Functional Compensation of Primary and Secondary Metabolites by Duplicate Genes in Arabidopsis thaliana
Open Access
- 24 August 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Molecular Biology and Evolution
- Vol. 28 (1), 377-382
- https://doi.org/10.1093/molbev/msq204
Abstract
It is well known that knocking out a gene in an organism often causes no phenotypic effect. One possible explanation is the existence of duplicate genes; that is, the effect of knocking out a gene is compensated by a duplicate copy. Another explanation is the existence of alternative pathways. In terms of metabolic products, the relative roles of the two mechanisms have been extensively studied in yeast but not in any multi-cellular organisms. Here, to address the functional compensation of metabolic products by duplicate genes, we quantified 35 metabolic products from 1,976 genes in knockout mutants of Arabidopsis thaliana by a high-throughput Liquid chromatography-Mass spectrometer (LC-MS) analysis. We found that knocking out either a singleton gene or a duplicate gene with distant paralogs in the genome tends to induce stronger metabolic effects than knocking out a duplicate gene with a close paralog in the genome, indicating that only duplicate genes with close paralogs play a significant role in functional compensation for metabolic products in A. thaliana. To extend the analysis, we examined metabolic products with either high or low connectivity in a metabolic network. We found that the compensatory role of duplicate genes is less important when the metabolite has a high connectivity, indicating that functional compensation by alternative pathways is common in the case of high connectivity. In conclusion, recently duplicated genes play an important role in the compensation of metabolic products only when the number of alternative pathways is small.Keywords
This publication has 30 references indexed in Scilit:
- Functional compensation by duplicated genes in mouseTrends in Genetics, 2009
- Evolutionary Persistence of Functional Compensation by Duplicate Genes in ArabidopsisGenome Biology and Evolution, 2009
- Abundant Indispensable Redundancies in Cellular Metabolic NetworksGenome Biology and Evolution, 2009
- Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental StimuliPlant Physiology, 2008
- The AtGenExpress hormone- and chemical-treatment data set: Experimental design, data evaluation, model data analysis, and data accessThe Plant Journal, 2008
- Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesisProceedings of the National Academy of Sciences of the United States of America, 2007
- Plasticity of genetic interactions in metabolic networks of yeastProceedings of the National Academy of Sciences of the United States of America, 2007
- A gene expression map of Arabidopsis thaliana developmentNature Genetics, 2005
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994