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López-Ruíz BA, García-Ponce B, de la Paz Sánchez M, Álvarez-Buylla ER, Urrutia AO, Garay-Arroyo A. Genome-wide association studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity. Mol Biol Rep 2024; 51:763. [PMID: 38874813 PMCID: PMC11178574 DOI: 10.1007/s11033-024-09623-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Arabidopsis thaliana primary root growth has become a model for evo-devo studies due to its simplicity and facility to record cell proliferation and differentiation. To identify new genetic components relevant to primary root growth, we used a Genome-Wide Association Studies (GWAS) meta-analysis approach using data published in the last decade. In this work, we performed intra and inter-studies analyses to discover new genetic components that could participate in primary root growth. METHODS AND RESULTS We used 639 accessions from nine different studies under control conditions and performed different GWAS tests. We found that primary root growth changes were associated with 41 genes, of which six (14.6%) have been previously described as inhibitors or promoters of primary root growth. The knockdown lines of two genes, Suppressor of Gene Silencing (SGS3), involved in tasiRNA processing, and a gene with a Sterile Alpha Motif (SAM) motif named NOJOCH MOOTS (NOJO), confirmed their role as repressors of primary root growth, none has been shown to participate in this developmental process before. CONCLUSIONS In summary, our GWAS analysis of different available studies identified new genes that participate in primary root growth; two of them were identified as repressors of primary root growth.
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Affiliation(s)
- Brenda Anabel López-Ruíz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
- Centro de Ciencias de la Complejidad, UNAM, CDMX, México
| | - Araxi O Urrutia
- Laboratorio de Genómica Evolutiva y Funcional, Instituto de Ecología, UNAM, Mexico City, México.
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK.
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México.
- Centro de Ciencias de la Complejidad, UNAM, CDMX, México.
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Mostafa I, Zhu N, Yoo MJ, Balmant KM, Misra BB, Dufresne C, Abou-Hashem M, Chen S, El-Domiaty M. New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants. J Proteomics 2016; 138:1-19. [PMID: 26915584 DOI: 10.1016/j.jprot.2016.02.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/07/2016] [Accepted: 02/17/2016] [Indexed: 12/24/2022]
Abstract
UNLABELLED Glucosinolates present in Brassicales are important for human health and plant defense against insects and pathogens. Here we investigate the proteomes and metabolomes of Arabidopsis myb28/29 and cyp79B2/B3 mutants deficient in aliphatic glucosinolates and indolic glucosinolates, respectively. Quantitative proteomics of the myb28/29 and cyp79B2/B3 mutants led to the identification of 2785 proteins, of which 142 proteins showed significant changes in the two mutants compared to wild type (WT). By mapping the differential proteins using STRING, we detected 59 new edges in the glucosinolate metabolic network. These connections can be classified as primary with direct roles in glucosinolate metabolism, secondary related to plant stress responses, and tertiary involved in other biological processes. Gene Ontology analysis of the differential proteins showed high level of enrichment in the nodes belonging to metabolic process including glucosinolate biosynthesis and response to stimulus. Using metabolomics, we quantified 292 metabolites covering a broad spectrum of metabolic pathways, and 89 exhibited differential accumulation patterns between the mutants and WT. The changing metabolites (e.g., γ-glutamyl amino acids, auxins and glucosinolate hydrolysis products) complement our proteomics findings. This study contributes toward engineering and breeding of glucosinolate profiles in plants in efforts to improve human health, crop quality and productivity. BIOLOGICAL SIGNIFICANCE Glucosinolates in Brassicales constitute an important group of natural metabolites important for plant defense and human health. Its biosynthetic pathways and transcriptional regulation have been well-studied. Using Arabidopsis mutants of important genes in glucosinolate biosynthesis, quantitative proteomics and metabolomics led to identification of many proteins and metabolites that are potentially related to glucosinolate metabolism. This study provides a comprehensive insight into the molecular networks of glucosinolate metabolism, and will facilitate efforts toward engineering and breeding of glucosinolate profiles for enhanced crop defense, and nutritional value.
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Affiliation(s)
- Islam Mostafa
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Ning Zhu
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mi-Jeong Yoo
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Kelly M Balmant
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Biswapriya B Misra
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Craig Dufresne
- Thermo Fisher Scientific, West Palm Beach, FL 33407, USA
| | - Maged Abou-Hashem
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA.
| | - Maher El-Domiaty
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
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