Circadian clocks allow organisms to predict environmental changes caused by the rotation of the Earth. Although circadian rhythms are widespread among different taxa, the core components of circadian oscillators are not conserved and differ between bacteria, plants, animals and fungi. Stramenopiles are a large group of organisms in which circadian rhythms have been only poorly characterized and no clock components have been identified. We have investigated cell division and molecular rhythms in
The circadian clock is an internal molecular oscillator and coordinates numerous physiological processes through regulation of molecular pathways. Tissue‐specific clocks connected by mobile signals have previously been found to run at different speeds in
- Award ID(s):
- 1950376
- NSF-PAR ID:
- 10369148
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Plant Direct
- Volume:
- 6
- Issue:
- 7
- ISSN:
- 2475-4455
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
Summary Nannochloropsis species. In the four strains tested, cell division occurred principally during the night period under diel conditions; however, these rhythms damped within 2–3 days after transfer to constant light. We developed firefly luciferase reporters for the long‐term monitoring ofin vivo transcriptional rhythms in twoNannochlropsis species,Nannochloropsis oceanica CCMP 1779 andNannochloropsis salina CCMP 537. The reporter lines express anticipatory behavior under light/dark cycles and free‐running bioluminescence rhythms with periods of ~21–31 h that damped within ~3–4 days under constant light. Using different entrainment regimes, we demonstrate that these rhythms are modulated by a circadian‐type oscillator. In addition, the phase of free‐running luminescence rhythms can be modulated pharmacologically using aCK 1 ε/δ inhibitor, suggesting a role of this kinase in theNannochloropsis clock. Together with the molecular and genomic tools available forNannochloropsis species, these reporter lines represent an excellent system for future studies on the molecular mechanisms of stramenopile circadian oscillators. -
Abstract Plant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plant
Arabidopsis thaliana (Arabidopsis ) and crop species, circadian clock factors are critical for growth, flowering, and circadian rhythms. Outside ofArabidopsis, however, little is known about the molecular function of clock gene products. Therefore, we sought to compare the function ofBrachypodium distachyon (Brachypodium ) andSetaria viridis (Setaria ) orthologs of a key clock gene inEARLY FLOWERING 3,Arabidopsis . To identify both cycling genes and putative functional orthologs inELF 3Setaria , a circadianRNA ‐seq dataset and online query tool (Diel Explorer) were generated to explore expression profiles ofSetaria genes under circadian conditions. The function of orthologs fromELF 3Arabidopsis, Brachypodium, andSetaria was tested for complementation of anelf3 mutation inArabidopsis . We find that both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time, and arrhythmic clock phenotypes. Using affinity purification and mass spectrometry, our data indicate that BdELF 3 and SvELF 3 could be integrated into similar complexesin vivo as AtELF 3. Thus, we find that, despite 180 million years of separation,Bd andELF 3Sv can functionally complement loss ofELF 3 at the molecular and physiological level.ELF 3 -
Organisms track time of day through the function of cell-autonomous molecular clocks. In addition to a central clock located in the brain, molecular clocks are present in most peripheral tissues. Circadian clocks are coordinated within and across tissues, but the manner through which this coordination is achieved is not well understood. We reasoned that the ability to track in vivo molecular clock activity in specific tissues of the fruit fly, Drosophila melanogaster, would facilitate an investigation into the relationship between different clock-containing tissues. Previous efforts to monitor clock gene expression in single flies in vivo have used regulatory elements of several different clock genes to dictate expression of a luciferase reporter enzyme, the activity of which can be monitored using a luminometer. Although these reporter lines have been instrumental in our understanding of the circadian system, they generally lack cell specificity, making it difficult to compare molecular clock oscillations between different tissues. Here, we report the generation of several novel lines of flies that allow for inducible expression of a luciferase reporter construct for clock gene transcriptional activity. We find that these lines faithfully report circadian transcription, as they exhibit rhythmic luciferase activity that is dependent on a functional molecular clock. Furthermore, we take advantage of our reporter lines’ tissue specificity to demonstrate that peripheral molecular clocks are able to retain rhythmicity for multiple days under constant environmental conditions.
-
Summary Relative to homozygous diploids, the presence of multiple homologs or homeologs in polyploids affords greater tolerance to mutations that can impact genome evolution. In this study, we describe sequence and structural variation in the genomes of six accessions of cultivated potato (
Solanum tuberosum L.), a vegetatively propagated autotetraploid and their impact on the transcriptome. Sequence diversity was high with a mean single nucleotide polymorphisms (SNP ) rate of approximately 1 per 50 bases suggestive of high levels of allelic diversity. Additive gene expression was observed in leaves (3605 genes) and tubers (6156 genes) that contrasted the preferential allele expression of between 2180 and 3502 and 3367 and 5270 genes in the leaf and tuber transcriptome, respectively. Preferential allele expression was significantly associated with evolutionarily conserved genes suggesting selection of specific alleles of genes responsible for biological processes common to angiosperms during the breeding selection process. Copy number variation was rampant with between 16 098 and 18 921 genes in each cultivar exhibiting duplication or deletion. Copy number variable genes tended to be evolutionarily recent, lowly expressed, and enriched in genes that show increased expression in response to biotic and abiotic stress treatments suggestive of a role in adaptation. Gene copy number impacts on gene expression were detected with 528 genes having correlations between copy number and gene expression. Collectively, these data suggest that in addition to allelic variation of coding sequence, the heterogenous nature of the tetraploid potato genome contributes to a highly dynamic transcriptome impacted by allele preferential and copy number‐dependent expression effects. -
Summary The altered carbon assimilation pathway of crassulacean acid metabolism (
CAM ) photosynthesis results in an up to 80% higher water‐use efficiency than C3photosynthesis in plants making it a potentially useful pathway for engineering crop plants with improved drought tolerance. Here we surveyed detailed temporal (diel time course) and spatial (across a leaf gradient) gene and microRNA (miRNA ) expression patterns in the obligateCAM plant pineapple [Ananas comosus (L.) Merr.]. The high‐resolution transcriptome atlas allowed us to distinguish betweenCAM ‐related and non‐CAM gene copies. A differential gene co‐expression network across green and white leaf diel datasets identified genes with circadian oscillation,CAM ‐related functions, and source‐sink relations. Gene co‐expression clusters containingCAM pathway genes are enriched with clock‐associatedcis ‐elements, suggesting circadian regulation ofCAM . About 20% of pineapple microRNA s have diel expression patterns, with several that target keyCAM ‐related genes. Expression and physiology data provide a model forCAM ‐specific carbohydrate flux and long‐distance hexose transport. Together these resources provide a list of candidate genes for targeted engineering ofCAM into C3photosynthesis crop species.