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Proceedings of the National Academy of... Feb 2020Light-environment signals, sensed by plant phytochrome photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF)...
Light-environment signals, sensed by plant phytochrome photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factor abundance and activity. Previous genome-wide DNA-binding and expression analysis has identified a set of genes that are direct targets of PIF transcriptional regulation. However, quantitative analysis of promoter occupancy versus expression level has suggested that unknown "trans factors" modulate the intrinsic transcriptional activation activity of DNA-bound PIF proteins. Here, using computational analysis of published data, we have identified PSEUDO-RESPONSE REGULATORS (PRR5 and PRR7) as displaying a high frequency of colocalization with the PIF proteins at their binding sites in the promoters of PIF Direct Target Genes (DTGs). We show that the PRRs function to suppress PIF-stimulated growth in the light and vegetative shade and that they repress the rapid PIF-induced expression of PIF-DTGs triggered by exposure to shade. The repressive action of the PRRs on both growth and DTG expression requires the PIFs, indicating direct action on PIF activity, rather than a parallel antagonistic pathway. Protein interaction assays indicate that the PRRs exert their repressive activity by binding directly to the PIF proteins in the nucleus. These findings support the conclusion that the PRRs function as direct outputs from the core circadian oscillator to regulate the expression of PIF-DTGs through modulation of PIF transcriptional activation activity, thus expanding the roles of the multifunctional PIF-signaling hub.
Topics: Arabidopsis Proteins; Basic Helix-Loop-Helix Transcription Factors; Circadian Clocks; Gene Expression Regulation, Plant; Photoreceptors, Plant; Photosynthesis; Phytochrome; Repressor Proteins; Transcription Factors; Transcriptional Activation
PubMed: 31988133
DOI: 10.1073/pnas.1918317117 -
Plant Biotechnology Journal Sep 2020Flowering time is a critical determinant of the geographic distribution and regional adaptability of soybean (Glycine max) and is strongly regulated by photoperiod and...
Flowering time is a critical determinant of the geographic distribution and regional adaptability of soybean (Glycine max) and is strongly regulated by photoperiod and temperature. In this study, quantitative trait locus (QTL) mapping and subsequent candidate gene analysis revealed that GmPRR37, encoding a pseudo-response regulator protein, is responsible for the major QTL qFT12-2, which was identified from a population of 308 recombinant inbred lines (RILs) derived from a cross between a very late-flowering soybean cultivar, 'Zigongdongdou (ZGDD)', and an extremely early-flowering cultivar, 'Heihe27 (HH27)', in multiple environments. Comparative analysis of parental sequencing data confirmed that HH27 contains a non-sense mutation that causes the loss of the CCT domain in the GmPRR37 protein. CRISPR/Cas9-induced Gmprr37-ZGDD mutants in soybean exhibited early flowering under natural long-day (NLD) conditions. Overexpression of GmPRR37 significantly delayed the flowering of transgenic soybean plants compared with wild-type under long photoperiod conditions. In addition, both the knockout and overexpression of GmPRR37 in soybean showed no significant phenotypic alterations in flowering time under short-day (SD) conditions. Furthermore, GmPRR37 down-regulated the expression of the flowering-promoting FT homologues GmFT2a and GmFT5a, and up-regulated flowering-inhibiting FT homologue GmFT1a expression under long-day (LD) conditions. We analysed haplotypes of GmPRR37 among 180 cultivars collected across China and found natural Gmprr37 mutants flower earlier and enable soybean to be cultivated at higher latitudes. This study demonstrates that GmPRR37 controls soybean photoperiodic flowering and provides opportunities to breed optimized cultivars with adaptation to specific regions and farming systems.
Topics: CRISPR-Cas Systems; China; Flowers; Gene Expression Regulation, Plant; Mutation; Photoperiod; Plant Proteins; Glycine max
PubMed: 31981443
DOI: 10.1111/pbi.13346 -
Molecular Plant Mar 2020Post-translational modifications play essential roles in finely modulating eukaryotic circadian clock systems. In plants, the effects of O-glycosylation on the circadian...
Post-translational modifications play essential roles in finely modulating eukaryotic circadian clock systems. In plants, the effects of O-glycosylation on the circadian clock and the underlying mechanisms remain largely unknown. The O-fucosyltransferase SPINDLY (SPY) and the O-GlcNAc transferase SECRET AGENT (SEC) are two prominent O-glycosylation enzymes in higher plants, with both overlapped and unique functions in plant growth and development. Unlike the critical role of O-GlcNAc in regulating the animal circadian clock, here we report that nuclear-localized SPY, but not SEC, specifically modulates the pace of the Arabidopsis circadian clock. By identifying the interactome of SPY, we identified PSEUDO-RESPONSE REGULATOR 5 (PRR5), one of the core circadian clock components, as a new SPY-interacting protein. PRR5 can be O-fucosylated by SPY in planta, while point mutation in the catalytic domain of SPY abolishes the O-fucosylation of PRR5. The protein abundance of PRR5 is strongly increased in spy mutants, while the degradation rate of PRR5 is much reduced, suggesting that PRR5 proteolysis is promoted by SPY-mediated O-fucosylation. Moreover, multiple lines of genetic evidence indicate that PRR5 is a major downstream target of SPY to specifically mediate its modulation of the circadian clock. Collectively, our findings provide novel insights into the specific role of the O-fucosyltransferase activity of SPY in modulating the circadian clock and implicate that O-glycosylation might play an evolutionarily conserved role in modulating the circadian clock system, via O-GlcNAcylation in mammals, but via O-fucosylation in higher plants.
Topics: Active Transport, Cell Nucleus; Arabidopsis; Arabidopsis Proteins; Cell Nucleus; Circadian Clocks; Glycosylation; Proteolysis; Repressor Proteins; Transcription Factors
PubMed: 31899321
DOI: 10.1016/j.molp.2019.12.013 -
Evolutionary Applications Jan 2020Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic...
Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pleiotropy and polygenic control, and parallel evidence from phenotypic-based experimental comparisons is required. In long-lived organisms, the detection of selective pressures might also be precluded by evolutionary lag times in response to the environment. Here, we used the English yew to showcase an example of a multiscale integrative approach in a nonmodel species with limited plant and genomic resources. We combined information from two independent sources, phenotypes in a common environment and genomic data in natural populations, to investigate the signature of selection. Growth differences among populations in a common environment, and phenological patterns of both shoot elongation and male strobili maturation, were associated with climate clines, providing evidence for local adaptation and guiding us in the selection of populations for genomic analyses. We used information on over 25,000 SNPs from c. 1,200 genes to infer the demographic history and to test for molecular signatures of selection at different levels: SNP, gene, and biological pathway. Our results confirmed an overall demographic history of population decline, but we also found evidence for putative local adaptation at the molecular level. We identified or confirmed several candidate genes for positive and negative selection in forest trees, including the (PRR7), an essential component of the circadian clock in plants. In addition, we successfully tested an approach to detect polygenic adaptation in biological pathways, allowing us to identify the pathway as a candidate stress-response pathway that deserves further attention in other plants. Finally, our study contributes to the emerging view that explaining contemporary standing genetic variation requires considering adaptation to past climates, especially for long-lived trees.
PubMed: 31892949
DOI: 10.1111/eva.12838 -
AJNR. American Journal of Neuroradiology Jan 2020The Response Assessment in Neuro-Oncology criteria were developed as an objective tool for radiologic assessment of treatment response in high-grade gliomas. Imaging... (Review)
Review
The Response Assessment in Neuro-Oncology criteria were developed as an objective tool for radiologic assessment of treatment response in high-grade gliomas. Imaging plays a critical role in the management of the patient with glioma, from initial diagnosis to posttreatment follow-up, which can be particularly challenging for radiologists. Interpreting findings after surgery, radiation, and chemotherapy requires profound knowledge about the tumor biology, as well as the peculiar changes expected to ensue as a consequence of each treatment technique. In this article, we discuss the imaging findings associated with tumor progression, tumor response, pseudoprogression, and pseudoresponse according to the Response Assessment in Neuro-Oncology criteria for high-grade and lower-grade gliomas. We describe relevant practical issues when evaluating patients with glioma, such as the need for imaging in the first 48 hours, the radiation therapy planning and isodose curves, the significance of T2/FLAIR hyperintense lesions, the impact of the timing for the evaluation after radiation therapy, and the definition of progressive disease on the histologic specimen. We also illustrate the correlation among the findings on conventional MR imaging with advanced techniques, such as perfusion, diffusion-weighted imaging, spectroscopy, and amino acid PET. Because many of the new lesions represent a mixture of tumor cells and tissue with radiation injury, the radiologist aims to identify the predominant component of the lesion and categorize the findings according to Response Assessment in Neuro-Oncology criteria so that the patient can receive the best treatment.
Topics: Brain Neoplasms; Glioma; Humans; Neuroimaging
PubMed: 31857322
DOI: 10.3174/ajnr.A6358 -
Plant Physiology Jan 2020The Evening Complex (EC) is a core component of the Arabidopsis () circadian clock, which represses target gene expression at the end of the day and integrates...
The Evening Complex (EC) is a core component of the Arabidopsis () circadian clock, which represses target gene expression at the end of the day and integrates temperature information to coordinate environmental and endogenous signals. Here we show that the EC induces repressive chromatin structure to regulate the evening transcriptome. The EC component ELF3 directly interacts with a protein from the SWI2/SNF2-RELATED (SWR1) complex to control deposition of H2A.Z-nucleosomes at the EC target genes. SWR1 components display circadian oscillation in gene expression with a peak at dusk. In turn, SWR1 is required for the circadian clockwork, as defects in SWR1 activity alter morning-expressed genes. The EC-SWR1 complex binds to the loci of the core clock genes - () and and catalyzes deposition of nucleosomes containing the histone variant H2A.Z coincident with the repression of these genes at dusk. This provides a mechanism by which the circadian clock temporally establishes repressive chromatin domains to shape oscillatory gene expression around dusk.
Topics: Arabidopsis; Arabidopsis Proteins; Chromatin; Circadian Clocks; Histones; Repressor Proteins; Transcription Factors
PubMed: 31712305
DOI: 10.1104/pp.19.00881 -
Plant & Cell Physiology Nov 2019The circadian clock is a timekeeping system for regulation of numerous biological daily rhythms. One characteristic of the circadian clock is that period length remains...
The circadian clock is a timekeeping system for regulation of numerous biological daily rhythms. One characteristic of the circadian clock is that period length remains relatively constant in spite of environmental fluctuations, such as temperature change. Here, using the curated collection of in-house small molecule chemical library (ITbM chemical library), we show that small molecule 3,4-dibromo-7-azaindole (B-AZ) lengthened the circadian period of Arabidopsis thaliana (Arabidopsis). B-AZ has not previously been reported to have any biological and biochemical activities. Target identification can elucidate the mode of action of small molecules, but we were unable to make a molecular probe of B-AZ for target identification. Instead, we performed other analysis, gene expression profiling that potentially reveals mode of action of molecules. Short-term treatment of B-AZ decreased the expression of four dawn- and morning-phased clock-associated genes, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7. Consistently, amounts of PRR5 and TIMING OF CAB EXPRESSION 1 (TOC1) proteins, transcriptional repressors of CCA1, LHY, PRR9 and PRR7 were increased upon B-AZ treatment. B-AZ inhibited Casein Kinase 1 family (CK1) that phosphorylates PRR5 and TOC1 for targeted degradation. A docking study and molecular dynamics simulation suggested that B-AZ interacts with the ATP-binding pocket of human CK1 delta, whose amino acid sequences are highly similar to those of Arabidopsis CK1. B-AZ-induced period-lengthening effect was attenuated in prr5 toc1 mutants. Collectively, this study provides a novel and simple structure CK1 inhibitor that modulates circadian clock via accumulation of PRR5 and TOC1.
Topics: Arabidopsis; Arabidopsis Proteins; Casein Kinase I; Circadian Clocks; Circadian Rhythm; Gene Expression Regulation, Plant; Transcription Factors
PubMed: 31529098
DOI: 10.1093/pcp/pcz183 -
Frontiers in Plant Science 2019[This corrects the article DOI: 10.3389/fpls.2019.00667.].
[This corrects the article DOI: 10.3389/fpls.2019.00667.].
PubMed: 31481969
DOI: 10.3389/fpls.2019.01057 -
Frontiers in Plant Science 2019Control of protein turnover is a key post-translational control point in the oscillatory network of the circadian clock. Some elements, such as TOC1 and PRR5 are engaged...
Control of protein turnover is a key post-translational control point in the oscillatory network of the circadian clock. Some elements, such as TOC1 and PRR5 are engaged by a well-described F-box protein, ZEITLUPE, dedicated to their proteolytic turnover to shape their expression profile to a specific time of night. For most other clock components the regulation of their protein abundance is unknown, though turnover is often rapid and often lags the cycling of the respective mRNA. Here we report the design and results of an unbiased genetic screen in Arabidopsis to uncover proteolytic regulatory factors of PSEUDO-RESPONSE REGULATOR 7 (PRR7), a transcriptional repressor that peaks in the late afternoon. We performed EMS mutagenesis on a transgenic line expressing a () translational fusion that accurately recapitulates the diurnal and circadian oscillations of the endogenous PRR7 protein. Using continuous luciferase imaging under constant light, we recovered mutants that alter the PRR7-LUC waveform and some that change period. We have identified novel alleles of and , core components of the ELF3-ELF4-LUX Evening Complex (EC), that dampen the oscillation of PRR7-LUC. We report the characterization of two new hypomorphic alleles of that help to understand the relationship between molecular potency and phenotype.
PubMed: 31191580
DOI: 10.3389/fpls.2019.00667 -
Frontiers in Neurology 2019Glioblastoma is the deadliest primary malignant brain neoplasm, and despite the availability of many treatment options, its prognosis remains somber. Enhancement... (Review)
Review
Glioblastoma is the deadliest primary malignant brain neoplasm, and despite the availability of many treatment options, its prognosis remains somber. Enhancement detected by magnetic resonance imaging (MRI) was considered the best imaging marker of tumor activity in glioblastoma for decades. However, its role as a surrogate marker of tumor viability has changed with the appearance of new treatment regimens and imaging modalities. The antiangiogenic therapy created an inflection point in the imaging assessment of glioblastoma response in clinical trials and clinical practice. Although BEV led to the improvement of enhancement, it did not necessarily mean tumor response. The decrease in the enhancement intensity represents a change in the permeability properties of the blood brain barrier, and presumably, the switch of the tumor growth pattern to an infiltrative non-enhancing phenotype. New imaging techniques for the assessment of cellularity, blood flow hemodynamics, and biochemistry have emerged to overcome this hurdle; nevertheless, designing tools to assess tumor response more accurately, and in so doing, improve the assessment of response to standard of care (SOC) therapies and to novel therapies, remains challenging.
PubMed: 31133966
DOI: 10.3389/fneur.2019.00460