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Núñez-Enríquez JC, Romo-Rodríguez R, Gaspar-Mendoza P, Zamora-Herrera G, Torres-Pineda L, Amador-Cardoso J, López-Blanco JA, Alfaro-Hernández L, López-García L, Rosas-Cruz A, Alberto-Aguilar DR, Trejo-Pichardo CO, Ramírez-Ramírez D, Cruz-Maza A, Flores-Lujano J, Luna-Silva N, Martínez-Martell A, Martínez-Jose K, Ramírez-Ramírez A, Solis-Poblano JC, Zagoya-Martínez P, Terán-Cerqueda V, Huerta-Moreno A, Montiel-Jarquín Á, Garrido-Hernández M, Hernández-Ramos R, Olvera-Caraza D, Cruz-Medina CS, Alvarez-Rodríguez E, Chávez-Aguilar LA, Herrera-Olivares W, García-Hidalgo B, Cano-Cuapio LS, Guevara-Espejel C, Juárez-Avendaño G, Balandrán JC, Baños-Lara MDR, Cárdenas-González M, Álvarez-Buylla ER, Pérez-Tapia SM, Casique-Aguirre D, Pelayo R. Implementation of a roadmap for the comprehensive diagnosis, follow-up, and research of childhood leukemias in vulnerable regions of Mexico: results from the PRONAII Strategy. Front Oncol 2024; 14:1304690. [PMID: 38634051 PMCID: PMC11022691 DOI: 10.3389/fonc.2024.1304690] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/28/2024] [Indexed: 04/19/2024] Open
Abstract
The main objective of the National Project for Research and Incidence of Childhood Leukemias is to reduce early mortality rates for these neoplasms in the vulnerable regions of Mexico. This project was conducted in the states of Oaxaca, Puebla, and Tlaxcala. A key strategy of the project is the implementation of an effective roadmap to ensure that leukemia patients are the target of maximum benefit of interdisciplinary collaboration between researchers, clinicians, surveyors, and laboratories. This strategy guarantees the comprehensive management of diagnosis and follow-up samples of pediatric patients with leukemia, centralizing, managing, and analyzing the information collected. Additionally, it allows for a precise diagnosis and monitoring of the disease through immunophenotype and measurable residual disease (MRD) studies, enhancing research and supporting informed clinical decisions for the first time in these regions through a population-based study. This initiative has significantly improved the diagnostic capacity of leukemia in girls, boys, and adolescents in the regions of Oaxaca, Puebla, and Tlaxcala, providing comprehensive, high-quality care with full coverage in the region. Likewise, it has strengthened collaboration between health institutions, researchers, and professionals in the sector, which contributes to reducing the impact of the disease on the community.
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Affiliation(s)
- Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría “Dr. Silvestre Frenk Freund” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Rubí Romo-Rodríguez
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Mexico City, Mexico
| | - Pedro Gaspar-Mendoza
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Gabriela Zamora-Herrera
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Lizeth Torres-Pineda
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Jiovanni Amador-Cardoso
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Jebea A. López-Blanco
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Laura Alfaro-Hernández
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Facultad de Ciencias Químicas. Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Lucero López-García
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Arely Rosas-Cruz
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Dulce Rosario Alberto-Aguilar
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Mexico City, Mexico
| | - César Omar Trejo-Pichardo
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Dalia Ramírez-Ramírez
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Astin Cruz-Maza
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
- Laboratorio Juárez, Medicina de Laboratorio Clínico de Alta Especialidad, Biología Molecular e Investigación Clínica, Oaxaca de Juárez, Oaxaca, Mexico
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría “Dr. Silvestre Frenk Freund” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Nuria Luna-Silva
- Servicio de Hemato-Oncología Pediátrica, Hospital de la Niñez Oaxaqueña, Secretaría de Salud, Oaxaca, Mexico
| | - Angélica Martínez-Martell
- Servicio de Hemato-Oncología Pediátrica, Hospital de la Niñez Oaxaqueña, Secretaría de Salud, Oaxaca, Mexico
| | - Karina Martínez-Jose
- Servicio de Hemato-Oncología Pediátrica, Hospital de la Niñez Oaxaqueña, Secretaría de Salud, Oaxaca, Mexico
| | - Anabel Ramírez-Ramírez
- Servicio de ONCOCREAN, Hospital General de Zona 01, Delegación Oaxaca, Instituto Mexicano del Seguro Social, Oaxaca, Mexico
| | - Juan Carlos Solis-Poblano
- Servicio de Hematología, Unidad Médica de Alta Especialidad, Hospital de Especialidades “Manuel Avila Camacho”, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Patricia Zagoya-Martínez
- Servicio de Hematología, Unidad Médica de Alta Especialidad, Hospital de Especialidades “Manuel Avila Camacho”, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Vanessa Terán-Cerqueda
- Servicio de Hematología, Unidad Médica de Alta Especialidad, Hospital de Especialidades “Manuel Avila Camacho”, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Andrea Huerta-Moreno
- Servicio de Hematología, Unidad Médica de Alta Especialidad, Hospital de Especialidades “Manuel Avila Camacho”, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Álvaro Montiel-Jarquín
- Servicio de Hematología, Unidad Médica de Alta Especialidad, Hospital de Especialidades “Manuel Avila Camacho”, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | | | - Raquel Hernández-Ramos
- Departamento de Oncología. Hospital para el Niño Poblano. Secretaría de Salud, Puebla, Mexico
| | - Daniela Olvera-Caraza
- Departamento de Oncología. Hospital para el Niño Poblano. Secretaría de Salud, Puebla, Mexico
| | - Cynthia Shanat Cruz-Medina
- Departamento de Oncología. Hospital para el Niño Poblano. Secretaría de Salud, Puebla, Mexico
- Servicio de Oncohematología Pediátrica, Instituto de Seguridad y Servicios Sociales de los Trabajadores al Servicio de los Poderes del Estado de Puebla (ISSSTEP), Puebla, Mexico
| | - Enoch Alvarez-Rodríguez
- Servicio de Oncohematología Pediátrica, Instituto de Seguridad y Servicios Sociales de los Trabajadores al Servicio de los Poderes del Estado de Puebla (ISSSTEP), Puebla, Mexico
- Servicio de Hematología Pediátrica, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Puebla, Mexico
| | - Lénica Anahí Chávez-Aguilar
- Servicio de Hematología Pediátrica, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Puebla, Mexico
| | - Wilfrido Herrera-Olivares
- Servicio de Hematología Pediátrica, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Puebla, Mexico
- Servicio de Oncohematología Pediátrica, Hospital General del Sur, Puebla, Mexico
| | | | | | | | - Gerardo Juárez-Avendaño
- Laboratorio Juárez, Medicina de Laboratorio Clínico de Alta Especialidad, Biología Molecular e Investigación Clínica, Oaxaca de Juárez, Oaxaca, Mexico
| | - Juan Carlos Balandrán
- Department of Pathology, New York University (NYU) School of Medicine, New York, NY, United States
| | - Ma. del Rocío Baños-Lara
- Centro de Investigación Oncológica, Una Nueva Esperanza, Universidad Popular Autónoma del Estado de Puebla, Puebla, Mexico
| | | | | | - Sonia Mayra Pérez-Tapia
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I+D+i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Mexico City, Mexico
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Diana Casique-Aguirre
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Mexico City, Mexico
| | - Rosana Pelayo
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Unidad de Educación e Investigación, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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Castañón-Suárez CA, Arrizubieta M, Castelán-Muñoz N, Sánchez-Rodríguez DB, Caballero-Cordero C, Zluhan-Martínez E, Patiño-Olvera SC, Arciniega-González J, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. The MADS-box genes SOC1 and AGL24 antagonize XAL2 functions in Arabidopsis thaliana root development. Front Plant Sci 2024; 15:1331269. [PMID: 38576790 PMCID: PMC10994003 DOI: 10.3389/fpls.2024.1331269] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/06/2024] [Indexed: 04/06/2024]
Abstract
MADS-domain transcription factors play pivotal roles in numerous developmental processes in Arabidopsis thaliana. While their involvement in flowering transition and floral development has been extensively examined, their functions in root development remain relatively unexplored. Here, we explored the function and genetic interaction of three MADS-box genes (XAL2, SOC1 and AGL24) in primary root development. By analyzing loss-of-function and overexpression lines, we found that SOC1 and AGL24, both critical components in flowering transition, redundantly act as repressors of primary root growth as the loss of function of either SOC1 or AGL24 partially recovers the primary root growth, meristem cell number, cell production rate, and the length of fully elongated cells of the short-root mutant xal2-2. Furthermore, we observed that the simultaneous overexpression of AGL24 and SOC1 leads to short-root phenotypes, affecting meristem cell number and fully elongated cell size, whereas SOC1 overexpression is sufficient to affect columella stem cell differentiation. Additionally, qPCR analyses revealed that these genes exhibit distinct modes of transcriptional regulation in roots compared to what has been previously reported for aerial tissues. We identified 100 differentially expressed genes in xal2-2 roots by RNA-seq. Moreover, our findings revealed that the expression of certain genes involved in cell differentiation, as well as stress responses, which are either upregulated or downregulated in the xal2-2 mutant, reverted to WT levels in the absence of SOC1 or AGL24.
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Affiliation(s)
- Claudio A. Castañón-Suárez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Maite Arrizubieta
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Natalia Castelán-Muñoz
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Postgrado en Recursos Genéticos y Productividad-Fisiología Vegetal, Colegio de Postgraduados, Texcoco, Estado de México, Mexico
| | - Diana Belén Sánchez-Rodríguez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Carolina Caballero-Cordero
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sandra C. Patiño-Olvera
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - J.Arturo Arciniega-González
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Bensussen A, Torres-Magallanes JA, Álvarez-Buylla ER, de Álvarez-Buylla ER. Hybrid lineages of CD4 + T cells: a handbook update. Front Immunol 2024; 15:1344078. [PMID: 38312841 PMCID: PMC10834732 DOI: 10.3389/fimmu.2024.1344078] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024] Open
Abstract
CD4+ T lymphocytes have been classified into several lineages, according to their gene expression profiles and their effector responses. Interestingly, recent evidence is showing that many lineages could yield hybrid phenotypes with unique properties and functions. It has been reported that such hybrid lineages might underlie pathologies or may function as effector cells with protection capacities against molecular threats. In this work, we reviewed the characteristics of the hybrid lineages reported in the literature, in order to identify the expression profiles that characterize them and the markers that could be used to identify them. We also review the differentiation cues that elicit their hybrid origin and what is known about their physiological roles.
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Affiliation(s)
- Antonio Bensussen
- Laboratorio de Neuroendocrinología, Centro Universitario de Investigaciones Biomédicas, Universidad de Colima, Colima, Mexico
| | - José Antonio Torres-Magallanes
- Laboratorio de Neuroendocrinología, Centro Universitario de Investigaciones Biomédicas, Universidad de Colima, Colima, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena Roces de Álvarez-Buylla
- Laboratorio de Neuroendocrinología, Centro Universitario de Investigaciones Biomédicas, Universidad de Colima, Colima, Mexico
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Romo-Rodríguez R, Zamora-Herrera G, López-Blanco JA, López-García L, Rosas-Cruz A, Alfaro-Hernández L, Trejo-Pichardo CO, Alberto-Aguilar DR, Casique-Aguirre D, Vilchis-Ordoñez A, Solis-Poblano JC, García-Stivalet LA, Terán-Cerqueda V, Luna-Silva NC, Garrido-Hernández MÁ, Cano-Cuapio LS, Ayala-Contreras K, Domínguez F, del Campo-Martínez MDLÁ, Juárez-Avendaño G, Balandrán JC, Pérez-Tapia SM, Fernández-Giménez C, Zárate-Rodríguez PA, López-Aguilar E, Treviño-García A, Duque-Molina C, Bonifaz LC, Núñez-Enríquez JC, Cárdenas-González M, Álvarez-Buylla ER, Ramírez-Ramírez D, Pelayo R. Subclassification of B-acute lymphoblastic leukemia according to age, immunophenotype and microenvironment, predicts MRD risk in Mexican children from vulnerable regions. Front Oncol 2024; 13:1304662. [PMID: 38250553 PMCID: PMC10796993 DOI: 10.3389/fonc.2023.1304662] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction The decisive key to disease-free survival in B-cell precursor acute lymphoblastic leukemia in children, is the combination of diagnostic timeliness and treatment efficacy, guided by accurate patient risk stratification. Implementation of standardized and high-precision diagnostic/prognostic systems is particularly important in the most marginalized geographic areas in Mexico, where high numbers of the pediatric population resides and the highest relapse and early death rates due to acute leukemias are recorded even in those cases diagnosed as standard risk. Methods By using a multidimensional and integrated analysis of the immunophenotype of leukemic cells, the immunological context and the tumor microenvironment, this study aim to capture the snapshot of acute leukemia at disease debut of a cohort of Mexican children from vulnerable regions in Puebla, Oaxaca and Tlaxcala and its potential use in risk stratification. Results and discussion Our findings highlight the existence of a distinct profile of ProB-ALL in children older than 10 years, which is associated with a six-fold increase in the risk of developing measurable residual disease (MRD). Along with the absence of CD34+ seminal cells for normal hematopoiesis, this ProB-ALL subtype exhibited several characteristics related to poor prognosis, including the high expression level of myeloid lineage markers such as MPO and CD33, as well as upregulation of CD19, CD34, CD24, CD20 and nuTdT. In contrast, it showed a trend towards decreased expression of CD9, CD81, CD123, CD13, CD15 and CD21. Of note, the mesenchymal stromal cell compartment constituting their leukemic niche in the bone marrow, displayed characteristics of potential suppressive microenvironment, such as the expression of Gal9 and IDO1, and the absence of the chemokine CXCL11. Accordingly, adaptive immunity components were poorly represented. Taken together, our results suggest, for the first time, that a biologically distinct subtype of ProB-ALL emerges in vulnerable adolescents, with a high risk of developing MRD. Rigorous research on potential enhancing factors, environmental or lifestyle, is crucial for its detection and prevention. The use of the reported profile for early risk stratification is suggested.
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Affiliation(s)
- Rubí Romo-Rodríguez
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Gabriela Zamora-Herrera
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Jebea A. López-Blanco
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Lucero López-García
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Arely Rosas-Cruz
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Laura Alfaro-Hernández
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - César Omar Trejo-Pichardo
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Dulce Rosario Alberto-Aguilar
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Mexico City, Mexico
| | - Diana Casique-Aguirre
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Mexico City, Mexico
| | - Armando Vilchis-Ordoñez
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Hospital Infantil de México ‘Federico Gómez’, Secretaría de Salud, Mexico City, Mexico
| | - Juan Carlos Solis-Poblano
- Servicio de Hematología, Unidad Médica de Alta Especialidad, Hospital de Especialidades “Manuel Avila Camacho”, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Lilia Adela García-Stivalet
- Servicio de Hematología, Unidad Médica de Alta Especialidad, Hospital de Especialidades “Manuel Avila Camacho”, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Vanessa Terán-Cerqueda
- Servicio de Hematología, Unidad Médica de Alta Especialidad, Hospital de Especialidades “Manuel Avila Camacho”, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | | | | | | | - Karen Ayala-Contreras
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Fabiola Domínguez
- Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | | | | | - Juan Carlos Balandrán
- Department of Pathology, New York University (NYU) School of Medicine, New York, NY, United States
| | - Sonia Mayra Pérez-Tapia
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Carlos Fernández-Giménez
- Cancer Research Center-Instituto de Biología Molecular y Celular del Cáncer-Universidad de Salamanca-Centro Superior de Investigaciones Científicas (IBMCC-USAL-CSIC), Department of Medicine and Cytometry Service-Nucleus Platform, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Biomedical Research Institute of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | | | - Enrique López-Aguilar
- Coordinación de Atención Oncológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Aurora Treviño-García
- Organo de Operación Administrativa Desconcentrada, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Célida Duque-Molina
- Dirección de Prestaciones Médicas, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Laura C. Bonifaz
- Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad Médica de Alta Especialidad (UMAE) Hospital de Pediatría “Dr. Silvestre Frenk Freund” Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | | | - Dalia Ramírez-Ramírez
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
| | - Rosana Pelayo
- Laboratorio de Citómica del Cáncer Infantil, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Puebla, Mexico
- Unidad de Educación e Investigación, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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5
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Rodríguez-Bolaños M, Martínez T, Juárez S, Quiroz S, Domínguez A, Garay-Arroyo A, Sanchez MDLP, Álvarez-Buylla ER, García-Ponce B. XAANTAL1 Reveals an Additional Level of Flowering Regulation in the Shoot Apical Meristem in Response to Light and Increased Temperature in Arabidopsis. Int J Mol Sci 2023; 24:12773. [PMID: 37628953 PMCID: PMC10454237 DOI: 10.3390/ijms241612773] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Light and photoperiod are environmental signals that regulate flowering transition. In plants like Arabidopsis thaliana, this regulation relies on CONSTANS, a transcription factor that is negatively posttranslational regulated by phytochrome B during the morning, while it is stabilized by PHYA and cryptochromes 1/2 at the end of daylight hours. CO induces the expression of FT, whose protein travels from the leaves to the apical meristem, where it binds to FD to regulate some flowering genes. Although PHYB delays flowering, we show that light and PHYB positively regulate XAANTAL1 and other flowering genes in the shoot apices. Also, the genetic data indicate that XAL1 and FD participate in the same signaling pathway in flowering promotion when plants are grown under a long-day photoperiod at 22 °C. By contrast, XAL1 functions independently of FD or PIF4 to induce flowering at higher temperatures (27 °C), even under long days. Furthermore, XAL1 directly binds to FD, SOC1, LFY, and AP1 promoters. Our findings lead us to propose that light and temperature influence the floral network at the meristem level in a partially independent way of the signaling generated from the leaves.
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Affiliation(s)
- Mónica Rodríguez-Bolaños
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Tania Martínez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Saray Juárez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Stella Quiroz
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
- Laboratory of Pathogens and Host Immunity, University of Montpellier, 34 090 Montpellier, France
| | - Andrea Domínguez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Adriana Garay-Arroyo
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - María de la Paz Sanchez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Elena R. Álvarez-Buylla
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Berenice García-Ponce
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
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6
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Ayala-Angulo M, González EJ, Ureta C, Chávez-Servia JL, González-Ortega E, Vandame R, de Ávila-Bloomberg A, Martínez-Guerra G, González-Díaz S, Ruíz-González RO, Diego-Flores P, Álvarez-Buylla ER, Piñeyro-Nelson A. Local and Regional Dynamics of Native Maize Seed Lot Use by Small-Scale Producers and Their Impact on Transgene Presence in Three Mexican States. Plants (Basel) 2023; 12:2514. [PMID: 37447074 DOI: 10.3390/plants12132514] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
Mexico harbors over 50% of maize's genetic diversity in the Americas. Native maize varieties are actively managed by small-scale producers within a diverse array of cultivation systems. Seed lot use, exchange and admixture has consequences for the in situ conservation of such varieties. Here we analyze native maize seed management dynamics from 906 small-scale producers surveyed in three Mexican states: Mexico City, Oaxaca and Chiapas. Furthermore, we analyze how their management practices can relate to transgene presence, which was experimentally documented for maize samples associated with the applied surveys. Through a data mining approach, we investigated which practices might be related with a higher probability of transgene presence. The variables found to have a strong spatial association with transgene presence were: for Mexico City, maize producers with larger parcels; for Oaxaca, producer's age (43-46 years) and the sale of seed; for Chiapas, the use of agricultural machinery and younger producers (37-43 years). Additionally, transgene presence and frequency within the socioeconomic regions of Oaxaca and Chiapas was analyzed. In Oaxaca, higher transgene frequencies occurred in regions where transgene presence had been previously reported. In Chiapas, the border regions with Guatemala as well as a region where reproduction of improved seed takes place, the highest proportion of positive samples were found. A detailed mapping of regional seed markets and seed exchange sites together with deployment of national and local biosecurity measures, could help prevent the further spread of transgenes into native maize varieties, as well as improve conservation efforts.
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Affiliation(s)
- Mariana Ayala-Angulo
- Doctorado en Ciencias Agropecuarias, Departamento de Producción Agrícola y Animal, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana-Unidad Xochimilco (UAM-X), Ciudad de México 04960, Mexico
- Departamento de Producción Agrícola y Animal, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana-Unidad Xochimilco (UAM-X), Ciudad de México 04960, Mexico
| | - Edgar J González
- Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
| | - Carolina Ureta
- Investigadora por México (Conahcyt)-Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
| | | | - Emmanuel González-Ortega
- Departamento de Producción Agrícola y Animal, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana-Unidad Xochimilco (UAM-X), Ciudad de México 04960, Mexico
| | - Remy Vandame
- Departamento de Agricultura Sociedad y Ambiente, El Colegio de la Frontera Sur (ECOSUR), San Cristóbal de las Casas 29290, Mexico
| | | | | | - Said González-Díaz
- Maestría en Sociedades Sustentables, División de Ciencias Sociales y Humanidades, Universidad Autónoma Metropolitana-Unidad Xochimilco (UAM-X), Ciudad de México 04960, Mexico
| | - Rosey Obet Ruíz-González
- Departamento de Agricultura Sociedad y Ambiente, El Colegio de la Frontera Sur (ECOSUR), San Cristóbal de las Casas 29290, Mexico
| | | | - Elena R Álvarez-Buylla
- Laboratorio de Genética molecular, Epigenética, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana-Unidad Xochimilco (UAM-X), Ciudad de México 04960, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
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7
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Timilsena PR, Barrett CF, Piñeyro-Nelson A, Wafula EK, Ayyampalayam S, McNeal JR, Yukawa T, Givnish TJ, Graham SW, Pires JC, Davis JI, Ané C, Stevenson DW, Leebens-Mack J, Martínez-Salas E, Álvarez-Buylla ER, dePamphilis CW. Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages. Genome Biol Evol 2022; 15:6965378. [PMID: 36582124 PMCID: PMC9887272 DOI: 10.1093/gbe/evac183] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/13/2022] [Accepted: 12/18/2022] [Indexed: 12/31/2022] Open
Abstract
Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have evolved repeatedly in plants, particularly in monocots. Although reductive evolution of plastomes in mycoheterotrophs is well documented, the dynamics of nuclear genome evolution remains largely unknown. Transcriptome datasets were generated from four mycoheterotrophs in three families (Orchidaceae, Burmanniaceae, Triuridaceae) and related green plants and used for phylogenomic analyses to resolve relationships among the mycoheterotrophs, their relatives, and representatives across the monocots. Phylogenetic trees based on 602 genes were mostly congruent with plastome phylogenies, except for an Asparagales + Liliales clade inferred in the nuclear trees. Reduction and loss of chlorophyll synthesis and photosynthetic gene expression and relaxation of purifying selection on retained genes were progressive, with greater loss in older nonphotosynthetic lineages. One hundred seventy-four of 1375 plant benchmark universally conserved orthologous genes were undetected in any mycoheterotroph transcriptome or the genome of the mycoheterotrophic orchid Gastrodia but were expressed in green relatives, providing evidence for massively convergent gene loss in nonphotosynthetic lineages. We designate this set of deleted or undetected genes Missing in Mycoheterotrophs (MIM). MIM genes encode not only mainly photosynthetic or plastid membrane proteins but also a diverse set of plastid processes, genes of unknown function, mitochondrial, and cellular processes. Transcription of a photosystem II gene (psb29) in all lineages implies a nonphotosynthetic function for this and other genes retained in mycoheterotrophs. Nonphotosynthetic plants enable novel insights into gene function as well as gene expression shifts, gene loss, and convergence in nuclear genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | | | - Joel R McNeal
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Georgia
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Museum of Nature and Science, 1-1, Amakubo 4, Tsukuba, 305-0005, Japan
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri–Columbia, Columbia, Missouri
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 1485
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin,Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin
| | | | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 3060
| | - Esteban Martínez-Salas
- Departmento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, México
| | - Elena R Álvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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8
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Ornelas-Ayala D, Cortés-Quiñones C, Olvera-Herrera J, García-Ponce B, Garay-Arroyo A, Álvarez-Buylla ER, Sanchez MDLP. A Green Light to Switch on Genes: Revisiting Trithorax on Plants. Plants (Basel) 2022; 12:75. [PMID: 36616203 PMCID: PMC9824250 DOI: 10.3390/plants12010075] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
The Trithorax Group (TrxG) is a highly conserved multiprotein activation complex, initially defined by its antagonistic activity with the PcG repressor complex. TrxG regulates transcriptional activation by the deposition of H3K4me3 and H3K36me3 marks. According to the function and evolutionary origin, several proteins have been defined as TrxG in plants; nevertheless, little is known about their interactions and if they can form TrxG complexes. Recent evidence suggests the existence of new TrxG components as well as new interactions of some TrxG complexes that may be acting in specific tissues in plants. In this review, we bring together the latest research on the topic, exploring the interactions and roles of TrxG proteins at different developmental stages, required for the fine-tuned transcriptional activation of genes at the right time and place. Shedding light on the molecular mechanism by which TrxG is recruited and regulates transcription.
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9
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López-Ruiz BA, Quezada-Rodríguez EH, Piñeyro-Nelson A, Tovar H, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. Combined Approach of GWAS and Phylogenetic Analyses to Identify New Candidate Genes That Participate in Arabidopsis thaliana Primary Root Development Using Cellular Measurements and Primary Root Length. Plants (Basel) 2022; 11:3162. [PMID: 36432890 PMCID: PMC9697774 DOI: 10.3390/plants11223162] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Genome-wide association studies (GWAS) have allowed the identification of different loci associated with primary root (PR) growth, and Arabidopsis is an excellent model for these studies. The PR length is controlled by cell proliferation, elongation, and differentiation; however, the specific contribution of proliferation and differentiation in the control of PR growth is still poorly studied. To this end, we analyzed 124 accessions and used a GWAS approach to identify potential causal genomic regions related to four traits: PR length, growth rate, cell proliferation and cell differentiation. Twenty-three genes and five statistically significant SNPs were identified. The SNP with the highest score mapped to the fifth exon of NAC048 and this change makes a missense variant in only 33.3% of the accessions with a large PR, compared with the accessions with a short PR length. Moreover, we detected five more SNPs in this gene and in NAC3 that allow us to discover closely related accessions according to the phylogenetic tree analysis. We also found that the association between genetic variants among the 18 genes with the highest scores in our GWAS and the phenotypic classes into which we divided our accessions are not straightforward and likely follow historical patterns.
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Affiliation(s)
- Brenda Anabel López-Ruiz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Elsa H. Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México 04510, Mexico
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Hugo Tovar
- División de Genómica Computacional, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México 14610, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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10
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Bensussen A, Valcarcel A, Álvarez-Buylla ER, Díaz J. ORF8 and Health Complications of COVID-19 in Down Syndrome Patients. Front Genet 2022; 13:830426. [PMID: 35222544 PMCID: PMC8864084 DOI: 10.3389/fgene.2022.830426] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Antonio Bensussen
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Antonio Valcarcel
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Elena R. Álvarez-Buylla
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- *Correspondence: Elena R. Álvarez-Buylla, ; José Díaz,
| | - José Díaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
- *Correspondence: Elena R. Álvarez-Buylla, ; José Díaz,
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11
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Hernández-Herrera P, Ugartechea-Chirino Y, Torres-Martínez HH, Arzola AV, Chairez-Veloz JE, García-Ponce B, Sánchez MDLP, Garay-Arroyo A, Álvarez-Buylla ER, Dubrovsky JG, Corkidi G. Live Plant Cell Tracking: Fiji plugin to analyze cell proliferation dynamics and understand morphogenesis. Plant Physiol 2022; 188:846-860. [PMID: 34791452 PMCID: PMC8825436 DOI: 10.1093/plphys/kiab530] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/19/2021] [Indexed: 05/13/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) primary and lateral roots (LRs) are well suited for 3D and 4D microscopy, and their development provides an ideal system for studying morphogenesis and cell proliferation dynamics. With fast-advancing microscopy techniques used for live-imaging, whole tissue data are increasingly available, yet present the great challenge of analyzing complex interactions within cell populations. We developed a plugin "Live Plant Cell Tracking" (LiPlaCeT) coupled to the publicly available ImageJ image analysis program and generated a pipeline that allows, with the aid of LiPlaCeT, 4D cell tracking and lineage analysis of populations of dividing and growing cells. The LiPlaCeT plugin contains ad hoc ergonomic curating tools, making it very simple to use for manual cell tracking, especially when the signal-to-noise ratio of images is low or variable in time or 3D space and when automated methods may fail. Performing time-lapse experiments and using cell-tracking data extracted with the assistance of LiPlaCeT, we accomplished deep analyses of cell proliferation and clonal relations in the whole developing LR primordia and constructed genealogical trees. We also used cell-tracking data for endodermis cells of the root apical meristem (RAM) and performed automated analyses of cell population dynamics using ParaView software (also publicly available). Using the RAM as an example, we also showed how LiPlaCeT can be used to generate information at the whole-tissue level regarding cell length, cell position, cell growth rate, cell displacement rate, and proliferation activity. The pipeline will be useful in live-imaging studies of roots and other plant organs to understand complex interactions within proliferating and growing cell populations. The plugin includes a step-by-step user manual and a dataset example that are available at https://www.ibt.unam.mx/documentos/diversos/LiPlaCeT.zip.
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Affiliation(s)
- Paul Hernández-Herrera
- Laboratorio de Imágenes y Visión por Computadora, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Yamel Ugartechea-Chirino
- Departamento de Ecología Funcional, Instituto de Ecología, Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Héctor H Torres-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Alejandro V Arzola
- Instituto de Física, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - José Eduardo Chairez-Veloz
- Departamento de Control Automático, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Cd. de México, C.P. 07350, Mexico
| | - Berenice García-Ponce
- Departamento de Ecología Funcional, Instituto de Ecología, Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - María de la Paz Sánchez
- Departamento de Ecología Funcional, Instituto de Ecología, Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Adriana Garay-Arroyo
- Departamento de Ecología Funcional, Instituto de Ecología, Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Elena R Álvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
| | - Gabriel Corkidi
- Laboratorio de Imágenes y Visión por Computadora, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cd. de México, C.P. 04510, Mexico
- Author for communication:
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12
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Alejo-Vinogradova MT, Ornelas-Ayala D, Vega-León R, Garay-Arroyo A, García-Ponce B, R Álvarez-Buylla E, Sanchez MDLP. Unraveling the role of epigenetic regulation in asymmetric cell division during plant development. J Exp Bot 2022; 73:38-49. [PMID: 34518884 DOI: 10.1093/jxb/erab421] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
Asymmetric cell divisions are essential to generate different cellular lineages. In plants, asymmetric cell divisions regulate the correct formation of the embryo, stomatal cells, apical and root meristems, and lateral roots. Current knowledge of regulation of asymmetric cell divisions suggests that, in addition to the function of key transcription factor networks, epigenetic mechanisms play crucial roles. Therefore, we highlight the importance of epigenetic regulation and chromatin dynamics for integration of signals and specification of cells that undergo asymmetric cell divisions, as well as for cell maintenance and cell fate establishment of both progenitor and daughter cells. We also discuss the polarization and segregation of cell components to ensure correct epigenetic memory or resetting of epigenetic marks during asymmetric cell divisions.
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Affiliation(s)
- M Teresa Alejo-Vinogradova
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - Diego Ornelas-Ayala
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - Rosario Vega-León
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
| | - María de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas. Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria. UNAM, México D.F. 04510, México
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13
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Chávez-Hernández EC, Quiroz S, García-Ponce B, Álvarez-Buylla ER. The flowering transition pathways converge into a complex gene regulatory network that underlies the phase changes of the shoot apical meristem in Arabidopsis thaliana. Front Plant Sci 2022; 13:852047. [PMID: 36017258 PMCID: PMC9396034 DOI: 10.3389/fpls.2022.852047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/04/2022] [Indexed: 05/08/2023]
Abstract
Post-embryonic plant development is characterized by a period of vegetative growth during which a combination of intrinsic and extrinsic signals triggers the transition to the reproductive phase. To understand how different flowering inducing and repressing signals are associated with phase transitions of the Shoot Apical Meristem (SAM), we incorporated available data into a dynamic gene regulatory network model for Arabidopsis thaliana. This Flowering Transition Gene Regulatory Network (FT-GRN) formally constitutes a dynamic system-level mechanism based on more than three decades of experimental data on flowering. We provide novel experimental data on the regulatory interactions of one of its twenty-three components: a MADS-box transcription factor XAANTAL2 (XAL2). These data complement the information regarding flowering transition under short days and provides an example of the type of questions that can be addressed by the FT-GRN. The resulting FT-GRN is highly connected and integrates developmental, hormonal, and environmental signals that affect developmental transitions at the SAM. The FT-GRN is a dynamic multi-stable Boolean system, with 223 possible initial states, yet it converges into only 32 attractors. The latter are coherent with the expression profiles of the FT-GRN components that have been experimentally described for the developmental stages of the SAM. Furthermore, the attractors are also highly robust to initial states and to simulated perturbations of the interaction functions. The model recovered the meristem phenotypes of previously described single mutants. We also analyzed the attractors landscape that emerges from the postulated FT-GRN, uncovering which set of signals or components are critical for reproductive competence and the time-order transitions observed in the SAM. Finally, in the context of such GRN, the role of XAL2 under short-day conditions could be understood. Therefore, this model constitutes a robust biological module and the first multi-stable, dynamical systems biology mechanism that integrates the genetic flowering pathways to explain SAM phase transitions.
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Affiliation(s)
- Elva C. Chávez-Hernández
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Stella Quiroz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Berenice García-Ponce,
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Elena R. Álvarez-Buylla,
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14
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Valcarcel A, Bensussen A, Álvarez-Buylla ER, Díaz J. Structural Analysis of SARS-CoV-2 ORF8 Protein: Pathogenic and Therapeutic Implications. Front Genet 2021; 12:693227. [PMID: 34552615 PMCID: PMC8450498 DOI: 10.3389/fgene.2021.693227] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 04/10/2021] [Accepted: 07/29/2021] [Indexed: 12/27/2022] Open
Abstract
Current therapeutic strategies and vaccines against SARS-CoV-2 are mainly focused on the Spike protein despite there are other viral proteins with important roles in COVID-19 pathogenicity. For example, ORF8 restructures vesicular trafficking in the host cell, impacts intracellular immunity through the IFN-I signaling, and growth pathways through the mitogen-activated protein kinases (MAPKs). In this mini-review, we analyze the main structural similarities of ORF8 with immunological molecules such as IL-1, contributing to the immunological deregulation observed in COVID-19. We also propose that the blockage of some effector functions of ORF8 with Rapamycin, such as the mTORC1 activation through MAPKs 40 pathway, with Rapamycin, can be a promising approach to reduce COVID-19 mortality.
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Affiliation(s)
- Antonio Valcarcel
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Antonio Bensussen
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Elena R Álvarez-Buylla
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evoluciónde Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - José Díaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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15
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Ornelas-Ayala D, Garay-Arroyo A, García-Ponce B, R. Álvarez-Buylla E, Sanchez MDLP. The Epigenetic Faces of ULTRAPETALA1. Front Plant Sci 2021; 12:637244. [PMID: 33719312 PMCID: PMC7947857 DOI: 10.3389/fpls.2021.637244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/21/2021] [Indexed: 05/27/2023]
Abstract
ULTRAPETALA1 (ULT1) is a versatile plant-exclusive protein, initially described as a trithorax group (TrxG) factor that regulates transcriptional activation and counteracts polycomb group (PcG) repressor function. As part of TrxG, ULT1 interacts with ARABIDOPSIS TRITHORAX1 (ATX1) to regulate H3K4me3 activation mark deposition. However, our recent studies indicate that ULT1 can also act independently of ATX1. Moreover, the ULT1 ability to interact with transcription factors (TFs) and PcG proteins indicates that it is a versatile protein with other roles. Therefore, in this work we revised recent information about the function of Arabidopsis ULT1 to understand the roles of ULT1 in plant development. Furthermore, we discuss the molecular mechanisms of ULT1, highlighting its epigenetic role, in which ULT1 seems to have characteristics of an epigenetic molecular switch that regulates repression and activation processes via TrxG and PcG complexes.
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Affiliation(s)
- Diego Ornelas-Ayala
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, Mexico
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16
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Díaz J, Álvarez-Buylla ER. Spatio-Temporal Dynamics of the Patterning of Arabidopsis Flower Meristem. Front Plant Sci 2021; 12:585139. [PMID: 33659013 PMCID: PMC7917056 DOI: 10.3389/fpls.2021.585139] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
The qualitative model presented in this work recovers the onset of the four fields that correspond to those of each floral organ whorl of Arabidopsis flower, suggesting a mechanism for the generation of the positional information required for the differential expression of the A, B, and C identity genes according to the ABC model for organ determination during early stages of flower development. Our model integrates a previous model for the emergence of WUS pattern in the floral meristem, and shows that this pre-pattern is a necessary but not sufficient condition for the posterior information of the four fields predicted by the ABC model. Furthermore, our model predicts that LFY diffusion along the L1 layer of cells is not a necessary condition for the patterning of the floral meristem.
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Affiliation(s)
- José Díaz
- Laboratorio de Dinámica de Redes Genéticas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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17
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García-Gómez ML, Garay-Arroyo A, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER. Hormonal Regulation of Stem Cell Proliferation at the Arabidopsis thaliana Root Stem Cell Niche. Front Plant Sci 2021; 12:628491. [PMID: 33747009 PMCID: PMC7966715 DOI: 10.3389/fpls.2021.628491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/12/2021] [Indexed: 05/13/2023]
Abstract
The root stem cell niche (SCN) of Arabidopsis thaliana consists of the quiescent center (QC) cells and the surrounding initial stem cells that produce progeny to replenish all the tissues of the root. The QC cells divide rather slowly relative to the initials, yet most root tissues can be formed from these cells, depending on the requirements of the plant. Hormones are fundamental cues that link such needs with the cell proliferation and differentiation dynamics at the root SCN. Nonetheless, the crosstalk between hormone signaling and the mechanisms that regulate developmental adjustments is still not fully understood. Developmental transcriptional regulatory networks modulate hormone biosynthesis, metabolism, and signaling, and conversely, hormonal responses can affect the expression of transcription factors involved in the spatiotemporal patterning at the root SCN. Hence, a complex genetic-hormonal regulatory network underlies root patterning, growth, and plasticity in response to changing environmental conditions. In this review, we summarize the scientific literature regarding the role of hormones in the regulation of QC cell proliferation and discuss how hormonal signaling pathways may be integrated with the gene regulatory network that underlies cell fate in the root SCN. The conceptual framework we present aims to contribute to the understanding of the mechanisms by which hormonal pathways act as integrators of environmental cues to impact on SCN activity.
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Affiliation(s)
- Mónica L. García-Gómez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- *Correspondence: Elena R. Álvarez-Buylla,
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18
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Zluhan-Martínez E, López-Ruíz BA, García-Gómez ML, García-Ponce B, de la Paz Sánchez M, Álvarez-Buylla ER, Garay-Arroyo A. Integrative Roles of Phytohormones on Cell Proliferation, Elongation and Differentiation in the Arabidopsis thaliana Primary Root. Front Plant Sci 2021; 12:659155. [PMID: 33981325 PMCID: PMC8107238 DOI: 10.3389/fpls.2021.659155] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/24/2021] [Indexed: 05/17/2023]
Abstract
The growth of multicellular organisms relies on cell proliferation, elongation and differentiation that are tightly regulated throughout development by internal and external stimuli. The plasticity of a growth response largely depends on the capacity of the organism to adjust the ratio between cell proliferation and cell differentiation. The primary root of Arabidopsis thaliana offers many advantages toward understanding growth homeostasis as root cells are continuously produced and move from cell proliferation to elongation and differentiation that are processes spatially separated and could be studied along the longitudinal axis. Hormones fine tune plant growth responses and a huge amount of information has been recently generated on the role of these compounds in Arabidopsis primary root development. In this review, we summarized the participation of nine hormones in the regulation of the different zones and domains of the Arabidopsis primary root. In some cases, we found synergism between hormones that function either positively or negatively in proliferation, elongation or differentiation. Intriguingly, there are other cases where the interaction between hormones exhibits unexpected results. Future analysis on the molecular mechanisms underlying crosstalk hormone action in specific zones and domains will unravel their coordination over PR development.
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Affiliation(s)
- Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Brenda Anabel López-Ruíz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Mónica L. García-Gómez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- *Correspondence: Adriana Garay-Arroyo,
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19
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López-Ruiz BA, Zluhan-Martínez E, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. Interplay between Hormones and Several Abiotic Stress Conditions on Arabidopsis thaliana Primary Root Development. Cells 2020; 9:E2576. [PMID: 33271980 PMCID: PMC7759812 DOI: 10.3390/cells9122576] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 01/17/2023] Open
Abstract
As sessile organisms, plants must adjust their growth to withstand several environmental conditions. The root is a crucial organ for plant survival as it is responsible for water and nutrient acquisition from the soil and has high phenotypic plasticity in response to a lack or excess of them. How plants sense and transduce their external conditions to achieve development, is still a matter of investigation and hormones play fundamental roles. Hormones are small molecules essential for plant growth and their function is modulated in response to stress environmental conditions and internal cues to adjust plant development. This review was motivated by the need to explore how Arabidopsis thaliana primary root differentially sense and transduce external conditions to modify its development and how hormone-mediated pathways contribute to achieve it. To accomplish this, we discuss available data of primary root growth phenotype under several hormone loss or gain of function mutants or exogenous application of compounds that affect hormone concentration in several abiotic stress conditions. This review shows how different hormones could promote or inhibit primary root development in A. thaliana depending on their growth in several environmental conditions. Interestingly, the only hormone that always acts as a promoter of primary root development is gibberellins.
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Affiliation(s)
- Brenda Anabel López-Ruiz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
| | - Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico
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20
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García-Gómez ML, Castillo-Jiménez A, Martínez-García JC, Álvarez-Buylla ER. Multi-level gene regulatory network models to understand complex mechanisms underlying plant development. Curr Opin Plant Biol 2020; 57:171-179. [PMID: 33171396 DOI: 10.1016/j.pbi.2020.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/12/2020] [Accepted: 09/24/2020] [Indexed: 05/07/2023]
Abstract
Patterning in plant development is the emergent outcome of the feedback-based interplay between tissue-coupled intracellular regulatory networks and physicochemical fields. This interplay gives rise to dynamics that evolve on a wide spectrum of spatiotemporal scales. This imposes important challenges for computational approaches to model the dynamics of plant development. These challenges are being tackled in recent times by computational and mathematical advances that have made progress in the modelling of regulatory networks, as well as in approaches to couple the latter to physicochemical fields. Efforts in this direction are fundamental to identify the dynamical constraints that emerge from non-cellular autonomous activity in cell-fate decisions and patterning, and requires an understanding of how multi-level and multi-scale processes are coupled. Here, we discuss the use of multi-level modeling and simulation tools for the study of multicellular systems, with emphasis on plants. As illustrative examples, we discuss recent works elucidating the mechanisms that underlie patterning in the root meristem of Arabidopsis thaliana, and in plant responses to environmental conditions.
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Affiliation(s)
- Mónica L García-Gómez
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, Mexico; Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, Mexico
| | - Aaron Castillo-Jiménez
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, Mexico; PhD Program on Biomedical Science, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, Mexico
| | | | - Elena R Álvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, Mexico; Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, Mexico.
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21
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Enciso J, Mendoza L, Álvarez-Buylla ER, Pelayo R. Dynamical modeling predicts an inflammation-inducible CXCR7+ B cell precursor with potential implications in lymphoid blockage pathologies. PeerJ 2020; 8:e9902. [PMID: 33062419 PMCID: PMC7531334 DOI: 10.7717/peerj.9902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 03/24/2020] [Accepted: 08/18/2020] [Indexed: 12/16/2022] Open
Abstract
Background The blockage at the early B lymphoid cell development pathway within the bone marrow is tightly associated with hematopoietic and immune diseases, where the disruption of basal regulatory networks prevents the continuous replenishment of functional B cells. Dynamic computational models may be instrumental for the comprehensive understanding of mechanisms underlying complex differentiation processes and provide novel prediction/intervention platforms to reinvigorate the system. Methods By reconstructing a three-module regulatory network including genetic transcription, intracellular transduction, and microenvironment communication, we have investigated the early B lineage cell fate decisions in normal and pathological settings. The early B cell differentiation network was simulated as a Boolean model and then transformed, using fuzzy logic, to a continuous model. We tested null and overexpression mutants to analyze the emergent behavior of the network. Due to its importance in inflammation, we investigated the effect of NFkB induction at different early B cell differentiation stages. Results While the exhaustive synchronous and asynchronous simulation of the early B cell regulatory network (eBCRN) reproduced the configurations of the hematopoietic progenitors and early B lymphoid precursors of the pathway, its simulation as a continuous model with fuzzy logics suggested a transient IL-7R+ ProB-to-Pre-B subset expressing pre-BCR and a series of dominant B-cell transcriptional factors. This conspicuous differentiating cell population up-regulated CXCR7 and reduced CXCR4 and FoxO1 expression levels. Strikingly, constant but intermediate NFkB signaling at specific B cell differentiation stages allowed stabilization of an aberrant CXCR7+ pre-B like phenotype with apparent affinity to proliferative signals, while under constitutive overactivation of NFkB, such cell phenotype was aberrantly exacerbated from the earliest stage of common lymphoid progenitors. Our mutant models revealed an abnormal delay in the BCR assembly upon NFkB activation, concomitant to sustained Flt3 signaling, down-regulation of Ebf1, Irf4 and Pax5 genes transcription, and reduced Ig recombination, pointing to a potential lineage commitment blockage. Discussion For the first time, an inducible CXCR7hi B cell precursor endowed with the potential capability of shifting central lymphoid niches, is inferred by computational modeling. Its phenotype is compatible with that of leukemia-initiating cells and might be the foundation that bridges inflammation with blockage-related malignancies and a wide range of immunological diseases. Besides the predicted differentiation impairment, inflammation-inducible phenotypes open the possibility of newly formed niches colonized by the reported precursor. Thus, emergent bone marrow ecosystems are predicted following a pro-inflammatory induction, that may lead to hematopoietic instability associated to blockage pathologies.
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Affiliation(s)
- Jennifer Enciso
- Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Metepec, Puebla, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, México.,Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, México
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, México
| | | | - Rosana Pelayo
- Centro de Investigación Biomédica de Oriente, Delegación Puebla, Instituto Mexicano del Seguro Social, Metepec, Puebla, Mexico
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22
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Zluhan-Martínez E, Pérez-Koldenkova V, Ponce-Castañeda MV, Sánchez MDLP, García-Ponce B, Miguel-Hernández S, Álvarez-Buylla ER, Garay-Arroyo A. Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation. Int J Mol Sci 2020; 21:E4925. [PMID: 32664691 PMCID: PMC7404004 DOI: 10.3390/ijms21144925] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/29/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
The Retinoblastoma protein (pRb) is a key cell cycle regulator conserved in a wide variety of organisms. Experimental analysis of pRb's functions in animals and plants has revealed that this protein participates in cell proliferation and differentiation processes. In addition, pRb in animals and its orthologs in plants (RBR), are part of highly conserved protein complexes which suggest the possibility that analogies exist not only between functions carried out by pRb orthologs themselves, but also in the structure and roles of the protein networks where these proteins are involved. Here, we present examples of pRb/RBR participation in cell cycle control, cell differentiation, and in the regulation of epigenetic changes and chromatin remodeling machinery, highlighting the similarities that exist between the composition of such networks in plants and animals.
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Affiliation(s)
- Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
- Posgrado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán 04510, Mexico
| | - Vadim Pérez-Koldenkova
- Laboratorio Nacional de Microscopía Avanzada, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc, 330. Col. Doctores, Alc. Cuauhtémoc 06720, Mexico;
| | - Martha Verónica Ponce-Castañeda
- Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico;
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Sergio Miguel-Hernández
- Laboratorio de Citopatología Ambiental, Departamento de Morfología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Zacatenco, Calle Wilfrido Massieu Esquina Cda, Manuel Stampa 07738, Mexico;
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
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23
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Abstract
The current pandemic has rocked the lives of human beings every-where in ways never imagined, forcing us to question where our civilization is headed. In this article, we explore and discuss scien-tifi c evidence that helps explain recent events in the context of the COVID-19 pandemic.COVID-19 is caused by infection with a zoonotic-origin novel virus, SARS-CoV-2, that is genetically close to two coronavirus types iso-lated in bats. The transmission dynamics to humans from the original and intermediary hosts remain poorly understood, but it is highly likely that the SARS-CoV-2 virus infected humans after undergoing an inter-species transfer from bats to an intermediate species, and from there to human beings. Crossing the species barrier is largely fostered by industrial-scale agricultural practices that simplify original ecosystem connections by reducing biodiversity, facilitating the emergence of new infectious diseases. The scientifi c community has played an exemplary role in responding to this global emergency, working to fi nd timely, relevant solutions for governments and society as a whole. We need to take this opportunity to promote a global and open science that delves into the interrelation-ships of the biological, environmental, social and economic dimen-sions of this and other diseases while questioning current modes of production and their impact on the environment, and thus on human health worldwide. Keywords: Coronavirus infections; communicable diseases; zoonoses; ecosystems; technology, industry, and agriculture; pandemics; global health; Mexico.
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24
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Abstract
Endothelial cells (ECs) form the lining of lymph and blood vessels. Changes in tissue requirements or wounds may cause ECs to behave as tip or stalk cells. Alternatively, they may differentiate into mesenchymal cells (MCs). These processes are known as EC activation and endothelial-to-mesenchymal transition (EndMT), respectively. EndMT, Tip, and Stalk EC behaviors all require SNAI1, SNAI2, and Matrix metallopeptidase (MMP) function. However, only EndMT inhibits the expression of VE-cadherin, PECAM1, and VEGFR2, and also leads to EC detachment. Physiologically, EndMT is involved in heart valve development, while a defective EndMT regulation is involved in the physiopathology of cardiovascular malformations, congenital heart disease, systemic and organ fibrosis, pulmonary arterial hypertension, and atherosclerosis. Therefore, the control of EndMT has many promising potential applications in regenerative medicine. Despite the fact that many molecular components involved in EC activation and EndMT have been characterized, the system-level molecular mechanisms involved in this process have not been elucidated. Toward this end, hereby we present Boolean network model of the molecular involved in the regulation of EC activation and EndMT. The simulated dynamic behavior of our model reaches fixed and cyclic patterns of activation that correspond to the expected EC and MC cell types and behaviors, recovering most of the specific effects of simple gain and loss-of-function mutations as well as the conditions associated with the progression of several diseases. Therefore, our model constitutes a theoretical framework that can be used to generate hypotheses and guide experimental inquiry to comprehend the regulatory mechanisms behind EndMT. Our main findings include that both the extracellular microevironment and the pattern of molecular activity within the cell regulate EndMT. EndMT requires a lack of VEGFA and sufficient oxygen in the extracellular microenvironment as well as no FLI1 and GATA2 activity within the cell. Additionally Tip cells cannot undergo EndMT directly. Furthermore, the specific conditions that are sufficient to trigger EndMT depend on the specific pattern of molecular activation within the cell.
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Affiliation(s)
- Nathan Weinstein
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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25
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Ornelas-Ayala D, Vega-León R, Petrone-Mendoza E, Garay-Arroyo A, García-Ponce B, Álvarez-Buylla ER, Sanchez MDLP. ULTRAPETALA1 maintains Arabidopsis root stem cell niche independently of ARABIDOPSIS TRITHORAX1. New Phytol 2020; 225:1261-1272. [PMID: 31545512 DOI: 10.1111/nph.16213] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 05/09/2019] [Accepted: 09/14/2019] [Indexed: 05/26/2023]
Abstract
During plant development, morphogenetic processes rely on the activity of meristems. Meristem homeostasis depends on a complex regulatory network constituted by different factors and hormone signaling that regulate gene expression to coordinate the correct balance between cell proliferation and differentiation. ULTRAPETALA1, a transcriptional regulatory protein described as an Arabidopsis Trithorax group factor, has been characterized as a regulator of the shoot and floral meristems activity. Here, we highlight the role of ULTRAPETALA1 in root stem cell niche maintenance. We found that ULTRAPETALA1 is required to regulate both the quiescent center cell division rate and auxin signaling at the root tip. Furthermore, ULTRAPETALA1 regulates columella stem cell differentiation. These roles are independent of the ARABIDOPSIS TRITHORAX1, suggesting a different mechanism by which ULTRAPETALA1 can act in the root apical meristem of Arabidopsis. This work introduces a new component of the regulatory network needed for the root stem cell niche maintenance.
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Affiliation(s)
- Diego Ornelas-Ayala
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, CdMex, 04510, Mexico
| | - Rosario Vega-León
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, CdMex, 04510, Mexico
| | - Emilio Petrone-Mendoza
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, CdMex, 04510, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, CdMex, 04510, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, CdMex, 04510, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, CdMex, 04510, Mexico
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, CdMex, 04510, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, CdMex, 04510, Mexico
| | - María de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, Mexico City, CdMex, 04510, Mexico
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Mexico City, CdMex, 04510, Mexico
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26
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Castelán-Muñoz N, Herrera J, Cajero-Sánchez W, Arrizubieta M, Trejo C, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. MADS-Box Genes Are Key Components of Genetic Regulatory Networks Involved in Abiotic Stress and Plastic Developmental Responses in Plants. Front Plant Sci 2019; 10:853. [PMID: 31354752 PMCID: PMC6636334 DOI: 10.3389/fpls.2019.00853] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 06/13/2019] [Indexed: 05/05/2023]
Abstract
Plants, as sessile organisms, adapt to different stressful conditions, such as drought, salinity, extreme temperatures, and nutrient deficiency, via plastic developmental and growth responses. Depending on the intensity and the developmental phase in which it is imposed, a stress condition may lead to a broad range of responses at the morphological, physiological, biochemical, and molecular levels. Transcription factors are key components of regulatory networks that integrate environmental cues and concert responses at the cellular level, including those that imply a stressful condition. Despite the fact that several studies have started to identify various members of the MADS-box gene family as important molecular components involved in different types of stress responses, we still lack an integrated view of their role in these processes. In this review, we analyze the function and regulation of MADS-box gene family members in response to drought, salt, cold, heat, and oxidative stress conditions in different developmental processes of several plants. In addition, we suggest that MADS-box genes are key components of gene regulatory networks involved in plant responses to stress and plant developmental plasticity in response to seasonal changes in environmental conditions.
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Affiliation(s)
- Natalia Castelán-Muñoz
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Postgrado en Recursos Genéticos y Productividad-Fisiología Vegetal, Colegio de Postgraduados, Texcoco, Mexico
| | - Joel Herrera
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wendy Cajero-Sánchez
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Maite Arrizubieta
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos Trejo
- Postgrado en Botánica, Colegio de Postgraduados, Texcoco, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética y Desarrollo de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Adriana Garay-Arroyo
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27
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Cajero Sánchez W, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. Identifying the transition to the maturation zone in three ecotypes of Arabidopsis thaliana roots. Commun Integr Biol 2017; 11:e1395993. [PMID: 29497470 PMCID: PMC5824961 DOI: 10.1080/19420889.2017.1395993] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 09/20/2017] [Revised: 10/17/2017] [Accepted: 10/18/2017] [Indexed: 11/23/2022] Open
Abstract
The Arabidopsis thaliana (hereafter Arabidopsis) root has become a useful model for studying how organ morphogenesis emerge from the coordination and balance of cell proliferation and differentiation, as both processes may be observed and quantified in the root at different stages of development. Hence, being able to objectively identify and delimit the different stages of root development has been very important. Up to now, three different zones along the longitudinal axis of the primary root of Arabidopsis, have been identified: the root apical meristematic zone (RAM) with two domains [the proliferative (PD) and the transition domain (TD)], the elongation zone (EZ) and the maturation zone (MZ). We previously reported a method to quantify the length of the cells of the meristematic and the elongation zone, as well as the boundaries or transitions between the root domains along the growing part of the Arabidopsis root. In this study, we provide a more accurate criterion to identify the MZ. Traditionally, the transition between the EZ to the MZ has been established by the emergence of the first root-hair bulge in the epidermis, because this emergence coincides with cell maturation in this cell type. But we have found here that after the emergence of the first root-hair bulge some cells continue to elongate and we have confirmed this in three different Arabidopsis ecotypes. We established the limit between the EZ and the MZ by looking for the closest cortical cell with a longer length than the average cell length of 10 cells after the cortical cell closest to the epidermal cell with the first root-hair bulge in these three ecotypes. In Col-0 and Ws this cell is four cells above the one with the root hair bulge and, in the Ler ecotype, this cell is five cells above. To unambiguously identifying the site at which cells stop elongating and attain their final length and fate at the MZ, we propose to calculate the length of completely elongated cortical cells counting 10 cells starting from the sixth cell above the cortical cell closest to the epidermal cell with the first root-hair bulge. We validated this proposal in the three ecotypes analyzed and consider that this proposal may aid at having a more objective way to characterize root phenotypes and compare among them.
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Affiliation(s)
- Wendy Cajero Sánchez
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, Ciudad de México, Mexico
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, Ciudad de México, Mexico
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28
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Azpeitia E, Muñoz S, González-Tokman D, Martínez-Sánchez ME, Weinstein N, Naldi A, Álvarez-Buylla ER, Rosenblueth DA, Mendoza L. Erratum: The combination of the functionalities of feedback circuits is determinant for the attractors’ number and size in pathway-like Boolean networks. Sci Rep 2017; 7:44964. [PMID: 28327650 PMCID: PMC5361093 DOI: 10.1038/srep44964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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García-Gómez ML, Azpeitia E, Álvarez-Buylla ER. A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana. PLoS Comput Biol 2017; 13:e1005488. [PMID: 28426669 PMCID: PMC5417714 DOI: 10.1371/journal.pcbi.1005488] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 08/26/2016] [Revised: 05/04/2017] [Accepted: 03/30/2017] [Indexed: 11/18/2022] Open
Abstract
The study of the concerted action of hormones and transcription factors is fundamental to understand cell differentiation and pattern formation during organ development. The root apical meristem of Arabidopsis thaliana is a useful model to address this. It has a stem cell niche near its tip conformed of a quiescent organizer and stem or initial cells around it, then a proliferation domain followed by a transition domain, where cells diminish division rate before transiting to the elongation zone; here, cells grow anisotropically prior to their final differentiation towards the plant base. A minimal model of the gene regulatory network that underlies cell-fate specification and patterning at the root stem cell niche was proposed before. In this study, we update and couple such network with both the auxin and cytokinin hormone signaling pathways to address how they collectively give rise to attractors that correspond to the genetic and hormonal activity profiles that are characteristic of different cell types along A. thaliana root apical meristem. We used a Boolean model of the genetic-hormonal regulatory network to integrate known and predicted regulatory interactions into alternative models. Our analyses show that, after adding some putative missing interactions, the model includes the necessary and sufficient components and regulatory interactions to recover attractors characteristic of the root cell types, including the auxin and cytokinin activity profiles that correlate with different cellular behaviors along the root apical meristem. Furthermore, the model predicts the existence of activity configurations that could correspond to the transition domain. The model also provides a possible explanation for apparently paradoxical cellular behaviors in the root meristem. For example, how auxin may induce and at the same time inhibit WOX5 expression. According to the model proposed here the hormonal regulation of WOX5 might depend on the cell type. Our results illustrate how non-linear multi-stable qualitative network models can aid at understanding how transcriptional regulators and hormonal signaling pathways are dynamically coupled and may underlie both the acquisition of cell fate and the emergence of hormonal activity profiles that arise during complex organ development.
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Affiliation(s)
- Mónica L. García-Gómez
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Eugenio Azpeitia
- INRIA project-team Virtual Plants, joint with CIRAD and INRA, Montpellier, France
| | - Elena R. Álvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
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30
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Azpeitia E, Muñoz S, González-Tokman D, Martínez-Sánchez ME, Weinstein N, Naldi A, Álvarez-Buylla ER, Rosenblueth DA, Mendoza L. The combination of the functionalities of feedback circuits is determinant for the attractors' number and size in pathway-like Boolean networks. Sci Rep 2017; 7:42023. [PMID: 28186191 PMCID: PMC5301197 DOI: 10.1038/srep42023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 01/04/2017] [Indexed: 02/06/2023] Open
Abstract
Molecular regulation was initially assumed to follow both a unidirectional and a hierarchical organization forming pathways. Regulatory processes, however, form highly interlinked networks with non-hierarchical and non-unidirectional structures that contain statistically overrepresented circuits or motifs. Here, we analyze the behavior of pathways containing non-unidirectional (i.e. bidirectional) and non-hierarchical interactions that create motifs. In comparison with unidirectional and hierarchical pathways, our pathways have a high diversity of behaviors, characterized by the size and number of attractors. Motifs have been studied individually showing that feedback circuit motifs regulate the number and size of attractors. It is less clear what happens in molecular networks that usually contain multiple feedbacks. Here, we find that the way feedback circuits couple to each other (i.e., the combination of the functionalities of feedback circuits) regulate both the number and size of the attractors. We show that the different expected results of epistasis analysis (a method to infer regulatory interactions) are produced by many non-hierarchical and non-unidirectional structures. Thus, these structures cannot be correctly inferred by epistasis analysis. Finally, we show that the combinations of functionalities, combined with other network properties, allow for a better characterization of regulatory structures.
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Affiliation(s)
- Eugenio Azpeitia
- INRIA project-team Virtual Plants, joint with CIRAD and INRA, Montpellier Cedex 5, France
| | - Stalin Muñoz
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Apdo. 20-126, 01000 México, D.F., México
| | - Daniel González-Tokman
- CONACYT, Instituto de Ecología, A. C., Antiguo camino a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, México
| | - Mariana Esther Martínez-Sánchez
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, México.,Instituto de Ecología, Universidad Nacional Autónoma de México, México
| | - Nathan Weinstein
- ABACUS: Laboratorio de Matemáticas Aplicadas y Cómputo de Alto Rendimiento del Departamento de Matemáticas, Centro de Investigación y de Estudios Avanzados CINVESTAV-IPN, Carretera México-Toluca Km 38.5, La Marquesa, Ocoyoacac, Estado de México, 52740 México
| | | | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, México.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México
| | - David A Rosenblueth
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Apdo. 20-126, 01000 México, D.F., México
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México
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Velderraín JD, Martínez-García JC, Álvarez-Buylla ER. Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction. Methods Mol Biol 2017. [PMID: 28623593 DOI: 10.1007/978-1-4939-7125-1_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mathematical models based on dynamical systems theory are well-suited tools for the integration of available molecular experimental data into coherent frameworks in order to propose hypotheses about the cooperative regulatory mechanisms driving developmental processes. Computational analysis of the proposed models using well-established methods enables testing the hypotheses by contrasting predictions with observations. Within such framework, Boolean gene regulatory network dynamical models have been extensively used in modeling plant development. Boolean models are simple and intuitively appealing, ideal tools for collaborative efforts between theorists and experimentalists. In this chapter we present protocols used in our group for the study of diverse plant developmental processes. We focus on conceptual clarity and practical implementation, providing directions to the corresponding technical literature.
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Affiliation(s)
- José Dávila Velderraín
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, México, DF, 04510, Mexico
| | | | - Elena R Álvarez-Buylla
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, México, DF, 04510, Mexico. .,Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 3000, Ciudad Universitaria, Mexico City, 4510, Mexico.
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Pacheco-Escobedo MA, Ivanov VB, Ransom-Rodríguez I, Arriaga-Mejía G, Ávila H, Baklanov IA, Pimentel A, Corkidi G, Doerner P, Dubrovsky JG, Álvarez-Buylla ER, Garay-Arroyo A. Longitudinal zonation pattern in Arabidopsis root tip defined by a multiple structural change algorithm. Ann Bot 2016; 118:763-776. [PMID: 27358290 PMCID: PMC5055628 DOI: 10.1093/aob/mcw101] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/08/2016] [Accepted: 04/08/2016] [Indexed: 05/23/2023]
Abstract
Background and Aims The Arabidopsis thaliana root is a key experimental system in developmental biology. Despite its importance, we are still lacking an objective and broadly applicable approach for identification of number and position of developmental domains or zones along the longitudinal axis of the root apex or boundaries between them, which is essential for understanding the mechanisms underlying cell proliferation, elongation and differentiation dynamics during root development. Methods We used a statistics approach, the multiple structural change algorithm (MSC), for estimating the number and position of developmental transitions in the growing portion of the root apex. Once the positions of the transitions between domains and zones were determined, linear models were used to estimate the critical size of dividing cells (LcritD) and other parameters. Key Results The MSC approach enabled identification of three discrete regions in the growing parts of the root that correspond to the proliferation domain (PD), the transition domain (TD) and the elongation zone (EZ). Simultaneous application of the MSC approach and G2-to-M transition (CycB1;1DB:GFP) and endoreduplication (pCCS52A1:GUS) molecular markers confirmed the presence and position of the TD. We also found that the MADS-box gene XAANTAL1 (XAL1) is required for the wild-type (wt) PD increase in length during the first 2 weeks of growth. Contrary to wt, in the xal1 loss-of-function mutant the increase and acceleration of root growth were not detected. We also found alterations in LcritD in xal1 compared with wt, which was associated with longer cell cycle duration in the mutant. Conclusions The MSC approach is a useful, objective and versatile tool for identification of the PD, TD and EZ and boundaries between them in the root apices and can be used for the phenotyping of different genetic backgrounds, experimental treatments or developmental changes within a genotype. The tool is publicly available at www.ibiologia.com.mx/MSC_analysis.
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Affiliation(s)
- Mario A. Pacheco-Escobedo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, Mexico
| | - Victor B. Ivanov
- Department of Root Physiology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, ul. Botanicheskaya 35, Moscow, 127276 Russia
| | - Iván Ransom-Rodríguez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, Mexico
| | - Germán Arriaga-Mejía
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, U.P. Adolfo López Mateos, México DF, México
| | - Hibels Ávila
- Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, U.P. Adolfo López Mateos, México DF, México
| | - Ilya A. Baklanov
- Department of Root Physiology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, ul. Botanicheskaya 35, Moscow, 127276 Russia
| | - Arturo Pimentel
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| | - Gabriel Corkidi
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| | - Peter Doerner
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Joseph G. Dubrovsky
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, Mexico
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Aceves-García P, Álvarez-Buylla ER, Garay-Arroyo A, García-Ponce B, Muñoz R, Sánchez MDLP. Root Architecture Diversity and Meristem Dynamics in Different Populations of Arabidopsis thaliana. Front Plant Sci 2016; 7:858. [PMID: 27379140 PMCID: PMC4910468 DOI: 10.3389/fpls.2016.00858] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/31/2016] [Indexed: 05/26/2023]
Abstract
Arabidopsis thaliana has been an excellent model system for molecular genetic approaches to development and physiology. More recently, the potential of studying various accessions collected from diverse habitats has been started to exploit. Col-0 has been the best-studied accession but we now know that several traits show significant divergences among them. In this work, we focused in the root that has become a key system for development. We studied root architecture and growth dynamics of 12 Arabidopsis accessions. Our data reveal a wide variability in root architecture and root length among accessions. We also found variability in the root apical meristem (RAM), explained mainly by cell size at the RAM transition domain and possibly by peculiar forms of organization at the stem cell niche in some accessions. Contrary to Col-0 reports, in some accessions the RAM size not always explains the variations in the root length; indicating that elongated cell size could be more relevant in the determination of root length than the RAM size itself. This study contributes to investigations dealing with understanding the molecular and cellular basis of phenotypic variation, the role of plasticity on adaptation, and the developmental mechanisms that may restrict phenotypic variation in response to contrasting environmental conditions.
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Affiliation(s)
- Pamela Aceves-García
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, MéxicoMexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, MéxicoMexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, MéxicoMexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, MéxicoMexico
| | - Rodrigo Muñoz
- Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, MéxicoMexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, MéxicoMexico
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Álvarez-Buylla ER, Dávila-Velderrain J, Martínez-García JC. Systems Biology Approaches to Development beyond Bioinformatics: Nonlinear Mechanistic Models Using Plant Systems. Bioscience 2016. [DOI: 10.1093/biosci/biw027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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de la Paz Sanchez M, Aceves-García P, Petrone E, Steckenborn S, Vega-León R, Álvarez-Buylla ER, Garay-Arroyo A, García-Ponce B. The impact of Polycomb group (PcG) and Trithorax group (TrxG) epigenetic factors in plant plasticity. New Phytol 2015; 208:684-694. [PMID: 26037337 DOI: 10.1111/nph.13486] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/25/2015] [Indexed: 06/04/2023]
Abstract
Current advances indicate that epigenetic mechanisms play important roles in the regulatory networks involved in plant developmental responses to environmental conditions. Hence, understanding the role of such components becomes crucial to understanding the mechanisms underlying the plasticity and variability of plant traits, and thus the ecology and evolution of plant development. We now know that important components of phenotypic variation may result from heritable and reversible epigenetic mechanisms without genetic alterations. The epigenetic factors Polycomb group (PcG) and Trithorax group (TrxG) are involved in developmental processes that respond to environmental signals, playing important roles in plant plasticity. In this review, we discuss current knowledge of TrxG and PcG functions in different developmental processes in response to internal and environmental cues and we also integrate the emerging evidence concerning their function in plant plasticity. Many such plastic responses rely on meristematic cell behavior, including stem cell niche maintenance, cellular reprogramming, flowering and dormancy as well as stress memory. This information will help to determine how to integrate the role of epigenetic regulation into models of gene regulatory networks, which have mostly included transcriptional interactions underlying various aspects of plant development and its plastic response to environmental conditions.
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Affiliation(s)
- Maria de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Pamela Aceves-García
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Emilio Petrone
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Stefan Steckenborn
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Rosario Vega-León
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
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Ortiz-Gutiérrez E, García-Cruz K, Azpeitia E, Castillo A, Sánchez MDLP, Álvarez-Buylla ER. A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle. PLoS Comput Biol 2015; 11:e1004486. [PMID: 26340681 PMCID: PMC4560428 DOI: 10.1371/journal.pcbi.1004486] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 08/03/2015] [Indexed: 01/02/2023] Open
Abstract
Cell cycle control is fundamental in eukaryotic development. Several modeling efforts have been used to integrate the complex network of interacting molecular components involved in cell cycle dynamics. In this paper, we aimed at recovering the regulatory logic upstream of previously known components of cell cycle control, with the aim of understanding the mechanisms underlying the emergence of the cyclic behavior of such components. We focus on Arabidopsis thaliana, but given that many components of cell cycle regulation are conserved among eukaryotes, when experimental data for this system was not available, we considered experimental results from yeast and animal systems. We are proposing a Boolean gene regulatory network (GRN) that converges into only one robust limit cycle attractor that closely resembles the cyclic behavior of the key cell-cycle molecular components and other regulators considered here. We validate the model by comparing our in silico configurations with data from loss- and gain-of-function mutants, where the endocyclic behavior also was recovered. Additionally, we approximate a continuous model and recovered the temporal periodic expression profiles of the cell-cycle molecular components involved, thus suggesting that the single limit cycle attractor recovered with the Boolean model is not an artifact of its discrete and synchronous nature, but rather an emergent consequence of the inherent characteristics of the regulatory logic proposed here. This dynamical model, hence provides a novel theoretical framework to address cell cycle regulation in plants, and it can also be used to propose novel predictions regarding cell cycle regulation in other eukaryotes. In multicellular organisms, cells undergo a cyclic behavior of DNA duplication and delivery of a copy to daughter cells during cell division. In each of the main cell-cycle (CC) stages different sets of proteins are active and genes are expressed. Understanding how such cycling cellular behavior emerges and is robustly maintained in the face of changing developmental and environmental conditions, remains a fundamental challenge of biology. The molecular components that cycle through DNA duplication and citokinesis are interconnected in a complex regulatory network. Several models of such network have been proposed, although the regulatory network that robustly recovers a limit-cycle steady state that resembles the behavior of CC molecular components has been recovered only in a few cases, and no comprehensive model exists for plants. In this paper we used the plant Arabidopsis thaliana, as a study system to propose a core regulatory network to recover a cyclic attractor that mimics the oscillatory behavior of the key CC components. Our analyses show that the proposed GRN model is robust to transient alterations, and is validated with the loss- and gain-of-function mutants of the CC components. The interactions proposed for Arabidopsis thaliana CC can inspire predictions for further uncovering regulatory motifs in the CC of other organisms including human.
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Affiliation(s)
- Elizabeth Ortiz-Gutiérrez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| | - Karla García-Cruz
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México
| | - Eugenio Azpeitia
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| | - Aaron Castillo
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
| | - María de la Paz Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México
| | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Junto a Jardín Botánico Exterior, México, D.F. CP 04510, México; Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, México, D.F. 04510, México
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Pérez-Ruiz RV, García-Ponce B, Marsch-Martínez N, Ugartechea-Chirino Y, Villajuana-Bonequi M, de Folter S, Azpeitia E, Dávila-Velderrain J, Cruz-Sánchez D, Garay-Arroyo A, Sánchez MDLP, Estévez-Palmas JM, Álvarez-Buylla ER. XAANTAL2 (AGL14) Is an Important Component of the Complex Gene Regulatory Network that Underlies Arabidopsis Shoot Apical Meristem Transitions. Mol Plant 2015; 8:796-813. [PMID: 25636918 DOI: 10.1016/j.molp.2015.01.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [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: 12/10/2014] [Revised: 12/10/2014] [Accepted: 01/05/2015] [Indexed: 05/21/2023]
Abstract
In Arabidopsis thaliana, multiple genes involved in shoot apical meristem (SAM) transitions have been characterized, but the mechanisms required for the dynamic attainment of vegetative, inflorescence, and floral meristem (VM, IM, FM) cell fates during SAM transitions are not well understood. Here we show that a MADS-box gene, XAANTAL2 (XAL2/AGL14), is necessary and sufficient to induce flowering, and its regulation is important in FM maintenance and determinacy. xal2 mutants are late flowering, particularly under short-day (SD) condition, while XAL2 overexpressing plants are early flowering, but their flowers have vegetative traits. Interestingly, inflorescences of the latter plants have higher expression levels of LFY, AP1, and TFL1 than wild-type plants. In addition we found that XAL2 is able to bind the TFL1 regulatory regions. On the other hand, the basipetal carpels of the 35S::XAL2 lines lose determinacy and maintain high levels of WUS expression under SD condition. To provide a mechanistic explanation for the complex roles of XAL2 in SAM transitions and the apparently paradoxical phenotypes of XAL2 and other MADS-box (SOC1, AGL24) overexpressors, we conducted dynamic gene regulatory network (GRN) and epigenetic landscape modeling. We uncovered a GRN module that underlies VM, IM, and FM gene configurations and transition patterns in wild-type plants as well as loss and gain of function lines characterized here and previously. Our approach thus provides a novel mechanistic framework for understanding the complex basis of SAM development.
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Affiliation(s)
- Rigoberto V Pérez-Ruiz
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Berenice García-Ponce
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico.
| | - Nayelli Marsch-Martínez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Yamel Ugartechea-Chirino
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Mitzi Villajuana-Bonequi
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Carretera Irapuato - León, AP 629, 36821 Irapuato, Guanajuato, Mexico
| | - Eugenio Azpeitia
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - José Dávila-Velderrain
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - David Cruz-Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Adriana Garay-Arroyo
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - María de la Paz Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Juan M Estévez-Palmas
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico
| | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/no, Junto al Jardín Botánico, and Centro de Ciencias de la Complejidad Ciudad Universitaria, Coyoacán 04510, México D.F., Mexico; University of California, 431 Koshland Hall, Berkeley, CA 94720, USA.
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Rodríguez-Mega E, Piñeyro-Nelson A, Gutierrez C, García-Ponce B, Sánchez MDLP, Zluhan-Martínez E, Álvarez-Buylla ER, Garay-Arroyo A. Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach. Dev Dyn 2015; 244:1074-1095. [PMID: 25733163 DOI: 10.1002/dvdy.24268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 10/16/2014] [Revised: 02/24/2015] [Accepted: 02/24/2015] [Indexed: 12/20/2022] Open
Abstract
A growing body of evidence suggests that alterations in transcriptional regulation of genes involved in modulating development are an important part of phenotypic evolution, and this can be documented among species and within populations. While the effects of differential transcriptional regulation in organismal development have been preferentially studied in animal systems, this phenomenon has also been addressed in plants. In this review, we summarize evidence for cis-regulatory mutations, trans-regulatory changes and epigenetic modifications as molecular events underlying important phenotypic alterations, and thus shaping the evolution of plant development. We postulate that a mechanistic understanding of why such molecular alterations have a key role in development, morphology and evolution will have to rely on dynamic models of complex regulatory networks that consider the concerted action of genetic and nongenetic components, and that also incorporate the restrictions underlying the genotype to phenotype mapping process. Developmental Dynamics 244:1074-1095, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Emiliano Rodríguez-Mega
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México
| | - Alma Piñeyro-Nelson
- Department of Plant and Microbial Biology, University of California, Berkeley, California
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México
| | - María De La Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México
| | - Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo, Evolución y Epigenética de Plantas, Universidad Nacional Autónoma de México, 3er Circuito Exterior junto al Jardín Botánico, Ciudad Universitaria, México.,Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolás Cabrera 1, Cantoblanco, 28049, Madrid, Spain
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Weinstein N, Ortiz-Gutiérrez E, Muñoz S, Rosenblueth DA, Álvarez-Buylla ER, Mendoza L. A model of the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva. BMC Bioinformatics 2015; 16:81. [PMID: 25884811 PMCID: PMC4367908 DOI: 10.1186/s12859-015-0498-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 02/16/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND There are recent experimental reports on the cross-regulation between molecules involved in the control of the cell cycle and the differentiation of the vulval precursor cells (VPCs) of Caenorhabditis elegans. Such discoveries provide novel clues on how the molecular mechanisms involved in the cell cycle and cell differentiation processes are coordinated during vulval development. Dynamic computational models are helpful to understand the integrated regulatory mechanisms affecting these cellular processes. RESULTS Here we propose a simplified model of the regulatory network that includes sufficient molecules involved in the control of both the cell cycle and cell differentiation in the C. elegans vulva to recover their dynamic behavior. We first infer both the topology and the update rules of the cell cycle module from an expected time series. Next, we use a symbolic algorithmic approach to find which interactions must be included in the regulatory network. Finally, we use a continuous-time version of the update rules for the cell cycle module to validate the cyclic behavior of the network, as well as to rule out the presence of potential artifacts due to the synchronous updating of the discrete model. We analyze the dynamical behavior of the model for the wild type and several mutants, finding that most of the results are consistent with published experimental results. CONCLUSIONS Our model shows that the regulation of Notch signaling by the cell cycle preserves the potential of the VPCs and the three vulval fates to differentiate and de-differentiate, allowing them to remain completely responsive to the concentration of LIN-3 and lateral signal in the extracellular microenvironment.
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Affiliation(s)
- Nathan Weinstein
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de, México, DF, México.
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, DF, México.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México, DF, México.
| | - Elizabeth Ortiz-Gutiérrez
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de, México, DF, México.
- Instituto de Ecología, Universidad Nacional Autónoma de México, México, DF, México.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México, DF, México.
| | - Stalin Muñoz
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad, Nacional Autónoma de México, México, DF, México.
| | - David A Rosenblueth
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad, Nacional Autónoma de México, México, DF, México.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México, DF, México.
| | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, México, DF, México.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México, DF, México.
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, DF, México.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México, DF, México.
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Garay-Arroyo A, Ortiz-Moreno E, de la Paz Sánchez M, Murphy AS, García-Ponce B, Marsch-Martínez N, de Folter S, Corvera-Poiré A, Jaimes-Miranda F, Pacheco-Escobedo MA, Dubrovsky JG, Pelaz S, Álvarez-Buylla ER. The MADS transcription factor XAL2/AGL14 modulates auxin transport during Arabidopsis root development by regulating PIN expression. EMBO J 2013; 32:2884-95. [PMID: 24121311 DOI: 10.1038/emboj.2013.216] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 08/28/2013] [Indexed: 12/29/2022] Open
Abstract
Elucidating molecular links between cell-fate regulatory networks and dynamic patterning modules is a key for understanding development. Auxin is important for plant patterning, particularly in roots, where it establishes positional information for cell-fate decisions. PIN genes encode plasma membrane proteins that serve as auxin efflux transporters; mutations in members of this gene family exhibit smaller roots with altered root meristems and stem-cell patterning. Direct regulators of PIN transcription have remained elusive. Here, we establish that a MADS-box gene (XAANTAL2, XAL2/AGL14) controls auxin transport via PIN transcriptional regulation during Arabidopsis root development; mutations in this gene exhibit altered stem-cell patterning, root meristem size, and root growth. XAL2 is necessary for normal shootward and rootward auxin transport, as well as for maintaining normal auxin distribution within the root. Furthermore, this MADS-domain transcription factor upregulates PIN1 and PIN4 by direct binding to regulatory regions and it is required for PIN4-dependent auxin response. In turn, XAL2 expression is regulated by auxin levels thus establishing a positive feedback loop between auxin levels and PIN regulation that is likely to be important for robust root patterning.
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Affiliation(s)
- Adriana Garay-Arroyo
- Depto. de Ecología Funcional. Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, México
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Barrio RA, Romero-Arias JR, Noguez MA, Azpeitia E, Ortiz-Gutiérrez E, Hernández-Hernández V, Cortes-Poza Y, Álvarez-Buylla ER. Cell patterns emerge from coupled chemical and physical fields with cell proliferation dynamics: the Arabidopsis thaliana root as a study system. PLoS Comput Biol 2013; 9:e1003026. [PMID: 23658505 PMCID: PMC3642054 DOI: 10.1371/journal.pcbi.1003026] [Citation(s) in RCA: 36] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 02/25/2013] [Indexed: 11/18/2022] Open
Abstract
A central issue in developmental biology is to uncover the mechanisms by which stem cells maintain their capacity to regenerate, yet at the same time produce daughter cells that differentiate and attain their ultimate fate as a functional part of a tissue or an organ. In this paper we propose that, during development, cells within growing organs obtain positional information from a macroscopic physical field that is produced in space while cells are proliferating. This dynamical interaction triggers and responds to chemical and genetic processes that are specific to each biological system. We chose the root apical meristem of Arabidopsis thaliana to develop our dynamical model because this system is well studied at the molecular, genetic and cellular levels and has the key traits of multicellular stem-cell niches. We built a dynamical model that couples fundamental molecular mechanisms of the cell cycle to a tension physical field and to auxin dynamics, both of which are known to play a role in root development. We perform extensive numerical calculations that allow for quantitative comparison with experimental measurements that consider the cellular patterns at the root tip. Our model recovers, as an emergent pattern, the transition from proliferative to transition and elongation domains, characteristic of stem-cell niches in multicellular organisms. In addition, we successfully predict altered cellular patterns that are expected under various applied auxin treatments or modified physical growth conditions. Our modeling platform may be extended to explicitly consider gene regulatory networks or to treat other developmental systems. The emergence of tumors results from altered cell differentiation and proliferation during organ and tissue development. Understanding how such altered or normal patterns are established is still a challenge. Molecular genetic approaches to understanding pattern formation have searched for key central genetic controllers. However, biological patterns emerge as a consequence of coupled complex genetic and non-genetic sub-systems operating at various spatial and temporal scales and levels of organization. We present a two-dimensional model and simulation benchmark that considers the integrated dynamics of physical and chemical fields that result from cell proliferation. We aim at understanding how the cellular patterns of stem-cell niches emerge. In these, organizer cells with very low rates of proliferation are surrounded by stem cells with slightly higher proliferation rates that transit to a domain of active proliferation and then of elongation and differentiation. We quantified such cellular patterns in the Arabidopsis thaliana root to test our theoretical propositions. The results of our simulations closely mimic observed root cellular patterns, thus providing a proof of principle that coupled physical fields and chemical processes under active cell proliferation give rise to stem-cell patterns. Our framework may be extended to other developmental systems and to consider gene regulatory networks.
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Affiliation(s)
- Rafael A. Barrio
- Instituto de Física, Universidad Nacional Autónoma de México (UNAM), México, Distrito Federal, México
- * E-mail: (RAB); (ERAB)
| | - José Roberto Romero-Arias
- Instituto de Física, Universidad Nacional Autónoma de México (UNAM), México, Distrito Federal, México
| | - Marco A. Noguez
- Universidad Autónoma de la Ciudad de México, Mexico, Distrito Federal, México
| | - Eugenio Azpeitia
- Instituto de Ecología, Universidad Nacional Autónoma de México, México, Distrito Federal, México
- Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Elizabeth Ortiz-Gutiérrez
- Instituto de Ecología, Universidad Nacional Autónoma de México, México, Distrito Federal, México
- Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Valeria Hernández-Hernández
- Instituto de Ecología, Universidad Nacional Autónoma de México, México, Distrito Federal, México
- Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Yuriria Cortes-Poza
- Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Elena R. Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, México, Distrito Federal, México
- Centro de Ciencias de la Complejidad-C3, Universidad Nacional Autónoma de México, Distrito Federal, México
- * E-mail: (RAB); (ERAB)
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42
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Garay-Arroyo A, De La Paz Sánchez M, García-Ponce B, Azpeitia E, Álvarez-Buylla ER. Hormone symphony during root growth and development. Dev Dyn 2012; 241:1867-85. [DOI: 10.1002/dvdy.23878] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2012] [Indexed: 01/29/2023] Open
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Abstract
Understanding how the information contained in genes is mapped onto the phenotypes, and deriving formal frameworks to search for generic aspects of developmental constraints and evolution remains one of the main challenges of contemporary biological research. The Mexican endemic triurid Lacandonia schismatica (Lacandoniaceae), a mycoheterotrophic monocotyledonous plant with hermaphroditic reproductive axes is alone among 250,000 species of angiosperms, as it has central stamens surrounded by a peripheral gynoecium, representing a natural instance of a homeotic mutant. Based on the classical ABC model of flower development, it has recently been shown that the B-function gene APETALA3 (AP3), essential for stamen identity, was displaced toward the flower centre in L. schismatica (ABC to ACB) from the early stages of flower development. A functional conservation of B-function genes from L. schismatica through the rescue of B-gene mutants in Arabidopsis thaliana, as well as conserved protein interactions, has also been demonstrated. Thus, it has been shown that relatively simple genetic alterations may underlie large morphological shifts fixed in extant natural populations. Nevertheless, critical questions remain in order to have a full and sufficient explanation of the molecular genetic mechanisms underlying L. schismatica's unique floral arrangement. Evolutionary approaches to developmental mechanisms and systems biology, including high-throughput functional genomic studies and models of complex developmental gene regulatory networks, constitute two main approaches to meet such a challenge. In this review, the aim is to address some of the pending questions with the ultimate goal of investigating further the mechanisms of L. schismatica's unique homeotic flower arrangement and its evolution.
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Affiliation(s)
- Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, México
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44
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Álvarez-Buylla ER, Ambrose BA, Flores-Sandoval E, Englund M, Garay-Arroyo A, García-Ponce B, de la Torre-Bárcena E, Espinosa-Matías S, Martínez E, Piñeyro-Nelson A, Engström P, Meyerowitz EM. B-function expression in the flower center underlies the homeotic phenotype of Lacandonia schismatica (Triuridaceae). Plant Cell 2010; 22:3543-59. [PMID: 21119062 PMCID: PMC3015125 DOI: 10.1105/tpc.109.069153] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 10/05/2010] [Accepted: 11/14/2010] [Indexed: 05/07/2023]
Abstract
Spontaneous homeotic transformations have been described in natural populations of both plants and animals, but little is known about the molecular-genetic mechanisms underlying these processes in plants. In the ABC model of floral organ identity in Arabidopsis thaliana, the B- and C-functions are necessary for stamen morphogenesis, and C alone is required for carpel identity. We provide ABC model-based molecular-genetic evidence that explains the unique inside-out homeotic floral organ arrangement of the monocotyledonous mycoheterotroph species Lacandonia schismatica (Triuridaceae) from Mexico. Whereas a quarter million flowering plant species bear central carpels surrounded by stamens, L. schismatica stamens occur in the center of the flower and are surrounded by carpels. The simplest explanation for this is that the B-function is displaced toward the flower center. Our analyses of the spatio-temporal pattern of B- and C-function gene expression are consistent with this hypothesis. The hypothesis is further supported by conservation between the B-function genes of L. schismatica and Arabidopsis, as the former are able to rescue stamens in Arabidopsis transgenic complementation lines, and Ls-AP3 and Ls-PI are able to interact with each other and with the corresponding Arabidopsis B-function proteins in yeast. Thus, relatively simple molecular modifications may underlie important morphological shifts in natural populations of extant plant taxa.
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Affiliation(s)
- Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, D.F. Mexico 04510, Mexico.
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45
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Álvarez-Buylla ER, Ambrose BA, Flores-Sandoval E, Englund M, Garay-Arroyo A, García-Ponce B, de la Torre-Bárcena E, Espinosa-Matías S, Martínez E, Piñeyro-Nelson A, Engström P, Meyerowitz EM. B-function expression in the flower center underlies the homeotic phenotype of Lacandonia schismatica (Triuridaceae). Plant Cell 2010. [PMID: 21119062 PMCID: PMC3051254 DOI: 10.1105/tpc.111.230160] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Spontaneous homeotic transformations have been described in natural populations of both plants and animals, but little is known about the molecular-genetic mechanisms underlying these processes in plants. In the ABC model of floral organ identity in Arabidopsis thaliana, the B- and C-functions are necessary for stamen morphogenesis, and C alone is required for carpel identity. We provide ABC model-based molecular-genetic evidence that explains the unique inside-out homeotic floral organ arrangement of the monocotyledonous mycoheterotroph species Lacandonia schismatica (Triuridaceae) from Mexico. Whereas a quarter million flowering plant species bear central carpels surrounded by stamens, L. schismatica stamens occur in the center of the flower and are surrounded by carpels. The simplest explanation for this is that the B-function is displaced toward the flower center. Our analyses of the spatio-temporal pattern of B- and C-function gene expression are consistent with this hypothesis. The hypothesis is further supported by conservation between the B-function genes of L. schismatica and Arabidopsis, as the former are able to rescue stamens in Arabidopsis transgenic complementation lines, and Ls-AP3 and Ls-PI are able to interact with each other and with the corresponding Arabidopsis B-function proteins in yeast. Thus, relatively simple molecular modifications may underlie important morphological shifts in natural populations of extant plant taxa.
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Affiliation(s)
- Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Tercer Circuito Exterior, Ciudad Universitaria, D.F. Mexico 04510, Mexico.
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Sánchez-Corrales YE, Álvarez-Buylla ER, Mendoza L. The Arabidopsis thaliana flower organ specification gene regulatory network determines a robust differentiation process. J Theor Biol 2010; 264:971-83. [DOI: 10.1016/j.jtbi.2010.03.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 02/18/2010] [Accepted: 03/02/2010] [Indexed: 01/22/2023]
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47
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Álvarez-Buylla ER, Chaos Á, Aldana M, Benítez M, Cortes-Poza Y, Espinosa-Soto C, Hartasánchez DA, Lotto RB, Malkin D, Escalera Santos GJ, Padilla-Longoria P. Floral morphogenesis: stochastic explorations of a gene network epigenetic landscape. PLoS One 2008; 3:e3626. [PMID: 18978941 PMCID: PMC2572848 DOI: 10.1371/journal.pone.0003626] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [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: 10/31/2007] [Accepted: 10/05/2008] [Indexed: 11/18/2022] Open
Abstract
In contrast to the classical view of development as a preprogrammed and deterministic process, recent studies have demonstrated that stochastic perturbations of highly non-linear systems may underlie the emergence and stability of biological patterns. Herein, we address the question of whether noise contributes to the generation of the stereotypical temporal pattern in gene expression during flower development. We modeled the regulatory network of organ identity genes in the Arabidopsis thaliana flower as a stochastic system. This network has previously been shown to converge to ten fixed-point attractors, each with gene expression arrays that characterize inflorescence cells and primordial cells of sepals, petals, stamens, and carpels. The network used is binary, and the logical rules that govern its dynamics are grounded in experimental evidence. We introduced different levels of uncertainty in the updating rules of the network. Interestingly, for a level of noise of around 0.5–10%, the system exhibited a sequence of transitions among attractors that mimics the sequence of gene activation configurations observed in real flowers. We also implemented the gene regulatory network as a continuous system using the Glass model of differential equations, that can be considered as a first approximation of kinetic-reaction equations, but which are not necessarily equivalent to the Boolean model. Interestingly, the Glass dynamics recover a temporal sequence of attractors, that is qualitatively similar, although not identical, to that obtained using the Boolean model. Thus, time ordering in the emergence of cell-fate patterns is not an artifact of synchronous updating in the Boolean model. Therefore, our model provides a novel explanation for the emergence and robustness of the ubiquitous temporal pattern of floral organ specification. It also constitutes a new approach to understanding morphogenesis, providing predictions on the population dynamics of cells with different genetic configurations during development.
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Affiliation(s)
- Elena R. Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. Universitaria, México, D. F., México
- C3, Centro de Ciencias de la Complejidad, Cd. Universitaria, UNAM, México, D. F., México
- * E-mail: (ERA-B); (PP-L)
| | - Álvaro Chaos
- Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. Universitaria, México, D. F., México
- C3, Centro de Ciencias de la Complejidad, Cd. Universitaria, UNAM, México, D. F., México
| | - Maximino Aldana
- C3, Centro de Ciencias de la Complejidad, Cd. Universitaria, UNAM, México, D. F., México
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mariana Benítez
- Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. Universitaria, México, D. F., México
- C3, Centro de Ciencias de la Complejidad, Cd. Universitaria, UNAM, México, D. F., México
| | - Yuriria Cortes-Poza
- C3, Centro de Ciencias de la Complejidad, Cd. Universitaria, UNAM, México, D. F., México
- Instituto de Investigación en Matemáticas Aplicadas y Sistemas, Universidad Nacional Autónoma de México, Cd. Universitaria, México, D. F., México
| | - Carlos Espinosa-Soto
- Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. Universitaria, México, D. F., México
- C3, Centro de Ciencias de la Complejidad, Cd. Universitaria, UNAM, México, D. F., México
| | - Diego A. Hartasánchez
- C3, Centro de Ciencias de la Complejidad, Cd. Universitaria, UNAM, México, D. F., México
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - R. Beau Lotto
- lottolab, University College, London, United Kingdom
| | - David Malkin
- lottolab, University College, London, United Kingdom
| | - Gerardo J. Escalera Santos
- Instituto de Ecología, Universidad Nacional Autónoma de México, Cd. Universitaria, México, D. F., México
- C3, Centro de Ciencias de la Complejidad, Cd. Universitaria, UNAM, México, D. F., México
| | - Pablo Padilla-Longoria
- C3, Centro de Ciencias de la Complejidad, Cd. Universitaria, UNAM, México, D. F., México
- Instituto de Investigación en Matemáticas Aplicadas y Sistemas, Universidad Nacional Autónoma de México, Cd. Universitaria, México, D. F., México
- * E-mail: (ERA-B); (PP-L)
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