Alternative polyadenylation (
Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work is unclear. In particular, the effect of auxin on pre‐
- NSF-PAR ID:
- 10048379
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- The Plant Journal
- Volume:
- 93
- Issue:
- 2
- ISSN:
- 0960-7412
- Page Range / eLocation ID:
- p. 246-258
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Summary APA ) is a widespread post‐transcriptional mechanism that regulates gene expression throughmRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about theAPA ‐mediated regulation underlying the distinct characteristics between two major rice subspecies,indica andjaponica . Using a poly(A)‐tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage betweenindica andjaponica , and extensive differentiation inAPA profiles was detected genome‐wide. Genes with subspecies‐specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance ofindica and cold‐stress tolerance ofjaponica . In most tissues, differential usage ofAPA sites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL ) related to yield traits, such as spikelet number and 1000‐seed weight. In leaves of the booting stage,APA site‐switching genes displayed global shortening of 3′ untranslated regions with increased expression inindica compared withjaponica , and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis inindica than injaponica , being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest thatAPA may be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post‐transcriptional genetic basis underlying the divergence of rice traits. -
more » « less
Summary The post‐transcriptional regulation involved in the responses of diatoms to silicon is poorly understood. Using a poly(A)‐tag sequencing (
PAT ‐seq) technique that interrogates only the junctions of 3′‐untranslated region (UTR) and the poly(A) tails at the transcriptome level, a comprehensive comparison of alternative polyadenylation (APA ) was performed to understand the role of post‐transcriptional regulation in various silicon‐related cellular responses for the marine diatomThalassiosira pseudonana . In total, 23 701 poly(A) clusters and 6894APA genes, treated with silicon starvation and replenishment, were identified at nine time points. SignificantAPA was found in numerous genes (e.g. five cingulin genes) closely associated with the silicon‐starvation response, girdle bands and valve synthesis, suggesting that many genes participated in the responses to silicon availability and biosilica formation through changes in transcript isoforms. The poly(A) site usage profiles were distinct during various stages of silicon biomineralization responses. Moreover, a correlation betweenAPA and expression levels ofAPA switching genes was also discovered. This is an interesting study that presents a genome‐wide profile of transcript ends in diatoms, which is distinct from that of higher plants, animals and other microalgae. This work provides an important resource to understand a different aspect of cell‐wall synthesis. -
more » « less
Summary Despite well established roles of micro
RNA s in plant development, few aspects have been addressed to understand their effects in seeds especially on lipid metabolism. In this study, we showed that overexpressing microRNA 167A (miR167OE ) in camelina (Camelina sativa ) under a seed‐specific promoter changed fatty acid composition and increased seed size. Specifically, the miR167OE seeds had a lower α‐linolenic acid with a concomitantly higher linoleic acid content than the wild‐type. This decreased level of fatty acid desaturation corresponded to a decreased transcriptional expression of the camelina fatty acid desaturase3 (Cs ) in developing seeds. MiR167 targeted the transcription factor auxin response factor (CsFAD 3ARF 8) in camelina, as had been reported previously in Arabidopsis. Chromatin immunoprecipitation experiments combined with transcriptome analysis indicated that CsARF 8 bound to promoters of camelinabZIP 67ABI 3ABI 3‐bZIP 12 pathway regulateCs expression and affect α‐linolenic acid accumulation. In addition, to decipher the miR167A‐CsFAD 3ARF 8 mediated transcriptional cascade forCs suppression, transcriptome analysis was conducted to implicate mechanisms that regulate seed size in camelina. Expression levels of many genes were altered in miR167FAD 3OE , including orthologs that have previously been identified to affect seed size in other plants. Most notably, genes for seed coat development such as suberin and lignin biosynthesis were down‐regulated. This study provides valuable insights into the regulatory mechanism of fatty acid metabolism and seed size determination, and suggests possible approaches to improve these important traits in camelina. -
more » « less
Summary Catabolism of fatty acids stored in oil bodies is essential for seed germination and seedling development in Arabidopsis. This fatty acid breakdown occurs in peroxisomes, organelles that sequester oxidative reactions. Import of peroxisomal enzymes is facilitated by peroxins including
PEX 5, a receptor that delivers cargo proteins from the cytosol to the peroxisomal matrix. After cargo delivery, a complex of thePEX 1 andPEX 6ATP ases and thePEX 26 tail‐anchored membrane protein removes ubiquitinatedPEX 5 from the peroxisomal membrane. We identified Arabidopsispex6 andpex26 mutants by screening for inefficient seedling β‐oxidation phenotypes. The mutants displayed distinct defects in growth, response to a peroxisomally metabolized auxin precursor, and peroxisomal protein import. The lowPEX 5 levels in these mutants were increased by treatment with a proteasome inhibitor or by combiningpex26 with peroxisome‐associated ubiquitination machinery mutants, suggesting that ubiquitinatedPEX 5 is degraded by the proteasome when the function ofPEX 6 orPEX 26 is reduced. Combiningpex26 with mutations that increasePEX 5 levels either worsened or improvedpex26 physiological and molecular defects, depending on the introduced lesion. Moreover, elevatingPEX 5 levels via a35S: transgene exacerbatedPEX 5pex26 defects and ameliorated the defects of only a subset ofpex6 alleles, implying that decreasedPEX 5 is not the sole molecular deficiency in these mutants. We found peroxisomes clustered around persisting oil bodies inpex6 andpex26 seedlings, suggesting a role for peroxisomal retrotranslocation machinery in oil body utilization. The disparate phenotypes of thesepex alleles may reflect unanticipated functions of the peroxisomalATP ase complex. -
more » « less
Abstract BACKGROUND Calmodulin (CaM) is an essential protein in cellular activity and plays important roles in many processes in insect development. RNA interference (RNAi) has been hypothesized to be a promising method for pest control. CaM is a good candidate for RNAi target. However, the sequence and function of CaM in
Nilaparvata lugens are unknown. Furthermore, the double‐stranded RNA (dsRNA) target to CaM gene in pest control is still unavailable.RESULTS In the present study, two alternatively spliced variants of
CaM transcripts, designatedNlCaM1 andNlCaM2 , were cloned fromN. lugens NlCaM includingNlCaM1 andNlCaM2 mRNA was detectable in all developmental stages and tissues ofN. lugens NlCaM expression by RNAi with different dsRNAs led to an inability to molt properly, increased mortality, which ranged from 49.7 to 92.5%, impacted development of the ovaries and led to female infertility. There were no significant reductions in the transcript levels of vitellogenin and its receptor or in the total vitellogenin protein level relative to the control group. However, a significant reduction in vitellogenin protein was detected in ovaries injected with dsNlCaM. In addition, a specific dsRNA ofNlCaM for control ofN. lugens CONCLUSION NlCaM plays important roles mainly in nymph development and uptake of vitellogenin by ovaries in vitellogenesis inN. lugens . dsRNA derived from the less conserved 3′‐UTR ofNlCaM shows great potential for RNAi‐basedN. lugens
