The declining water availability for agriculture is becoming problematic for many countries. Therefore the study of plants under water restriction is acquiring extraordinary importance. Botanists currently follow the dehydration of plants comparing the fresh and dry weight of excised organs, or measuring their osmotic or water potentials; these are destructive methods inappropriate for in-vivo determination of plants' hydration dynamics. Water is opaque in the terahertz band, while dehydrated biological tissues are partially transparent. We used terahertz spectroscopy to study the water dynamics of Arabidopsis thaliana by comparing the dehydration kinetics of leaves from plants under well-irrigated and water deficit conditions. We also present measurements of the effect of dark-light cycles and abscisic acid on its water dynamics. The measurements we present provide a new perspective on the water dynamics of plants under different external stimuli and confirm that terahertz can be an excellent non-contact probe of in-vivo tissue hydration.
Highlight Phaseolus vulgaris miR1514a, a non-conserved microRNA that is induced by drought, targets a NAC transcription factor transcript for degradation, consequently triggering phasiRNA production and affecting downstream genes, thus revealing their involvement in responses to drought.
As sessile organisms, plants have to cope with the ever-changing environment as well as with numerous forms of stress. To react to these external cues, plants have evolved a suite of response mechanisms operating at many different levels, ranging from physiological to molecular processes that provide the organism with a wide phenotypic plasticity, allowing for fine tuning of the reactions to these adverse circumstances. During the past decade, non-coding RNAs (ncRNAs) have emerged as key regulatory molecules, which contribute to a significant portion of the transcriptome in eukaryotes and are involved in the control of transcriptional and post-transcriptional gene regulatory pathways. Although accumulated evidence supports an important role for ncRNAs in plant response and adaptation to abiotic stress, their mechanism(s) of action still remains obscure and a functional characterization of the ncRNA repertoire in plants is still needed. Moreover, common features in the biogenesis of different small ncRNAs, and in some cases, cross talk between different gene regulatory pathways may add to the complexity of these pathways and could play important roles in modulating stress responses. Here we review the various ncRNAs that have been reported to participate in the response to abiotic stress in plants, focusing on their importance in plant adaptation and evolution. Understanding how ncRNAs work may reveal novel mechanisms involved in the plant responses to the environment.
SUMMARY Plastids contain their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial‐type, multi‐subunit polymerase encoded by the plastid genome. The plastid‐encoded RNA polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome‐wide scale at high resolution. We established a highly specific approach to detect the genome‐wide pattern of PEP binding to chloroplast DNA using plastid chromatin immunoprecipitation–sequencing (ptChIP‐seq). We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with levels of RNA accumulation, which demonstrates the impact of PEP on chloroplast gene expression. Presented data are available through a publicly available Plastid Genome Visualization Tool (Plavisto) at https://plavisto.mcdb.lsa.umich.edu/.
Plastids are endosymbiotic organelles containing their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid encoded RNA polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplasts DNA using ptChIP-seq. We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with the levels of RNA accumulation, which allowed estimating the quantitative contribution of transcription to RNA accumulation.
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