Linking molecular insight and ecological research (original) (raw)
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Genome-Wide Patterns of Arabidopsis Gene Expression in Nature
Organisms in the wild are subject to multiple, fluctuating environmental factors, and it is in complex natural environments that genetic regulatory networks actually function and evolve. We assessed genome-wide gene expression patterns in the wild in two natural accessions of the model plant Arabidopsis thaliana and examined the nature of transcriptional variation throughout its life cycle and gene expression correlations with natural environmental fluctuations. We grew plants in a natural field environment and measured genome-wide time-series gene expression from the plant shoot every three days, spanning the seedling to reproductive stages. We find that 15,352 genes were expressed in the A. thaliana shoot in the field, and accession and flowering status (vegetative versus flowering) were strong components of transcriptional variation in this plant. We identified between ,110 and 190 time-varying gene expression clusters in the field, many of which were significantly overrepresented by genes regulated by abiotic and biotic environmental stresses. The two main principal components of vegetative shoot gene expression (PCveg) correlate to temperature and precipitation occurrence in the field. The largest PCveg axes included thermoregulatory genes while the second major PCveg was associated with precipitation and contained drought-responsive genes. By exposing A. thaliana to natural environments in an open field, we provide a framework for further understanding the genetic networks that are deployed in natural environments, and we connect plant molecular genetics in the laboratory to plant organismal ecology in the wild.
Genes to ecosystems: exploring the frontiers of ecology with one of the smallest biological units
New Phytologist, 2011
Genes and their expression levels in individual species can structure whole communities and affect ecosystem processes. Although much has been written about community and ecosystem phenotypes with a few model systems, such as poplar and goldenrod, here we explore the potential application of a community genetics approach with systems involving invasive species, climate change and pollution. We argue that community genetics can reveal patterns and processes that otherwise might remain undetected. To further facilitate the community genetics or genes-to-ecosystem concept, we propose four community genetics postulates that allow for the conclusion of a causal relationship between the gene and its effect on the ecosystem. Although most current studies do not satisfy these criteria completely, several come close and, in so doing, begin to provide a genetic-based understanding of communities and ecosystems, as well as a sound basis for conservation and management practices.
Molecular plant responses to combined abiotic stresses put a spotlight on unknown and abundant genes
Journal of Experimental Botany
Environmental stresses such as drought, heat, and salinity limit plant development and agricultural productivity. While individual stresses have been studied extensively, much less is known about the molecular interaction of responses to multiple stresses. To address this problem, we investigated molecular responses of Arabidopsis to single, double, and triple combinations of salt, osmotic, and heat stresses. A metabolite profiling analysis indicated the production of specific compatible solutes depending on the nature of the stress applied. We found that in combination with other stresses, heat has a dominant effect on global gene expression and metabolite level patterns. Treatments that include heat stress lead to strongly reduced transcription of genes coding for abundant photosynthetic proteins and proteins regulating the cell life cycle, while genes involved in protein degradation are up-regulated. Under combined stress conditions, the plants shifted their metabolism to a survi...
Plant, Cell and Environment, 2005
The purpose of plant functional genomics is to describe the patterns of gene expression and internal plant function underlying the ecological functions that sustain plant growth and reproduction. Plants function as integrated systems in which metabolic and developmental pathways draw on common resource pools and respond to a relatively small number of signal/response systems. Plants are also integrated with their environment, exchanging energy and matter with their surroundings and are consequently sensitive to changes in energy and resource fluxes. These two levels of integration complicate the description of gene function. Internal integration results in single genes often affecting multiple characteristics (pleiotropy) and interacting with multiple other genes (epistasis). Integration with the external environment leads to gene expression and the genes' phenotypic effects varying across environmental backgrounds (gene-environment interaction). An accurate description of the function of all genes requires an augmentation, already underway, of the study of isolated developmental and metabolic pathways to a more integrated approach involving the study of genetic effects across scales of variation usually regarded as the purview of ecological and evolutionary research. Since the evolution of gene function also depends on this complex of gene effects, progress in evolutionary genetics will also require understanding the nature of gene interactions and pleiotropy and the constraints and patterns they impose on adaptive evolution. Studying gene function in the context of the integrated organism is a major challenge, best met by developing co-ordinated research efforts in model systems. This review highlights natural variation in A. thaliana as a system for understanding integrated gene function in an ecological and evolutionary context. The current state of this research integration in A. thaliana is described by summarizing relevant approaches, current knowledge, and some potentially fruitful future studies. By introducing some of the fundamental questions of ecological and evo-lutionary research, experimental approaches and systems that can reveal new facets of gene function and gene effect are also described. A glossary is included in the Appendix.
Abiotic stresses are a primary cause of crop loss worldwide. The convergence of stress signalling pathways to a common set of transcription factors suggests the existence of upstream regulatory genes that control plant responses to multiple abiotic stresses. To identify such genes, data from published Arabidopsis thaliana abiotic stress microarray analyses were combined with our presented global analysis of early heat stress-responsive gene expression, in a relational database. A set of Multiple Stress (MST) genes was identified by scoring each gene for the number of abiotic stresses affecting expression of that gene. ErmineJ overrepresentation analysis of the MST gene set identified significantly enriched gene ontology biological processes for multiple abiotic stresses and regulatory genes, particularly transcription factors. A subset of MST genes including only regulatory genes that were designated 'Multiple Stress Regulatory' (MSTR) genes, was identified. To validate this strategy for identifying MSTR genes, mutants of the highest-scoring MSTR gene encoding the circadian clock protein CCA1, were tested for altered sensitivity to stress. A double mutant of CCA1 and its structural and functional homolog, LATE ELONGLATED HYPOCOTYL, exhibited greater sensitivity to salt, osmotic and heat stress than wild-type plants. This work provides a reference data set for further study of MSTR genes.
Functional ecological genomics to demonstrate general and specific responses to abiotic stress
Functional Ecology, 2007
1. Stress is a major component of natural selection in soil ecosystems. The most prominent abiotic stress factors in the field are temperature extremes (heat, cold), dehydration (drought), high salinity and specific toxic compounds such as heavy metals. Organisms are able to deal with these stresses to a certain extent, which determines the limits of their ecological amplitudes. Functional genomic tools are now becoming available to study stress in ecologically relevant soil organisms.