المؤلفون: Hu, Wei, Lagarias, J Clark

المصدر: Plant Molecular Biology. 114(4)

مصطلحات موضوعية: Plant Biology, Biological Sciences, Genetics, Aetiology, 2.1 Biological and endogenous factors, Phytochrome B, Arabidopsis, Cytosol, Arabidopsis Proteins, Signal Transduction, Basic Helix-Loop-Helix Transcription Factors, Hypocotyl, Plants, Genetically Modified, Light, Mutation, Gene Expression Regulation, Plant, Seedlings, Phenotype, Light-independent phyB signaling, Cytoplasmic phytochrome signaling, Photomorphogenesis, Subcellular localization, Plant photoreceptors, Biochemistry and Cell Biology, Plant Biology & Botany, Plant biology

الوصف: The red and far-red light photoreceptor phytochrome B (phyB) transmits light signals following cytosol-to-nuclear translocation to regulate transcriptional networks therein. This necessitates changes in protein-protein interactions of phyB in the cytosol, about which little is presently known. Via introduction of a nucleus-excluding G767R mutation into the dominant, constitutively active phyBY276H (YHB) allele, we explore the functional consequences of expressing a cytosol-localized YHBG767R variant in transgenic Arabidopsis seedlings. We show that YHBG767R elicits selective constitutive photomorphogenic phenotypes in dark-grown phyABCDE null mutants, wild type and other phy-deficient genotypes. These responses include light-independent apical hook opening, cotyledon unfolding, seed germination and agravitropic hypocotyl growth with minimal suppression of hypocotyl elongation. Such phenotypes correlate with reduced PIF3 levels, which implicates cytosolic targeting of PIF3 turnover or PIF3 translational inhibition by YHBG767R. However, as expected for a cytoplasm-tethered phyB, YHBG767R elicits reduced light-mediated signaling activity compared with similarly expressed wild-type phyB in phyABCDE mutant backgrounds. YHBG767R also interferes with wild-type phyB light signaling, presumably by formation of cytosol-retained and/or otherwise inactivated heterodimers. Our results suggest that cytosolic interactions with PIFs play an important role in phyB signaling even under physiological conditions.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/7tv4w411Test
https://escholarship.org/content/qt7tv4w411/qt7tv4w411.pdfTest

المؤلفون: Du, Juan, Kim, Keunhwa, Chen, Meng

المصدر: Nature Communications. 15(1)

مصطلحات موضوعية: Phytochrome B, Arabidopsis, Arabidopsis Proteins, Cell Nucleus, Temperature, Plants, Genetically Modified, Organelles

الوصف: Photobodies (PBs) are membraneless subnuclear organelles that self-assemble via concentration-dependent liquid-liquid phase separation (LLPS) of the plant photoreceptor and thermosensor phytochrome B (PHYB). The current PHYB LLPS model posits that PHYB phase separates randomly in the nucleoplasm regardless of the cellular or nuclear context. Here, we established a robust Oligopaints method in Arabidopsis to determine the positioning of individual PBs. We show surprisingly that even in PHYB overexpression lines - where PHYB condensation would be more likely to occur randomly - PBs positioned at twelve distinct subnuclear locations distinguishable by chromocenter and nucleolus landmarks, suggesting that PHYB condensation occurs nonrandomly at preferred seeding sites. Intriguingly, warm temperatures reduce PB number by inducing the disappearance of specific thermo-sensitive PBs, demonstrating that individual PBs possess different thermosensitivities. These results reveal a nonrandom PB nucleation model, which provides the framework for the biogenesis of spatially distinct individual PBs with diverse environmental sensitivities within a single plant nucleus.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/8523c21tTest

المؤلفون: Kim, Ruth, Fan, De, He, Jiangman, Kim, Keunhwa, Du, Juan, Chen, Meng

المصدر: Nature Communications. 15(1)

مصطلحات موضوعية: Phytochrome B, Arabidopsis Proteins, Arabidopsis, Basic Helix-Loop-Helix Transcription Factors, Signal Transduction, Proteolysis, Light, Protein Stability, Gene Expression Regulation, Plant, Cell Nucleus, Plants, Genetically Modified

الوصف: Photoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear membraneless organelles named photobodies (PBs). However, the function of PBs in PHYB signaling remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. Conversely, reducing PB size by dim light, which enhanced PB dynamics and nucleoplasmic PHYB and PIF5, switched the balance towards PIF5 degradation. Together, these results reveal that PB formation spatially segregates two antagonistic PHYB signaling actions - PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm - which could enable an environmentally sensitive, counterbalancing mechanism to titrate nucleoplasmic PIF5 and environmental responses.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/5601b6qtTest

المؤلفون: Soy Platero, Judit

المساهمون: University/Department: Universitat de Barcelona. Facultat de Biologia

مرشدي الرسالة: Monte Collado, Elena, Valls i Matheu, Marc

المصدر: TDX (Tesis Doctorals en Xarxa)

مصطلحات موضوعية: Arabidopsis, Ritmes circadiaris, Ritmos circadianos, Circadian rhythms, Factors de transcripció, Factores de transcripción, Transcription factors, Fitocrom, Fitocromo, Phytochrome, Genómica, Genomics, Ciències Experimentals i Matemàtiques

الوصف: Arabidopsis thaliana seedling growth and development is influenced by both external (such as light and temperature) and internal (like hormones or circadian clock) factors. In short-day (SD) growing conditions, it is known that both light and clock have a pivotal role in the regulation of hypocotyl elongation, as mutations in members of the two pathways result in altered lengthening of the hypocotyl. The main objective of the thesis was to determine the function of PIF transcription factors, as light-signaling pathway intermediates, in the regulation of hypocotyl elongation of SD-grown seedlings, together with the possible interplay between them and TOC1 protein, a central component of the circadian clock. Phenotypic and molecular data obtained along the thesis allowed us to conclude that PIF1 and PIF3 proteins, together with the other members PIF4 and PIF5 which had previously been related with the process, act as positive regulators of hypocotyl growth at the end of the dark period in SD conditions. Moreover, several phenotypic studies, gene expression and protein accumulation analysis, together with chromatin immunoprecipitation assays performed in multiple combinations of PIFs and TOC1 mutants allows us to determine that there is a previously unknown direct crosstalk point between light and circadian clock in the regulation of hypocotyl elongation. Together, the work indicates the existence of a new regulatory mechanism by which clock gates hypocotyl elongation at the end of the dark period in SD-grown seedlings by repressing the transcriptional activity of PIF3 protein during the rest of the night.

الوصف (مترجم): El desenvolupament i creixement de plàntules d’Arabidopsis thaliana està influenciat tant per factors ambientals, com la llum o la temperatura, com per factors interns, com per exemple les hormones o el rellotge circadià. Es coneix que, en condicions de dia curt (cicles de 8h de llum i 16h de foscor), tant la llum com el rellotge circadià realitzen un paper clau en la regulació de l’elongació de l’hipocòtil ja que mutacions en components de les dues vies tenen com a conseqüència alteracions en la llargada d’aquest òrgan. L’objectiu principal d’estudi en aquesta tesi ha estat determinar la funció dels factors de transcripció PIF, intermediaris de la via de senyalització lumínica, en la regulació de l’elongació de l’hipocòtil en plàntules crescudes en dia curt i la connexió que existeix entre aquestes proteïnes i la proteïna TOC1, component central del rellotge circadià. Les dades fenotípiques i moleculars obtingudes al llarg de la tesi ens han permès concloure que les proteïnes PIF1 i PIF3, conjuntament amb PIF4 i PIF5 les quals ja havien estat prèviament involucrades en el procés, actuen com a reguladors positius de l’elongació de l’hipocòtil al final del període de foscor en condicions de dia curt. A més, diferents estudis fenotípics i anàlisis genòmics i bioquímics, conjuntament amb experiments d’immunoprecipitació de la cromatina, realitzats en diferents combinacions de mutants PIFs i TOC1 han permès determinar que existeix un nou punt de relació directa entre la llum i el rellotge circadià en la regulació de l’elongació de l’hipocòtil. Aquest treball ha permès demostrar l’existència d’un nou mecanisme de regulació pel qual el rellotge circadià restringeix el creixement de l’hipocòtil just al final del període de foscor en plàntules crescudes en condicions de dia curt. Tal mecanisme regulatori es basa en la repressió feta per la proteïna TOC1 sobre l’activitat transcripcional de la proteïna PIF3 durant la primera meitat del període de foscor.

وصف الملف: application/pdf

الوصول الحر: http://hdl.handle.net/10803/277536Test

المؤلفون: Rockwell, Nathan C, Martin, Shelley S, Lagarias, J Clark

المصدر: Proceedings of the National Academy of Sciences of the United States of America. 120(17)

مصطلحات موضوعية: Biochemistry and Cell Biology, Biological Sciences, Humans, Phylogeny, Phycobiliproteins, Oxidoreductases, Ecosystem, Bile Pigments, Cyanobacteria, phytochrome, cyanobacteriochrome, phylogenetic analysis, phycobilisome, light harvesting antennae

الوصف: Terrestrial ecosystems and human societies depend on oxygenic photosynthesis, which began to reshape our atmosphere approximately 2.5 billion years ago. The earliest known organisms carrying out oxygenic photosynthesis are the cyanobacteria, which use large complexes of phycobiliproteins as light-harvesting antennae. Phycobiliproteins rely on phycocyanobilin (PCB), a linear tetrapyrrole (bilin) chromophore, as the light-harvesting pigment that transfers absorbed light energy from phycobilisomes to the chlorophyll-based photosynthetic apparatus. Cyanobacteria synthesize PCB from heme in two steps: A heme oxygenase converts heme into biliverdin IXα (BV), and the ferredoxin-dependent bilin reductase (FDBR) PcyA then converts BV into PCB. In the current work, we examine the origins of this pathway. We demonstrate that PcyA evolved from pre-PcyA proteins found in nonphotosynthetic bacteria and that pre-PcyA enzymes are active FDBRs that do not yield PCB. Pre-PcyA genes are associated with two gene clusters. Both clusters encode bilin-binding globin proteins, phycobiliprotein paralogs that we designate as BBAGs (bilin biosynthesis-associated globins). Some cyanobacteria also contain one such gene cluster, including a BBAG, two V4R proteins, and an iron-sulfur protein. Phylogenetic analysis shows that this cluster is descended from those associated with pre-PcyA proteins and that light-harvesting phycobiliproteins are also descended from BBAGs found in other bacteria. We propose that PcyA and phycobiliproteins originated in heterotrophic, nonphotosynthetic bacteria and were subsequently acquired by cyanobacteria.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/83r83543Test

المؤلفون: Alvarez, Maria Alejandra, Li, Chengxia, Lin, Huiqiong, Joe, Anna, Padilla, Mariana, Woods, Daniel P, Dubcovsky, Jorge

المصدر: PLOS Genetics. 19(5)

مصطلحات موضوعية: Biological Sciences, Genetics, Biotechnology, Neurosciences, Phytochrome B, Triticum, Flowers, Circadian Rhythm, Photoperiod, Gene Expression Regulation, Plant, Plant Proteins, Developmental Biology

الوصف: The photoperiodic response is critical for plants to adjust their reproductive phase to the most favorable season. Wheat heads earlier under long days (LD) than under short days (SD) and this difference is mainly regulated by the PHOTOPERIOD1 (PPD1) gene. Tetraploid wheat plants carrying the Ppd-A1a allele with a large deletion in the promoter head earlier under SD than plants carrying the wildtype Ppd-A1b allele with an intact promoter. Phytochromes PHYB and PHYC are necessary for the light activation of PPD1, and mutations in either of these genes result in the downregulation of PPD1 and very late heading time. We show here that both effects are reverted when the phyB mutant is combined with loss-of-function mutations in EARLY FLOWERING 3 (ELF3), a component of the Evening Complex (EC) in the circadian clock. We also show that the wheat ELF3 protein interacts with PHYB and PHYC, is rapidly modified by light, and binds to the PPD1 promoter in planta (likely as part of the EC). Deletion of the ELF3 binding region in the Ppd-A1a promoter results in PPD1 upregulation at dawn, similar to PPD1 alleles with intact promoters in the elf3 mutant background. The upregulation of PPD1 is correlated with the upregulation of the florigen gene FLOWERING LOCUS T1 (FT1) and early heading time. Loss-of-function mutations in PPD1 result in the downregulation of FT1 and delayed heading, even when combined with the elf3 mutation. Taken together, these results indicate that ELF3 operates downstream of PHYB as a direct transcriptional repressor of PPD1, and that this repression is relaxed both by light and by the deletion of the ELF3 binding region in the Ppd-A1a promoter. In summary, the regulation of the light mediated activation of PPD1 by ELF3 is critical for the photoperiodic regulation of wheat heading time.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/547630prTest

المؤلفون: Woods, Daniel P, Li, Weiya, Sibout, Richard, Shao, Mingqin, Laudencia-Chingcuanco, Debbie, Vogel, John P, Dubcovsky, Jorge, Amasino, Richard M

المصدر: PLOS Genetics. 19(5)

مصطلحات موضوعية: Biotechnology, Brachypodium, Phytochrome, Plant Proteins, Photoperiod, Transcription Factors, Epistasis, Genetic, Mutation, Gene Expression Profiling, Flowers, Genetics, Developmental Biology

الوصف: Daylength sensing in many plants is critical for coordinating the timing of flowering with the appropriate season. Temperate climate-adapted grasses such as Brachypodium distachyon flower during the spring when days are becoming longer. The photoreceptor PHYTOCHROME C is essential for long-day (LD) flowering in B. distachyon. PHYC is required for the LD activation of a suite of genes in the photoperiod pathway including PHOTOPERIOD1 (PPD1) that, in turn, result in the activation of FLOWERING LOCUS T (FT1)/FLORIGEN, which causes flowering. Thus, B. distachyon phyC mutants are extremely delayed in flowering. Here we show that PHYC-mediated activation of PPD1 occurs via EARLY FLOWERING 3 (ELF3), a component of the evening complex in the circadian clock. The extreme delay of flowering of the phyC mutant disappears when combined with an elf3 loss-of-function mutation. Moreover, the dampened PPD1 expression in phyC mutant plants is elevated in phyC/elf3 mutant plants consistent with the rapid flowering of the double mutant. We show that loss of PPD1 function also results in reduced FT1 expression and extremely delayed flowering consistent with results from wheat and barley. Additionally, elf3 mutant plants have elevated expression levels of PPD1, and we show that overexpression of ELF3 results in delayed flowering associated with a reduction of PPD1 and FT1 expression, indicating that ELF3 represses PPD1 transcription consistent with previous studies showing that ELF3 binds to the PPD1 promoter. Indeed, PPD1 is the main target of ELF3-mediated flowering as elf3/ppd1 double mutant plants are delayed flowering. Our results indicate that ELF3 operates downstream from PHYC and acts as a repressor of PPD1 in the photoperiod flowering pathway of B. distachyon.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/5193d3r4Test

المؤلفون: Calderon, Robert H, Dalton, Jutta, Zhang, Yu, Quail, Peter H

المصدر: Plant Physiology. 190(3)

مصطلحات موضوعية: Genetics, Phytochrome, Arabidopsis Proteins, Gene Expression Regulation, Plant, Light, Arabidopsis, Biological Sciences, Agricultural and Veterinary Sciences, Plant Biology & Botany

الوصف: The phytochrome (phy)-PHYTOCHROME-INTERACTING FACTOR (PIF) sensory module perceives and transduces light signals to direct target genes (DTGs), which then drive the adaptational responses in plant growth and development appropriate to the prevailing environment. These signals include the first exposure of etiolated seedlings to sunlight upon emergence from subterranean darkness and the change in color of the light that is filtered through, or reflected from, neighboring vegetation ("shade"). Previously, we identified three broad categories of rapidly signal-responsive genes: those repressed by light and conversely induced by shade; those repressed by light, but subsequently unresponsive to shade; and those responsive to shade only. Here, we investigate the potential role of epigenetic chromatin modifications in regulating these contrasting patterns of phy-PIF module-induced expression of DTGs in Arabidopsis (Arabidopsis thaliana). Using RNA-seq and ChIP-seq to determine time-resolved profiling of transcript and histone 3 lysine 4 trimethylation (H3K4me3) levels, respectively, we show that, whereas the initial dark-to-light transition triggers a rapid, apparently temporally coincident decline of both parameters, the light-to-shade transition induces similarly rapid increases in transcript levels that precede increases in H3K4me3 levels. Together with other recent findings, these data raise the possibility that, rather than being causal in the shade-induced expression changes, H3K4me3 may function to buffer the rapidly fluctuating shade/light switching that is intrinsic to vegetational canopies under natural sunlight conditions.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/9dk7z6kjTest

المؤلفون: Ota, Keisuke, Qian, Yong, Zhu, Wenchao, Drobizhev, Mikhail, Nasu, Yusuke, Zhang, Jin, Bito, Haruhiko, Campbell, Robert, Hashizume, Rina, Fujii, Hajime, Mehta, Sohum

المصدر: Protein Science. 31(10)

مصطلحات موضوعية: bacterial phytochrome-derived fluorescent proteins, calcium ion imaging, far-red fluorescence, protein engineering, Animals, Biliverdine, Biosensing Techniques, Calcium, Carrier Proteins, HEK293 Cells, Humans, Ions, Luminescent Proteins, Mice

الوصف: Far-red and near-infrared (NIR) genetically encoded calcium ion (Ca2+ ) indicators (GECIs) are powerful tools for in vivo and multiplexed imaging of neural activity and cell signaling. Inspired by a previous report to engineer a far-red fluorescent protein (FP) from a biliverdin (BV)-binding NIR FP, we have developed a far-red fluorescent GECI, designated iBB-GECO1, from a previously reported NIR GECI. iBB-GECO1 exhibits a relatively high molecular brightness, an inverse response to Ca2+ with ΔF/Fmin  = -13, and a near-optimal dissociation constant (Kd ) for Ca2+ of 105 nM. We demonstrate the utility of iBB-GECO1 for four-color multiplexed imaging in MIN6 cells and five-color imaging in HEK293T cells. Like other BV-binding GECIs, iBB-GECO1 did not give robust signals during in vivo imaging of neural activity in mice, but did provide promising results that will guide future engineering efforts. SIGNIFICANCE: Genetically encoded calcium ion (Ca2+ ) indicators (GECIs) compatible with common far-red laser lines (~630-640 nm) on commercial microscopes are of critical importance for their widespread application to deep-tissue multiplexed imaging of neural activity. In this study, we engineered a far-red excitable fluorescent GECI, designated iBB-GECO1, that exhibits a range of preferable specifications such as high brightness, large fluorescence response to Ca2+ , and compatibility with multiplexed imaging in mammalian cells.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/37h2d2b6Test

المؤلفون: Huang, Zhuo, Tang, Rong, Yi, Xin, Xu, Wenxin, Zhu, Peilei, Jiang, Cai-Zhong

المصدر: International Journal of Molecular Sciences. 23(15)

مصطلحات موضوعية: Plant Biology, Biological Sciences, Biotechnology, Arabidopsis, Basic Helix-Loop-Helix Transcription Factors, Droughts, Gene Expression Regulation, Plant, Phytochrome, Plant Proteins, Plants, Genetically Modified, Salt Tolerance, Stress, Physiological, Myrothamnus flabellifolia, resurrection plant, drought tolerance, basic helix-loop-helix, phytochrome interacting factor, basic helix–loop–helix, Other Chemical Sciences, Genetics, Other Biological Sciences, Chemical Physics, Biochemistry and cell biology, Microbiology, Medicinal and biomolecular chemistry

الوصف: Myrothamnus flabellifolia is the only woody resurrection plant found in the world and can survive from long-term desiccation. Therefore, M. flabellifolia could be considered as a valuable resource for study of plant adaptation to abiotic stress. However, few genes related to its drought tolerance have been functionally characterized and the molecular mechanisms underlying the stress tolerance of M. flabellifolia are largely unknown. The phytochrome interacting factor (PIF) family is a group of basic helix-loop-helix (bHLH) transcription factors and functions as the core regulator in plant growth and development. However, less is known of its participation in abiotic stress response. In this study, we isolated and characterized a dehydration-inducible PIF gene MfPIF8 from M. flabellifolia. Heterologous expression of MfPIF8 in Arabidopsis enhanced tolerance to drought and salinity stresses at seedling and adult stages. It significantly increased primary root length and stomatal aperture (ration of length/width) under stress treatments and decreased water loss rate. Compared with WT, the transgenic lines overexpressing MfPIF8 exhibited higher chlorophyll content and lower malondialdehyde accumulation. The abilities of osmotic adjustment and reactive oxygen species scavenging were also enhanced in MfPIF8 transgenic lines. These results suggest that MfPIF8 may participate in the positive regulation of abiotic stress responses. Additional investigation of its mechanism is needed in the future.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/98z4m145Test