662. [PMID: 32814773 PMCID: PMC7438517 DOI: 10.1038/s41419-020-02899-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022]
Abstract
Arginine auxotrophy due to the silencing of argininosuccinate synthetase 1 (ASS1) occurs in many carcinomas and in the majority of sarcomas. Arginine deiminase (ADI-PEG20) therapy exploits this metabolic vulnerability by depleting extracellular arginine, causing arginine starvation. ASS1-negative cells develop resistance to ADI-PEG20 through a metabolic adaptation that includes re-expressing ASS1. As arginine-based multiagent therapies are being developed, further characterization of the changes induced by arginine starvation is needed. In order to develop a systems-level understanding of these changes, activity-based proteomic profiling (ABPP) and phosphoproteomic profiling were performed before and after ADI-PEG20 treatment in ADI-PEG20-sensitive and resistant sarcoma cells. When integrated with metabolomic profiling, this multi-omic analysis reveals that cellular response to arginine starvation is mediated by adaptive ERK signaling and activation of the Myc–Max transcriptional network. Concomitantly, these data elucidate proteomic changes that facilitate oxaloacetate production by enhancing glutamine and pyruvate anaplerosis and altering lipid metabolism to recycle citrate for oxidative glutaminolysis. Based on the complexity of metabolic and cellular signaling interactions, these multi-omic approaches could provide valuable tools for evaluating response to metabolically targeted therapies.
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