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Andrade-Marcial M, Pacheco-Arjona R, Hernández-Castellano S, Che-Aguilar L, De-la-Peña C. Transcriptome analysis reveals molecular mechanisms underlying chloroplast biogenesis in albino Agave angustifolia plantlets. Physiol Plant 2024; 176:e14289. [PMID: 38606618 DOI: 10.1111/ppl.14289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/13/2024]
Abstract
Albino plants display partial or complete loss of photosynthetic pigments and defective thylakoid membrane development, consequently impairing plastid function and development. These distinctive attributes render albino plants excellent models for investigating chloroplast biogenesis. Despite their potential, limited exploration has been conducted regarding the molecular alterations underlying these phenotypes, extending beyond photosynthetic metabolism. In this study, we present a novel de novo transcriptome assembly of an albino somaclonal variant of Agave angustifolia Haw., which spontaneously emerged during the micropropagation of green plantlets. Additionally, RT-qPCR analysis was employed to validate the expression of genes associated with chloroplast biogenesis, and plastome copy numbers were quantified. This research aims to gain insight into the molecular disruptions affecting chloroplast development and ascertain whether the expression of critical genes involved in plastid development and differentiation is compromised in albino tissues of A. angustifolia. Our transcriptomic findings suggest that albino Agave plastids exhibit high proliferation, activation of the protein import machinery, altered transcription directed by PEP and NEP, dysregulation of plastome expression genes, reduced expression of photosynthesis-associated nuclear genes, disruption in the tetrapyrrole and carotenoid biosynthesis pathway, alterations in the plastid ribosome, and an increased number of plastome copies, among other alterations.
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Affiliation(s)
| | - Ramón Pacheco-Arjona
- Consejo Nacional de Ciencia y Tecnología- Universidad Autónoma de Yucatán, Facultad de Medicina Veterinaria y Zootecnia, Mérida, México
| | | | - Ligia Che-Aguilar
- Tecnológico Nacional de México. Instituto Tecnológico de Mérida, Mérida, Yucatán, México
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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2
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Cadena-Ramos AI, De-la-Peña C. Picky eaters: selective autophagy in plant cells. Plant J 2024; 117:364-384. [PMID: 37864806 DOI: 10.1111/tpj.16508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/21/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Autophagy, a fundamental cellular process, plays a vital role in maintaining cellular homeostasis by degrading damaged or unnecessary components. While selective autophagy has been extensively studied in animal cells, its significance in plant cells has only recently gained attention. In this review, we delve into the intriguing realm selective autophagy in plants, with specific focus on its involvement in nutrient recycling, organelle turnover, and stress response. Moreover, recent studies have unveiled the interesting interplay between selective autophagy and epigenetic mechanisms in plants, elucidating the significance of epigenetic regulation in modulating autophagy-related gene expression and finely tuning the selective autophagy process in plants. By synthesizing existing knowledge, this review highlights the emerging field of selective autophagy in plant cells, emphasizing its pivotal role in maintaining nutrient homeostasis, facilitating cellular adaptation, and shedding light on the epigenetic regulation that governs these processes. Our comprehensive study provides the way for a deeper understanding of the dynamic control of cellular responses to nutrient availability and stress conditions, opening new avenues for future research in this field of autophagy in plant physiology.
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Affiliation(s)
- Alexis I Cadena-Ramos
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34 Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
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3
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Andrade-Marcial M, Ruíz-May E, Elizalde-Contreras JM, Pacheco N, Herrera-Pool E, De-la-Peña C. Proteome of Agave angustifolia Haw.: Uncovering metabolic alterations, over-accumulation of amino acids, and compensatory pathways in chloroplast-deficient albino plantlets. Plant Physiol Biochem 2023; 201:107902. [PMID: 37506650 DOI: 10.1016/j.plaphy.2023.107902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
Amino acids (AA) are essential molecules for plant physiology, acting as precursor molecules for proteins and other organic compounds. Chloroplasts play a vital role in AA metabolism, yet little is known about the impact on AA metabolism of albino plants' lack of chloroplasts. In this study, we conducted a quantitative proteome analysis on albino and variegated somaclonal variants of Agave angustifolia Haw. to investigate metabolic alterations in chloroplast-deficient plants, with a focus on AA metabolic pathways. We identified 82 enzymes involved in AA metabolism, with 32 showing differential accumulation between the somaclonal variants. AaCM, AaALS, AaBCAT, AaIPMS1, AaSHMT, AaAST, AaCGS, and AaMS enzymes were particularly relevant in chloroplast-deficient Agave plantlets. Both variegated and albino phenotypes exhibited excessive synthesis of AA typically associated with chloroplasts (aromatic AAs, BCAAs, Asp, Lys, Pro and Met). Consistent trends were observed for AaBCAT and AaCM at mRNA and protein levels in albino plantlets. These findings highlight the critical activation and reprogramming of AA metabolic pathways in plants lacking chloroplasts. This study contributes to unraveling the intricate relationship between AA metabolism and chloroplast absence, offering insights into survival mechanisms of albino plants.
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Affiliation(s)
- M Andrade-Marcial
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - E Ruíz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Congregación el Haya, 91070, Xalapa, Veracruz, México
| | - J M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Congregación el Haya, 91070, Xalapa, Veracruz, México
| | - N Pacheco
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Unidad Sureste, Tablaje Catastral 31264 Km 5.5 Carretera Sierra Papacal-Chuburná Puerto, Parque Científico Tecnológico de Yucatán, CP, 97302, Mérida, Yucatán, México
| | - E Herrera-Pool
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Unidad Sureste, Tablaje Catastral 31264 Km 5.5 Carretera Sierra Papacal-Chuburná Puerto, Parque Científico Tecnológico de Yucatán, CP, 97302, Mérida, Yucatán, México
| | - C De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México.
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Duarte-Aké F, Us-Camas R, De-la-Peña C. Epigenetic Regulation in Heterosis and Environmental Stress: The Challenge of Producing Hybrid Epigenomes to Face Climate Change. Epigenomes 2023; 7:14. [PMID: 37489402 PMCID: PMC10366763 DOI: 10.3390/epigenomes7030014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/26/2023] Open
Abstract
Epigenetic regulation has the potential to revolutionize plant breeding and improve crop yields by regulating gene expression in plants. DNA methylation and histone modifications are key epigenetic modifications that can impact plant development, stress responses, productivity, and yields. Higher-yielding crops not only generate greater profits for farmers and seed producers, but also require less land, water, fuel, and fertilizer than traditional crops for equivalent yields. The use of heterosis in crops can influence productivity and food quality, but producing hybrids with superior agronomic traits to their parents remains challenging. However, epigenetic markers, such as histone methylation and acetylation, may help select parental and hybrid combinations with better performances than the parental plants. This review assesses the potential applications of epigenetics in crop breeding and improvement, rendering agriculture more efficient, sustainable, and adaptable to changing environmental conditions.
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Affiliation(s)
- Fátima Duarte-Aké
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, Mérida 97205, Mexico
| | - Rosa Us-Camas
- Departamento de Estudios de Posgrado e Investigación del Instituto Tecnológico Superior del Calkiní en el Estado de Campeche (ITESCAM), Av. AH Canun S/N San Felipe, Calkiní 24900, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, Mérida 97205, Mexico
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Fortini EA, Batista DS, Felipe SHS, Silva TD, Correia LNF, Farias LM, Faria DV, Pinto VB, Santa-Catarina C, Silveira V, De-la-Peña C, Castillo-Castro E, Otoni WC. Physiological, epigenetic, and proteomic responses in Pfaffia glomerata growth in vitro under salt stress and 5-azacytidine. Protoplasma 2023; 260:467-482. [PMID: 35788779 DOI: 10.1007/s00709-022-01789-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Plants adjust their complex molecular, biochemical, and metabolic processes to overcome salt stress. Here, we investigated the proteomic and epigenetic alterations involved in the morphophysiological responses of Pfaffia glomerata, a medicinal plant, to salt stress and the demethylating agent 5-azacytidine (5-azaC). Moreover, we investigated how these changes affected the biosynthesis of 20-hydroxyecdysone (20-E), a pharmacologically important specialized metabolite. Plants were cultivated in vitro for 40 days in Murashige and Skoog medium supplemented with NaCl (50 mM), 5-azaC (25 μM), and NaCl + 5-azaC. Compared with the control (medium only), the treatments reduced growth, photosynthetic rates, and photosynthetic pigment content, with increase in sucrose, total amino acids, and proline contents, but a reduction in starch and protein. Comparative proteomic analysis revealed 282 common differentially accumulated proteins involved in 87 metabolic pathways, most of them related to amino acid and carbohydrate metabolism, and specialized metabolism. 5-azaC and NaCl + 5-azaC lowered global DNA methylation levels and 20-E content, suggesting that 20-E biosynthesis may be regulated by epigenetic mechanisms. Moreover, downregulation of a key protein in jasmonate biosynthesis indicates the fundamental role of this hormone in the 20-E biosynthesis. Taken together, our results highlight possible regulatory proteins and epigenetic changes related to salt stress tolerance and 20-E biosynthesis in P. glomerata, paving the way for future studies of the mechanisms involved in this regulation.
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Affiliation(s)
- Evandro Alexandre Fortini
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Diego Silva Batista
- Departamento de Agricultura, Universidade Federal da Paraíba, Campus III, Bananeiras, PB, 58220-000, Brazil
| | - Sérgio Heitor Sousa Felipe
- PPG em Agroecologia, Universidade Estadual do Maranhão, Av. Lourenço Vieira da Silva, s/nº, Cidade Universitária Paulo VI, São Luís, MA, Brazil
| | - Tatiane Dulcineia Silva
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Ludmila Nayara Freitas Correia
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Letícia Monteiro Farias
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Daniele Vidal Faria
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Vitor Batista Pinto
- Laboratório de Biotecnologia (LBT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual (LBCT), CBB-UENF, Campos dos Goytacazes, RJ, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia (LBT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A. C. (CICY), 97205, Mérida, Yucatán, Mexico
| | - Eduardo Castillo-Castro
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A. C. (CICY), 97205, Mérida, Yucatán, Mexico
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil.
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Andrade-Marcial M, Pacheco-Arjona R, Góngora-Castillo E, De-la-Peña C. Chloroplastic pentatricopeptide repeat proteins (PPR) in albino plantlets of Agave angustifolia Haw. reveal unexpected behavior. BMC Plant Biol 2022; 22:352. [PMID: 35850575 PMCID: PMC9295523 DOI: 10.1186/s12870-022-03742-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pentatricopeptide repeat (PPR) proteins play an essential role in the post-transcriptional regulation of genes in plastid genomes. Although important advances have been made in understanding the functions of these genes, there is little information available on chloroplastic PPR genes in non-model plants and less in plants without chloroplasts. In the present study, a comprehensive and multifactorial bioinformatic strategy was applied to search for putative PPR genes in the foliar and meristematic tissues of green and albino plantlets of the non-model plant Agave angustifolia Haw. RESULTS A total of 1581 PPR transcripts were identified, of which 282 were chloroplastic. Leaf tissue in the albino plantlets showed the highest levels of expression of chloroplastic PPRs. The search for hypothetical targets of 12 PPR sequences in the chloroplast genes of A. angustifolia revealed their action on transcripts related to ribosomes and translation, photosystems, ATP synthase, plastid-encoded RNA polymerase and RuBisCO. CONCLUSIONS Our results suggest that the expression of PPR genes depends on the state of cell differentiation and plastid development. In the case of the albino leaf tissue, which lacks functional chloroplasts, it is possible that anterograde and retrograde signaling networks are severely compromised, leading to a compensatory anterograde response characterized by an increase in the expression of PPR genes.
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Affiliation(s)
- M Andrade-Marcial
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - R Pacheco-Arjona
- Facultad de Medicina Veterinaria y Zootecnia, Consejo Nacional de Ciencia y Tecnología- Universidad Autónoma de Yucatán, Mérida, Mexico
| | - E Góngora-Castillo
- Consejo Nacional de Ciencia y Tecnología-Unidad De Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - C De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico.
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Jiménez-Ramírez IA, Pijeira-Fernández G, Moreno-Cálix DM, De-la-Peña C. Same modification, different location: the mythical role of N 6-adenine methylation in plant genomes. Planta 2022; 256:9. [PMID: 35696004 DOI: 10.1007/s00425-022-03926-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The present review summarizes recent advances in the understanding of 6mA in DNA as an emergent epigenetic mark with distinctive characteristics, discusses its importance in plant genomes, and highlights its chemical nature and functions. Adenine methylation is an epigenetic modification present in DNA (6mA) and RNA (m6A) that has a regulatory function in many cellular processes. This modification occurs through a reversible reaction that covalently binds a methyl group, usually at the N6 position of the purine ring. This modification carries biophysical properties that affect the stability of nucleic acids as well as their binding affinity with other molecules. DNA 6mA has been related to genome stability, gene expression, DNA replication, and repair mechanisms. Recent advances have shown that 6mA in plant genomes is related to development and stress response. In this review, we present recent advances in the understanding of 6mA in DNA as an emergent epigenetic mark with distinctive characteristics. We discuss the key elements of this modification, focusing mainly on its importance in plant genomes. Furthermore, we highlight its chemical nature and the regulatory effects that it exerts on gene expression and plant development. Finally, we emphasize the functions of 6mA in photosynthesis, stress, and flowering.
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Affiliation(s)
- Irma A Jiménez-Ramírez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Gema Pijeira-Fernández
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Delia M Moreno-Cálix
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico.
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De-la-Peña C, León P, Sharkey TD. Editorial: Chloroplast Biotechnology for Crop Improvement. Front Plant Sci 2022; 13:848034. [PMID: 35178064 PMCID: PMC8843820 DOI: 10.3389/fpls.2022.848034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Patricia León
- Instituto de Biotecnología Universidad Nacional Autónoma de Mexico, Cuernavaca, Mexico
| | - Thomas D. Sharkey
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States
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Abstract
Throughout decades of plant research, the plant hormones known as auxins have been found to be of vital importance in most plant development processes. Indole-3-acetic acid (IAA) represents the most common auxin in plants and can be synthesized from its tryptophan precursor, which is synthesized in the chloroplast. The chloroplast constitutes an organelle of great relevance to plants since the photosynthesis process by which plants get most of their energy is carried out there. The role of auxins in photosynthesis has been studied for at least 50 years, and in this time, it has been shown that auxins have an effect on several of the essential components and structure of the chloroplast. In recent decades, a high number of genes have been reported to be expressed in the chloroplast and some of their mutants have been shown to alter different auxin-mediated pathways. Genes in signaling pathways such as IAA/AUX, ARF, GH.3, SAUR and TIR, biosynthesis-related genes such as YUCCA and transport-related genes such as PIN have been identified among the most regulated genes in mutants related to alterations in the chloroplast. This review aims to provide a complete and updated summary of the relationship between auxins and several processes that involve the chloroplast, including chloroplast development, plant albinism, redox regulation and pigment synthesis.
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Affiliation(s)
- Alexis Salazar-Iribe
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico.
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Osorio-Montalvo P, De-la-Peña C, Oropeza C, Nic-Can G, Córdova-Lara I, Castillo-Castro E, Sáenz-Carbonell L. A peak in global DNA methylation is a key step to initiate the somatic embryogenesis of coconut palm (Cocos nucifera L). Plant Cell Rep 2020; 39:1345-1357. [PMID: 32789543 DOI: 10.1007/s00299-020-02568-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/25/2020] [Accepted: 07/10/2020] [Indexed: 05/08/2023]
Abstract
DNA methylation, morphogenesis and gene expression during the somatic embryogenesis of Coconut are affected by 5-Azacytidine pretreatments, indicating that DNA methylation is an important factor throughout this process. Somatic embryogenesis (SE) is a process that can aid in the production of elite Cocos nucifera palms. It has been well established that epigenetic mechanisms are regulators of cell differentiation programs; however, their role in the coconut somatic embryogenesis has not yet been addressed. To this end, the morphogenetic changes, the global DNA methylation and the expression profiles of the SE-related genes and DNA methyltransferases genes were evaluated during the SE process, with and without the presence of 5-Azacytidine (AzaC). The results show that three days of pretreatments with 15 µM and 20 µM of AzaC significantly increased early somatic embryo formation (four- and tenfold, respectively). A clear peak of the global percentage of DNA methylation (approximately 13%) was determined at the beginning of the culture, followed by a re-establishing stage and a steady increase thereafter; in all cases, the levels of DNA methylation were lower after the pretreatments with AzaC. Additionally, the expression profiles of the SERK, WUS, BBM and LEC genes are modulated during the SE process and the pretreatments with AzaC affect the expression profiles of these genes, even at early stages. Furthermore, increased levels of expression were observed for the genes encoding for DNA methyltransferases (MET, CMT and DRM) at early and late stages of SE, indicating that DNA methylation is an important factor throughout the SE.
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Affiliation(s)
- Pedro Osorio-Montalvo
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - Clelia De-la-Peña
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - Carlos Oropeza
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - Geovanny Nic-Can
- CONACYT-Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Iván Córdova-Lara
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - Eduardo Castillo-Castro
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - Luis Sáenz-Carbonell
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México.
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Pastrana-Trejo JC, Duarte-Aké F, Us-Camas R, De-la-Peña C, Parker L, Pertwee RG, Murillo-Rodríguez E. Effects on the post-translational modification of H3K4Me3, H3K9ac, H3K9Me2, H3K27Me3, and H3K36Me2 levels in cerebral cortex, hypothalamus and pons of rats after a systemic administration of cannabidiol: A Preliminary Study. Cent Nerv Syst Agents Med Chem 2020; 21:142-147. [PMID: 32972354 DOI: 10.2174/1871524920666200924114524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cannabidiol (CBD), a non-psychotropic constituent of Cannabis sativa, has shown therapeutic promises by modulating several pathological conditions, including pain, epilepsy autism, among others. However, the molecular mechanism of action of CBD remains unknown and recent data suggest the engagement on CBD´s effects of nuclear elements, such as histone activity. AIM This study assessed the changes on the post-translational modification (PTM) on the histones H3K4Me3, H3K9ac, H3K9Me2, H3K27Me3, and H3K36Me2 in several brain regions of rats after the administration of CBD (20mg/Kg/i.p.). OBJECTIVE To evaluate the effects on the PTM of histones H3K4Me3, H3K9ac, H3K9Me2, H3K27Me3, and H3K36Me2 levels in the cerebral cortex, hypothalamus and pons of CBD-treated rats. METHOD Ten adult rats were randomly assigned into 2 groups: Control or CBD (20mg/Kg/i.p). Animals were sacrificed after treatments and brains were collected for dissections of the cerebral cortex, hypothalamus and pons. Samples were analyzed for PTM on the histones H3K4Me3, H3K9ac, H3K9Me2, H3K27Me3, and H3K36Me2 levels by Western blot procedure. RESULTS CBD increased the PTM levels on the histones H3K4Me3, H3K9ac, and H3K27Me3 in the cerebral cortex whereas no significant differences were found in H3K9Me2 and H3K36Me2. In addition, in the hypothalamus, CBD decreased the contents of H3K9ac while no significant effects were observed in H3K4Me3, H3K9Me2, H3K27Me3, and H3K36Me2. Lastly, in the pons, CBD-treated rats showed a significant decline on the PTM levels of H3K4Me3 whereas no statistical differences were found in H3K9ac, H3K9Me2, H3K27Me3, and H3K36Me2. CONCLUSION The study showed that CBD induced differential effects in levels of PTM on the histones H3K4Me3, H3K9ac, H3K9Me2, H3K27Me3, and H3K36Me2 in several brain regions.
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Affiliation(s)
- José Carlos Pastrana-Trejo
- Laboratorio de Neurociencias Moleculares e Integrativas. Escuela de Medicina, División Ciencias de la Salud. Universidad Anáhuac Mayab Mérida, Yucatán. Mexico
| | - Fátima Duarte-Aké
- Centro de Investigación Científica de Yucatán. A.C. Unidad de Biotecnología. Mérida, Yucatán. Mexico
| | - Rosa Us-Camas
- Centro de Investigación Científica de Yucatán. A.C. Unidad de Biotecnología. Mérida, Yucatán. Mexico
| | - Clelia De-la-Peña
- Centro de Investigación Científica de Yucatán. A.C. Unidad de Biotecnología. Mérida, Yucatán. Mexico
| | - Linda Parker
- Department of Psychology and Neuroscience Graduate Program. University of Guelph. Guelph, Ontario. Canada
| | - Roger G Pertwee
- School of Medicine, Medical Sciences and Nutrition. Institute of Medical Sciences, University of Aberdeen. Aberdeen. United Kingdom
| | - Eric Murillo-Rodríguez
- Laboratorio de Neurociencias Moleculares e Integrativas. Escuela de Medicina, División Ciencias de la Salud. Universidad Anáhuac Mayab Mérida, Yucatán. Mexico
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12
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Méndez-Hernández HA, Ledezma-Rodríguez M, Avilez-Montalvo RN, Juárez-Gómez YL, Skeete A, Avilez-Montalvo J, De-la-Peña C, Loyola-Vargas VM. Signaling Overview of Plant Somatic Embryogenesis. Front Plant Sci 2019; 10:77. [PMID: 30792725 PMCID: PMC6375091 DOI: 10.3389/fpls.2019.00077] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/17/2019] [Indexed: 05/17/2023]
Abstract
Somatic embryogenesis (SE) is a means by which plants can regenerate bipolar structures from a somatic cell. During the process of cell differentiation, the explant responds to endogenous stimuli, which trigger the induction of a signaling response and, consequently, modify the gene program of the cell. SE is probably the most studied plant regeneration model, but to date it is the least understood due to the unclear mechanisms that occur at a cellular level. In this review, the authors seek to emphasize the importance of signaling on plant SE, highlighting the interactions between the different plant growth regulators (PGR), mainly auxins, cytokinins (CKs), ethylene and abscisic acid (ABA), during the induction of SE. The role of signaling is examined from the start of cell differentiation through the early steps on the embryogenic pathway, as well as its relation to a plant's tolerance of different types of stress. Furthermore, the role of genes encoded to transcription factors (TFs) during the embryogenic process such as the LEAFY COTYLEDON (LEC), WUSCHEL (WUS), BABY BOOM (BBM) and CLAVATA (CLV) genes, Arabinogalactan-proteins (AGPs), APETALA 2 (AP2) and epigenetic factors is discussed.
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Affiliation(s)
- Hugo A. Méndez-Hernández
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Maharshi Ledezma-Rodríguez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Randy N. Avilez-Montalvo
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Yary L. Juárez-Gómez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Analesa Skeete
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Johny Avilez-Montalvo
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Víctor M. Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
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13
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Osorio-Montalvo P, Sáenz-Carbonell L, De-la-Peña C. 5-Azacytidine: A Promoter of Epigenetic Changes in the Quest to Improve Plant Somatic Embryogenesis. Int J Mol Sci 2018; 19:E3182. [PMID: 30332727 PMCID: PMC6214027 DOI: 10.3390/ijms19103182] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023] Open
Abstract
Somatic embryogenesis (SE) is a widely studied process due to its biotechnological potential to generate large quantities of plants in short time frames and from different sources of explants. The success of SE depends on many factors, such as the nature of the explant, the microenvironment generated by in vitro culture conditions, and the regulation of gene expression, among others. Epigenetics has recently been identified as an important factor influencing SE outcome. DNA methylation is one of the most studied epigenetic mechanisms due to its essential role in gene expression, and its participation in SE is crucial. DNA methylation levels can be modified through the use of drugs such as 5-Azacytidine (5-AzaC), an inhibitor of DNA methylation, which has been used during SE protocols. The balance between hypomethylation and hypermethylation seems to be the key to SE success. Here, we discuss the most prominent recent research on the role of 5-AzaC in the regulation of DNA methylation, highlighting its importance during the SE process. Also, the molecular implications that this inhibitor might have for the increase or decrease in the embryogenic potential of various explants are reviewed.
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Affiliation(s)
- Pedro Osorio-Montalvo
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
| | - Luis Sáenz-Carbonell
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
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14
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Hernández-Castellano S, Nic-Can GI, De-la-Peña C. Localization of miRNAs by In Situ Hybridization in Plants Using Conventional Oligonucleotide Probes. Methods Mol Biol 2018; 1456:51-62. [PMID: 27770356 DOI: 10.1007/978-1-4899-7708-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Among the epigenetic mechanisms studied with a greater interest in the last decade are the microRNAs (miRNAs). These small noncoding RNA sequences that are approximately 17-22 nucleotides in length play an essential role in many biological processes of various organisms, including plants. The analysis of spatiotemporal expression of miRNAs provides a better understanding of the role of these small molecules in plant development, cell differentiation, and other processes; but such analysis is also an important method for the validation of biological functions. In this work, we describe the optimization of an efficient protocol for the spatiotemporal analysis of miRNA by in situ hybridization using different plant tissues embedded in paraffin. Instead of LNA-modified probes that are typically used for this work, we use conventional oligonucleotide probes that yield a high specificity and clean distribution of miRNAs.
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Affiliation(s)
- Sara Hernández-Castellano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Merida, Yucatán, 97200, Mexico
| | - Geovanny I Nic-Can
- Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Periférico Norte. Km 33.5, Tablaje catastral 13615 Col. Chuburná de Hidalgo In, Merida, Yucatán, CP 97200, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Merida, Yucatán, 97200, Mexico.
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15
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Us-Camas R, De-la-Peña C. Chromatin Immunoprecipitation (ChiP) Protocol for the Analysis of Gene Regulation by Histone Modifications in Agave angustifolia Haw. Methods Mol Biol 2018; 1815:371-383. [PMID: 29981136 DOI: 10.1007/978-1-4939-8594-4_26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Chromatin is a dynamic entity that regulates different biological processes crucial for the proper functioning of the cell. Chromatin regulation depends largely on the interactions that occur between DNA with histones and nonhistone proteins. The chromatin immunoprecipitation assay (ChiP) is a widely used technique for the study of these DNA-histone and DNA-nonhistone interactions and their biological repercussions. Here we describe a ChiP protocol that allows in vivo analysis of the associations of histone modifications with genomic DNA in Agave angustifolia Haw. Although this protocol is established for A. angustifolia, it can be used in other species to obtain similar results. We also propose a strategy to shorten the times in some steps of the standard protocol.
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Affiliation(s)
- Rosa Us-Camas
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 #130 x 32 y 34, Col.Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 #130 x 32 y 34, Col.Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico.
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16
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Rodas-Junco BA, Canul-Chan M, Rojas-Herrera RA, De-la-Peña C, Nic-Can GI. Stem Cells from Dental Pulp: What Epigenetics Can Do with Your Tooth. Front Physiol 2017; 8:999. [PMID: 29270128 PMCID: PMC5724083 DOI: 10.3389/fphys.2017.00999] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/20/2017] [Indexed: 12/16/2022] Open
Abstract
Adult stem cells have attracted scientific attention because they are able to self-renew and differentiate into several specialized cell types. In this context, human dental tissue-derived mesenchymal stem cells (hDT-MSCs) have emerged as a possible solution for repairing or regenerating damaged tissues. These cells can be isolated from primary teeth that are naturally replaced, third molars, or other dental tissues and exhibit self-renewal, a high proliferative rate and a great multilineage potential. However, the cellular and molecular mechanisms that determine lineage specification are still largely unknown. It is known that a change in cell fate requires the deletion of existing transcriptional programs, followed by the establishment of a new developmental program to give rise to a new cell lineage. Increasing evidence indicates that chromatin structure conformation can influence cell fate. In this way, reversible chemical modifications at the DNA or histone level, and combinations thereof can activate or inactivate cell-type-specific gene sequences, giving rise to an alternative cell fates. On the other hand, miRNAs are starting to emerge as a possible player in establishing particular somatic lineages. In this review, we discuss two new and promising research fields in medicine and biology, epigenetics and stem cells, by summarizing the properties of hDT-MSCs and highlighting the recent findings on epigenetic contributions to the regulation of cellular differentiation.
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Affiliation(s)
- Beatriz A Rodas-Junco
- CONACYT-Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Michel Canul-Chan
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Rafael A Rojas-Herrera
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Geovanny I Nic-Can
- CONACYT-Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Mexico
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17
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Mukul-López HG, De-la-Peña C, Galaz-Ávalos RM, Loyola-Vargas VM. Evaluation of the Extracellular Proteome Profile During the Somatic Embryogenesis Process of Coffea spp. J MEX CHEM SOC 2017. [DOI: 10.29356/jmcs.v56i1.278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The somatic embryogenesis (SE) has been used as an important tool for the study of molecular events in plant cell differentiation. Some studies have revealed that suspensions of somatic embryos secrete a vast array of proteins that could be involved in the regulation of this process. Many of these molecules have been suggested to work as inductors and others as inhibitors of the process. In the present work, suspension cultures of both <em>Coffea canephora</em> and <em>Coffea arabica</em> were used to study the population of proteins secreted into the media. Two types of cultures were used; one for the propagation of suspension cultures (non-embryogenic) and another for the induction of SE (embryogenic). The evaluated days were 14 and 42 for non-embryogenic condition and 21, 42, and 98 for the embryogenic condition. An embryogenic system was established in the <em>C. arabica</em> species, obtaining 4,000 embryos per liter. We analyzed the proteins secreted into the culture media, both under non-embryogenic and SE induction conditions. In <em>C. canephora</em> medium, we found 173 proteins after 14 d of culture under non-embryogenic conditions. In <em>C. arabica</em> we found 523 after 14 d under non-embryogenic conditions. Under embryogenic conditions we found 379, 409 and 175 proteins after 21, 42 and 98 d, respectively. We also determined that some proteins are secreted exclusively under embryogenic conditions and others proteins under non-embryogenic conditions.
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18
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Us-Camas R, Castillo-Castro E, Aguilar-Espinosa M, Limones-Briones V, Rivera-Madrid R, Robert-Díaz ML, De-la-Peña C. Assessment of molecular and epigenetic changes in the albinism of Agave angustifolia Haw. Plant Sci 2017; 263:156-167. [PMID: 28818371 DOI: 10.1016/j.plantsci.2017.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 06/09/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
Albinism in plants is a rare phenomenon that occurs in nature and is characterized by the total or partial loss of photosynthetic pigments. Although progress has been made in understanding the nature of this phenomenon, the precise causes and biological basis are still unexplored. Here, we study the genetic and epigenetic differences between green (G), variegated (V) and albino (A) A. angustifolia Haw. plantlets obtained by in vitro propagation in order to present new insights into albinism from a plant system that offers a unique set of biological phenotypic characteristics. Low transcript levels of genes involved in carotenoids and photosynthesis such as PSY, PDS, LCYƐ, rubS, PEPCase and LHCP suggest a disruption in these processes in albino plants. Due to a high level of genetic similarity being found between the three phenotypes, we analyzed global DNA methylation and different histone marks (H3K4me2, H3K36me2, H3K9ac, H3K9me2 and H3K27me3). Although no significant differences in global 5-methyl deoxicytidine were found, almost a 2-4.5-fold increase in H3K9ac was observed in albino plants in comparison with variegated or green plants, suggesting a change in chromatin compaction related to A. angustifolia albinism.
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Affiliation(s)
- Rosa Us-Camas
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico
| | - Eduardo Castillo-Castro
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico
| | - Margarita Aguilar-Espinosa
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico
| | - Verónica Limones-Briones
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico
| | - Renata Rivera-Madrid
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico
| | - Manuel L Robert-Díaz
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán, Mexico.
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19
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Campos-Rivero G, Osorio-Montalvo P, Sánchez-Borges R, Us-Camas R, Duarte-Aké F, De-la-Peña C. Plant hormone signaling in flowering: An epigenetic point of view. J Plant Physiol 2017; 214:16-27. [PMID: 28419906 DOI: 10.1016/j.jplph.2017.03.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/06/2017] [Accepted: 03/29/2017] [Indexed: 05/19/2023]
Abstract
Reproduction is one of the most important phases in an organism's lifecycle. In the case of angiosperm plants, flowering provides the major developmental transition from the vegetative to the reproductive stage, and requires genetic and epigenetic reprogramming to ensure the success of seed production. Flowering is regulated by a complex network of genes that integrate multiple environmental cues and endogenous signals so that flowering occurs at the right time; hormone regulation, signaling and homeostasis are very important in this process. Working alone or in combination, hormones are able to promote flowering by epigenetic regulation. Some plant hormones, such as gibberellins, jasmonic acid, abscisic acid and auxins, have important effects on chromatin compaction mediated by DNA methylation and histone posttranslational modifications, which hints at the role that epigenetic regulation may play in flowering through hormone action. miRNAs have been viewed as acting independently from DNA methylation and histone modification, ignoring their potential to interact with hormone signaling - including the signaling of auxins, gibberellins, ethylene, jasmonic acid, salicylic acid and others - to regulate flowering. Therefore, in this review we examine new findings about interactions between epigenetic mechanisms and key players in hormone signaling to coordinate flowering.
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Affiliation(s)
| | | | | | - Rosa Us-Camas
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mexico.
| | - Fátima Duarte-Aké
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mexico.
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mexico.
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20
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Morales-Lara D, De-la-Peña C, Murillo-Rodríguez E. Dad's Snoring May Have Left Molecular Scars in Your DNA: the Emerging Role of Epigenetics in Sleep Disorders. Mol Neurobiol 2017; 55:2713-2724. [PMID: 28155201 DOI: 10.1007/s12035-017-0409-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/13/2017] [Indexed: 12/16/2022]
Abstract
The sleep-wake cycle is a biological phenomena under the orchestration of neurophysiological, neurochemical, neuroanatomical, and genetical mechanisms. Moreover, homeostatic and circadian processes participate in the regulation of sleep across the light-dark period. Further complexity of the understanding of the genesis of sleep engages disturbances which have been characterized and classified in a variety of sleep-wake cycle disorders. The most prominent sleep alterations include insomnia as well as excessive daytime sleepiness. On the other side, several human diseases have been linked with direct changes in DNA, such as chromatin configuration, genomic imprinting, DNA methylation, histone modifications (acetylation, methylation, ubiquitylation or sumoylation, etc.), and activating RNA molecules that are transcribed from DNA but not translated into proteins. Epigenetic theories primarily emphasize the interaction between the environment and gene expression. According to these approaches, the environment to which mammals are exposed has a significant role in determining the epigenetic modifications occurring in chromosomes that ultimately would influence not only development but also the descendants' physiology and behavior. Thus, what makes epigenetics intriguing is that, unlike genetic variation, modifications in DNA are altered directly by the environment and, in some cases, these epigenetic changes may be inherited by future generations. Thus, it is likely that epigenetic phenomena might contribute to the homeostatic and/or circadian control of sleep and, possibly, have an undescribed link with sleep disorders. An exciting new horizon of research is arising between sleep and epigenetics since it represents the relevance of the study of how the genome learns from its experiences and modulates behavior, including sleep.
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Affiliation(s)
- Daniela Morales-Lara
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina, División Ciencias de la Salud, Universidad Anáhuac Mayab, Carretera Mérida-Progreso Km. 15.5, A.P. 96 Cordemex, C.P. 97310, Mérida, Yucatán, Mexico.,Grupo de Investigación en Envejecimiento, División Ciencias de la Salud, Universidad Anáhuac Mayab, Mérida, Yucatán, Mexico.,Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C, Mérida, Yucatán, Mexico
| | - Eric Murillo-Rodríguez
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina, División Ciencias de la Salud, Universidad Anáhuac Mayab, Carretera Mérida-Progreso Km. 15.5, A.P. 96 Cordemex, C.P. 97310, Mérida, Yucatán, Mexico. .,Grupo de Investigación en Envejecimiento, División Ciencias de la Salud, Universidad Anáhuac Mayab, Mérida, Yucatán, Mexico. .,Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico. .,Grupo de Investigación Desarrollos Tecnológicos para la Salud, División de Ingeniería y Ciencias Exactas, Universidad Anáhuac Mayab, Mérida, Yucatán, Mexico.
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21
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Duarte-Aké F, Castillo-Castro E, Pool FB, Espadas F, Santamaría JM, Robert ML, De-la-Peña C. Erratum to: Physiological differences and changes in global DNA methylation levels in Agave angustifolia Haw. albino variant somaclones during the micropropagation process. Plant Cell Rep 2017; 36:389. [PMID: 27999975 DOI: 10.1007/s00299-016-2086-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Fátima Duarte-Aké
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Eduardo Castillo-Castro
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Felipe Barredo Pool
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Francisco Espadas
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Jorge M Santamaría
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Manuel L Robert
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico.
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Duarte-Aké F, Castillo-Castro E, Pool FB, Espadas F, Santamaría JM, Robert ML, De-la-Peña C. Physiological differences and changes in global DNA methylation levels in Agave angustifolia Haw. albino variant somaclones during the micropropagation process. Plant Cell Rep 2016; 35:2489-2502. [PMID: 27590059 DOI: 10.1007/s00299-016-2049-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 08/27/2016] [Indexed: 06/06/2023]
Abstract
Global DNA methylation changes caused by in vitro conditions are associated with the subculturing and phenotypic variation in Agave angustifolia Haw. While the relationship between the development of albinism and in vitro culture is well documented, the role of epigenetic processes in this development leaves some important questions unanswered. During the micropropagation of Agave angustifolia Haw., we found three different phenotypes, green (G), variegated (V) and albino (A). To understand the physiological and epigenetic differences among the somaclones, we analyzed several morphophysiological parameters and changes in the DNA methylation patterns in the three phenotypes during their in vitro development. We found that under in vitro conditions, the V plantlets maintained their CAM photosynthetic capacity, while the A variant showed no pigments and lost its CAM photosynthetic ability. Epigenetic analysis revealed that global DNA methylation increased in the G phenotype during the first two subcultures. However, after that time, DNA methylation levels declined. This hypomethylation correlated with the appearance of V shoots in the G plantlets. A similar correlation occurred in the V phenotype, where an increase of 2 % in the global DNA methylation levels was correlated with the generation of A shoots in the V plantlets. This suggests that an "epigenetic stress memory" during in vitro conditions causes a chromatin shift that favors the generation of variegated and albino shoots.
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Affiliation(s)
- Fátima Duarte-Aké
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Eduardo Castillo-Castro
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Felipe Barredo Pool
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Francisco Espadas
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Jorge M Santamaría
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Manuel L Robert
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico.
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Álvarez-Venegas R, De-la-Peña C. Editorial: Recent Advances of Epigenetics in Crop Biotechnology. Front Plant Sci 2016; 7:413. [PMID: 27066049 PMCID: PMC4815029 DOI: 10.3389/fpls.2016.00413] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 03/17/2016] [Indexed: 05/14/2023]
Affiliation(s)
- Raúl Álvarez-Venegas
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalGuanajuato, México
- *Correspondence: Raúl Álvarez-Venegas
| | - Clelia De-la-Peña
- Centro de Investigación Científica de Yucatán, Unidad de BiotecnologíaMérida, México
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De-la-Peña C, Nic-Can GI, Galaz-Ávalos RM, Avilez-Montalvo R, Loyola-Vargas VM. The role of chromatin modifications in somatic embryogenesis in plants. Front Plant Sci 2015; 6:635. [PMID: 26347757 PMCID: PMC4539545 DOI: 10.3389/fpls.2015.00635] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/31/2015] [Indexed: 05/20/2023]
Abstract
Somatic embryogenesis (SE) is a powerful tool for plant genetic improvement when used in combination with traditional agricultural techniques, and it is also an important technique to understand the different processes that occur during the development of plant embryogenesis. SE onset depends on a complex network of interactions among plant growth regulators, mainly auxins and cytokinins, during the proembryogenic early stages, and ethylene and gibberellic and abscisic acids later in the development of the somatic embryos. These growth regulators control spatial and temporal regulation of multiple genes in order to initiate change in the genetic program of somatic cells, as well as moderating the transition between embryo developmental stages. In recent years, epigenetic mechanisms have emerged as critical factors during SE. Some early reports indicate that auxins and in vitro conditions modify the levels of DNA methylation in embryogenic cells. The changes in DNA methylation patterns are associated with the regulation of several genes involved in SE, such as WUS, BBM1, LEC, and several others. In this review, we highlight the more recent discoveries in the understanding of the role of epigenetic regulation of SE. In addition, we include a survey of different approaches to the study of SE, and new opportunities to focus SE studies.
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Affiliation(s)
- Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, MéridaMexico
| | - Geovanny I. Nic-Can
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, MéridaMexico
| | - Rosa M. Galaz-Ávalos
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, MéridaMexico
| | - Randy Avilez-Montalvo
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, MéridaMexico
| | - Víctor M. Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, MéridaMexico
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Nic-Can GI, Galaz-Ávalos RM, De-la-Peña C, Alcazar-Magaña A, Wrobel K, Loyola-Vargas VM. Somatic Embryogenesis: Identified Factors that Lead to Embryogenic Repression. A Case of Species of the Same Genus. PLoS One 2015; 10:e0126414. [PMID: 26038822 PMCID: PMC4454440 DOI: 10.1371/journal.pone.0126414] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/01/2015] [Indexed: 11/19/2022] Open
Abstract
Somatic embryogenesis is a powerful biotechnological tool for the mass production of economically important cultivars. Due to the cellular totipotency of plants, somatic cells under appropriate conditions are able to develop a complete functional embryo. During the induction of somatic embryogenesis, there are different factors involved in the success or failure of the somatic embryogenesis response. Among these factors, the origin of the explant, the culture medium and the in vitro environmental conditions have been the most studied. However, the secretion of molecules into the media has not been fully addressed. We found that the somatic embryogenesis of Coffea canephora, a highly direct embryogenic species, is disrupted by the metabolites secreted from C. arabica, a poorly direct embryogenic species. These metabolites also affect DNA methylation. Our results show that the abundance of two major phenolic compounds, caffeine and chlorogenic acid, are responsible for inhibiting somatic embryogenesis in C. canephora.
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Affiliation(s)
- Geovanny I. Nic-Can
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, CP 97200, Mérida, Yucatán, México
| | - Rosa M. Galaz-Ávalos
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, CP 97200, Mérida, Yucatán, México
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, CP 97200, Mérida, Yucatán, México
| | - Armando Alcazar-Magaña
- Department of Chemistry, University of Guanajuato, L. de Retana 5, CP 36000 Guanajuato, Mexico
| | - Kazimierz Wrobel
- Department of Chemistry, University of Guanajuato, L. de Retana 5, CP 36000 Guanajuato, Mexico
| | - Víctor M. Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, CP 97200, Mérida, Yucatán, México
- * E-mail:
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De-la-Peña C, Loyola-Vargas VM. Biotic interactions in the rhizosphere: a diverse cooperative enterprise for plant productivity. Plant Physiol 2014; 166:701-19. [PMID: 25118253 PMCID: PMC4213099 DOI: 10.1104/pp.114.241810] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/10/2014] [Indexed: 05/08/2023]
Abstract
Microbes and plants have evolved biochemical mechanisms to communicate with each other. The molecules responsible for such communication are secreted during beneficial or harmful interactions. Hundreds of these molecules secreted into the rhizosphere have been identified, and their functions are being studied in order to understand the mechanisms of interaction and communication among the different members of the rhizosphere community. The importance of root and microbe secretion to the underground habitat in improving crop productivity is increasingly recognized, with the discovery and characterization of new secreting compounds found in the rhizosphere. Different omic approaches, such as genomics, transcriptomics, proteomics, and metabolomics, have expanded our understanding of the first signals between microbes and plants. In this review, we highlight the more recent discoveries related to molecules secreted into the rhizosphere and how they affect plant productivity, either negatively or positively. In addition, we include a survey of novel approaches to studying the rhizosphere and emerging opportunities to direct future studies.
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Affiliation(s)
- Clelia De-la-Peña
- Unidad de Biotecnología (C.D.) and Unidad de Bioquímica y Biología Molecular de Plantas (V.M.L.-V.), Centro de Investigación Científica de Yucatán, 97200 Merida, Yucatan, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Biotecnología (C.D.) and Unidad de Bioquímica y Biología Molecular de Plantas (V.M.L.-V.), Centro de Investigación Científica de Yucatán, 97200 Merida, Yucatan, Mexico
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Nic-Can G, Hernández-Castellano S, Kú-González A, Loyola-Vargas VM, De-la-Peña C. An efficient immunodetection method for histone modifications in plants. Plant Methods 2013; 9:47. [PMID: 24341414 PMCID: PMC3868413 DOI: 10.1186/1746-4811-9-47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/02/2013] [Indexed: 05/08/2023]
Abstract
BACKGROUND Epigenetic mechanisms can be highly dynamic, but the cross-talk among them and with the genome is still poorly understood. Many of these mechanisms work at different places in the cell and at different times of organism development. Covalent histone modifications are one of the most complex and studied epigenetic mechanisms involved in cellular reprogramming and development in plants. Therefore, the knowledge of the spatial distribution of histone methylation in different tissues is important to understand their behavior on specific cells. RESULTS Based on the importance of epigenetic marks for biology, we present a simplified, inexpensive and efficient protocol for in situ immunolocalization on different tissues such as flowers, buds, callus, somatic embryo and meristematic tissue from several plants of agronomical and biological importance. Here, we fully describe all the steps to perform the localization of histone modifications. Using this method, we were able to visualize the distribution of H3K4me3 and H3K9me2 without loss of histological integrity of tissues from several plants, including Agave tequilana, Capsicum chinense, Coffea canephora and Cedrela odorata, as well as Arabidopsis thaliana. CONCLUSIONS There are many protocols to study chromatin modifications; however, most of them are expensive, difficult and require sophisticated equipment. Here, we provide an efficient protocol for in situ localization of histone methylation that dispenses with the use of expensive and sensitive enzymes. The present method can be used to investigate the cellular distribution and localization of a wide array of proteins, which could help to clarify the biological role that they play at specific times and places in different tissues of various plant species.
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Affiliation(s)
- Geovanny Nic-Can
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida CP 97200, Yucatán, México
| | - Sara Hernández-Castellano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida CP 97200, Yucatán, México
| | - Angela Kú-González
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida CP 97200, Yucatán, México
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida CP 97200, Yucatán, México
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida CP 97200, Yucatán, México
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Nic-Can GI, López-Torres A, Barredo-Pool F, Wrobel K, Loyola-Vargas VM, Rojas-Herrera R, De-la-Peña C. New insights into somatic embryogenesis: leafy cotyledon1, baby boom1 and WUSCHEL-related homeobox4 are epigenetically regulated in Coffea canephora. PLoS One 2013; 8:e72160. [PMID: 23977240 PMCID: PMC3748027 DOI: 10.1371/journal.pone.0072160] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/07/2013] [Indexed: 01/09/2023] Open
Abstract
Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY cotyledon1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-related homeobox4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed.
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Affiliation(s)
- Geovanny I. Nic-Can
- Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | | | - Felipe Barredo-Pool
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Kazimierz Wrobel
- Facultad de Química, Universidad de Guanajuato, Guanajuato, México
| | - Víctor M. Loyola-Vargas
- Centro de Investigación Científica de Yucatán, Unidad de Bioquímica y Biología Molecular de Plantas, Mérida, Yucatán, México
| | - Rafael Rojas-Herrera
- Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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De-la-Peña C, Nic-Can G, Ojeda G, Herrera-Herrera JL, López-Torres A, Wrobel K, Robert-Díaz ML. KNOX1 is expressed and epigenetically regulated during in vitro conditions in Agave spp. BMC Plant Biol 2012; 12:203. [PMID: 23126409 PMCID: PMC3541254 DOI: 10.1186/1471-2229-12-203] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 10/23/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND The micropropagation is a powerful tool to scale up plants of economical and agronomical importance, enhancing crop productivity. However, a small but growing body of evidence suggests that epigenetic mechanisms, such as DNA methylation and histone modifications, can be affected under the in vitro conditions characteristic of micropropagation. Here, we tested whether the adaptation to different in vitro systems (Magenta boxes and Bioreactors) modified epigenetically different clones of Agave fourcroydes and A. angustifolia. Furthermore, we assessed whether these epigenetic changes affect the regulatory expression of KNOTTED1-like HOMEOBOX (KNOX) transcription factors. RESULTS To gain a better understanding of epigenetic changes during in vitro and ex vitro conditions in Agave fourcroydes and A. angustifolia, we analyzed global DNA methylation, as well as different histone modification marks, in two different systems: semisolid in Magenta boxes (M) and temporary immersion in modular Bioreactors (B). No significant difference was found in DNA methylation in A. fourcroydes grown in either M or B. However, when A. fourcroydes was compared with A. angustifolia, there was a two-fold difference in DNA methylation between the species, independent of the in vitro system used. Furthermore, we detected an absence or a low amount of the repressive mark H3K9me2 in ex vitro conditions in plants that were cultured earlier either in M or B. Moreover, the expression of AtqKNOX1 and AtqKNOX2, on A. fourcroydes and A. angustifolia clones, is affected during in vitro conditions. Therefore, we used Chromatin ImmunoPrecipitation (ChIP) to know whether these genes were epigenetically regulated. In the case of AtqKNOX1, the H3K4me3 and H3K9me2 were affected during in vitro conditions in comparison with AtqKNOX2. CONCLUSIONS Agave clones plants with higher DNA methylation during in vitro conditions were better adapted to ex vitro conditions. In addition, A. fourcroydes and A. angustifolia clones displayed differential expression of the KNOX1 gene during in vitro conditions, which is epigenetically regulated by the H3K4me3 and H3K9me2 marks. The finding of an epigenetic regulation in key developmental genes will make it important in future studies to identify factors that help to find climate-resistant micropropagated plants.
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Affiliation(s)
- Clelia De-la-Peña
- Unidad Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida, Yucatán, CP 97200, México
| | - Geovanny Nic-Can
- Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Periférico Norte. Km 33.5, Tablaje catastral 13615 Col. Chuburná de Hidalgo Inn, Merida, Yucatán, C. P. 97203, Mexico
| | - Gabriel Ojeda
- Unidad Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida, Yucatán, CP 97200, México
| | - José L Herrera-Herrera
- Unidad Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida, Yucatán, CP 97200, México
| | | | - Kazimierz Wrobel
- Facultad de Química, Universidad de Guanajuato, Guanajuato, 36000, México
| | - Manuel L Robert-Díaz
- Unidad Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, Mérida, Yucatán, CP 97200, México
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Badri DV, De-la-Peña C, Lei Z, Manter DK, Chaparro JM, Guimarães RL, Sumner LW, Vivanco JM. Root secreted metabolites and proteins are involved in the early events of plant-plant recognition prior to competition. PLoS One 2012; 7:e46640. [PMID: 23056382 PMCID: PMC3462798 DOI: 10.1371/journal.pone.0046640] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 09/05/2012] [Indexed: 11/18/2022] Open
Abstract
The mechanism whereby organisms interact and differentiate between others has been at the forefront of scientific inquiry, particularly in humans and certain animals. It is widely accepted that plants also interact, but the degree of this interaction has been constricted to competition for space, nutrients, water and light. Here, we analyzed the root secreted metabolites and proteins involved in early plant neighbor recognition by using Arabidopsis thaliana Col-0 ecotype (Col) as our focal plant co-cultured in vitro with different neighbors [A. thaliana Ler ecotype (Ler) or Capsella rubella (Cap)]. Principal component and cluster analyses revealed that both root secreted secondary metabolites and proteins clustered separately between the plants grown individually (Col-0, Ler and Cap grown alone) and the plants co-cultured with two homozygous individuals (Col-Col, Ler-Ler and Cap-Cap) or with different individuals (Col-Ler and Col-Cap). In particularly, we observed that a greater number of defense- and stress- related proteins were secreted when our control plant, Col, was grown alone as compared to when it was co-cultured with another homozygous individual (Col-Col) or with a different individual (Col-Ler and Col-Cap). However, the total amount of defense proteins in the exudates of the co-cultures was higher than in the plant alone. The opposite pattern of expression was identified for stress-related proteins. These data suggest that plants can sense and respond to the presence of different plant neighbors and that the level of relatedness is perceived upon initial interaction. Furthermore, the role of secondary metabolites and defense- and stress-related proteins widely involved in plant-microbe associations and abiotic responses warrants reassessment for plant-plant interactions.
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Affiliation(s)
- Dayakar V. Badri
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Clelia De-la-Peña
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Zhentian Lei
- The Samuel Roberts Noble Foundation, Plant Biology Division, Oklahoma, United States of America
| | - Daniel K. Manter
- U.S. Department of Agriculture - Agricultural Research Service, Soil-Plant-Nutrient Research Unit, Fort Collins, Colorado, United States of America
| | - Jacqueline M. Chaparro
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | | | - Lloyd W. Sumner
- The Samuel Roberts Noble Foundation, Plant Biology Division, Oklahoma, United States of America
| | - Jorge M. Vivanco
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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Abstract
Methyl jasmonate (MeJA) produces an important reduction in the accumulation of proteins related to energy metabolism. The treatment of hairy roots (HR) with MeJA increased the accumulation of H2O2 during the first 48 h and this H2O2 accumulation was also observed in isolated mitochondria. Peroxidase and catalase activities decreased in the presence of MeJA, and this decrease directly correlated with the increase of H2O2 in HR treated with MeJA. This suggests that the H2O2 burst due to MeJA is the initial response to mitochondria disruption in the roots.
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Affiliation(s)
- Victor Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México.
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Ruiz-May E, De-la-Peña C, Galaz-Ávalos RM, Lei Z, Watson BS, Sumner LW, Loyola-Vargas VM. Methyl jasmonate induces ATP biosynthesis deficiency and accumulation of proteins related to secondary metabolism in Catharanthus roseus (L.) G. hairy roots. Plant Cell Physiol 2011; 52:1401-21. [PMID: 21727181 DOI: 10.1093/pcp/pcr086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Jasmonates are specific signal molecules in plants that are involved in a diverse set of physiological and developmental processes. However, methyl jasmonate (MeJA) has been shown to have a negative effect on root growth and, so far, the biochemical mechanism for this is unknown. Using Catharanthus roseus hairy roots, we were able to observe the effect of MeJA on growth inhibition, cell disorganization and cell death of the root cap. Hairy roots treated with MeJA induced the perturbation of mitochondrial membrane integrity and a diminution in ATP biosynthesis. Furthermore, several proteins were identified that were involved in energy and secondary metabolism; the changes in accumulation of these proteins were observed with 100 μM MeJA. In conclusion, our results suggest that a switch of the metabolic fate of hairy roots in response to MeJA could cause an increase in the accumulation of secondary metabolites. This is likely to have important consequences in the production of specific alkaloids important for the pharmaceutical industry.
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Affiliation(s)
- Eliel Ruiz-May
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Col. Chuburná de Hidalgo, CP 97200, Mérida, Yucatán, México
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De-la-Peña C, Badri DV, Lei Z, Watson BS, Brandão MM, Silva-Filho MC, Sumner LW, Vivanco JM. Root secretion of defense-related proteins is development-dependent and correlated with flowering time. J Biol Chem 2010; 285:30654-65. [PMID: 20682788 PMCID: PMC2945560 DOI: 10.1074/jbc.m110.119040] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 07/22/2010] [Indexed: 01/14/2023] Open
Abstract
Proteins found in the root exudates are thought to play a role in the interactions between plants and soil organisms. To gain a better understanding of protein secretion by roots, we conducted a systematic proteomic analysis of the root exudates of Arabidopsis thaliana at different plant developmental stages. In total, we identified 111 proteins secreted by roots, the majority of which were exuded constitutively during all stages of development. However, defense-related proteins such as chitinases, glucanases, myrosinases, and others showed enhanced secretion during flowering. Defense-impaired mutants npr1-1 and NahG showed lower levels of secretion of defense proteins at flowering compared with the wild type. The flowering-defective mutants fca-1, stm-4, and co-1 showed almost undetectable levels of defense proteins in their root exudates at similar time points. In contrast, root secretions of defense-enhanced cpr5-2 mutants showed higher levels of defense proteins. The proteomics data were positively correlated with enzymatic activity assays for defense proteins and with in silico gene expression analysis of genes specifically expressed in roots of Arabidopsis. In conclusion, our results show a clear correlation between defense-related proteins secreted by roots and flowering time.
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Affiliation(s)
- Clelia De-la-Peña
- From the Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Dayakar V. Badri
- From the Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Zhentian Lei
- The Samuel Roberts Noble Foundation, Plant Biology Division, Ardmore, Oklahoma 73401, and
| | - Bonnie S. Watson
- The Samuel Roberts Noble Foundation, Plant Biology Division, Ardmore, Oklahoma 73401, and
| | - Marcelo M. Brandão
- the Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, C.P. 83, 13400-970 Piracicaba São Paulo, Brazil
| | - Marcio C. Silva-Filho
- the Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, C.P. 83, 13400-970 Piracicaba São Paulo, Brazil
| | - Lloyd W. Sumner
- The Samuel Roberts Noble Foundation, Plant Biology Division, Ardmore, Oklahoma 73401, and
| | - Jorge M. Vivanco
- From the Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, Colorado 80523
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Broz AK, Broeckling CD, De-la-Peña C, Lewis MR, Greene E, Callaway RM, Sumner LW, Vivanco JM. Plant neighbor identity influences plant biochemistry and physiology related to defense. BMC Plant Biol 2010; 10:115. [PMID: 20565801 PMCID: PMC3095278 DOI: 10.1186/1471-2229-10-115] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 06/17/2010] [Indexed: 05/22/2023]
Abstract
BACKGROUND Chemical and biological processes dictate an individual organism's ability to recognize and respond to other organisms. A small but growing body of evidence suggests that plants may be capable of recognizing and responding to neighboring plants in a species specific fashion. Here we tested whether or not individuals of the invasive exotic weed, Centaurea maculosa, would modulate their defensive strategy in response to different plant neighbors. RESULTS In the greenhouse, C. maculosa individuals were paired with either conspecific (C. maculosa) or heterospecific (Festuca idahoensis) plant neighbors and elicited with the plant defense signaling molecule methyl jasmonate to mimic insect herbivory. We found that elicited C. maculosa plants grown with conspecific neighbors exhibited increased levels of total phenolics, whereas those grown with heterospecific neighbors allocated more resources towards growth. To further investigate these results in the field, we conducted a metabolomics analysis to explore chemical differences between individuals of C. maculosa growing in naturally occurring conspecific and heterospecific field stands. Similar to the greenhouse results, C. maculosa individuals accumulated higher levels of defense-related secondary metabolites and lower levels of primary metabolites when growing in conspecific versus heterospecific field stands. Leaf herbivory was similar in both stand types; however, a separate field study positively correlated specialist herbivore load with higher densities of C. maculosa conspecifics. CONCLUSIONS Our results suggest that an individual C. maculosa plant can change its defensive strategy based on the identity of its plant neighbors. This is likely to have important consequences for individual and community success.
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Affiliation(s)
- Amanda K Broz
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Corey D Broeckling
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO, 80523, USA
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, 80523, USA
| | - Clelia De-la-Peña
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Matthew R Lewis
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, 80523, USA
| | - Erick Greene
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Ragan M Callaway
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Lloyd W Sumner
- The Samuel Roberts Noble Foundation, Plant Biology, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO, 80523, USA
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De-la-Peña C, Badri DV, Vivanco JM. Novel role for pectin methylesterase in Arabidopsis: A new function showing ribosome-inactivating protein (RIP) activity. Biochim Biophys Acta Gen Subj 2008; 1780:773-83. [DOI: 10.1016/j.bbagen.2007.12.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Revised: 12/14/2007] [Accepted: 12/26/2007] [Indexed: 11/29/2022]
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Badri DV, Loyola-Vargas VM, Broeckling CD, De-la-Peña C, Jasinski M, Santelia D, Martinoia E, Sumner LW, Banta LM, Stermitz F, Vivanco JM. Altered profile of secondary metabolites in the root exudates of Arabidopsis ATP-binding cassette transporter mutants. Plant Physiol 2008; 146:762-71. [PMID: 18065561 PMCID: PMC2245854 DOI: 10.1104/pp.107.109587] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2007] [Accepted: 11/27/2007] [Indexed: 05/18/2023]
Abstract
Following recent indirect evidence suggesting a role for ATP-binding cassette (ABC) transporters in root exudation of phytochemicals, we identified 25 ABC transporter genes highly expressed in the root cells most likely to be involved in secretion processes. Of these 25 genes, we also selected six full-length ABC transporters and a half-size transporter for in-depth molecular and biochemical analyses. We compared the exuded root phytochemical profiles of these seven ABC transporter mutants to those of the wild type. There were three nonpolar phytochemicals missing in various ABC transporter mutants compared to the wild type when the samples were analyzed by high-performance liquid chromatography-mass spectrometry. These data suggest that more than one ABC transporter can be involved in the secretion of a given phytochemical and that a transporter can be involved in the secretion of more than one secondary metabolite. The primary and secondary metabolites present in the root exudates of the mutants were also analyzed by gas chromatography-mass spectrometry, which allowed for the identification of groups of compounds differentially found in some of the mutants compared to the wild type. For instance, the mutant Atpdr6 secreted a lower level of organic acids and Atmrp2 secreted a higher level of amino acids as compared to the wild type. We conclude that the release of phytochemicals by roots is partially controlled by ABC transporters.
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Affiliation(s)
- Dayakar V Badri
- Center for Rhizosphere Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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