scholarly journals A synthetic peptide encoded by a random DNA sequence inhibits discrete red light responses

Plant Direct ◽  
2019 ◽  
Vol 3 (10) ◽  
Author(s):  
Tautvydas Shuipys ◽  
Raquel F. Carvalho ◽  
Maureen A. Clancy ◽  
Zhilong Bao ◽  
Kevin M. Folta
Keyword(s):  
Dna Sequence ◽  
Synthetic Peptide ◽  
Red Light ◽  
Light Responses

scholarly journals A Synthetic Peptide Encoded by a Random DNA Sequence Inhibits Discrete Red Light Responses

2019 ◽  
Author(s):  
Tautvydas Shuipys ◽  
Raquel F. Carvalho ◽  
Maureen A. Clancy ◽  
Zhilong Bao ◽  
Kevin M. Folta
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Synthetic Peptide ◽  
Red Light ◽  
Seedling Development ◽  
Light Responses ◽  
Random Peptide ◽  
Peptide Expression ◽  
Early Seedling ◽  
Cotyledon Expansion

AbstractWe have identified a synthetic peptide that interrupts discrete aspects of seedling development under red light. Previous reports have demonstrated that plants transformed with random DNA sequences produce synthetic peptides that affect plant biology. In this report one specific peptide is characterized that inhibits discrete aspects of red-light-mediated Arabidopsis thaliana development during photomorphogenesis. Seedlings expressing the PEP6-32 peptide presented longer hypocotyls and diminished cotyledon expansion when grown under red light. Other red-light-mediated seedling processes such as induction of Lhcb (cab) transcripts or loss of vertical growth remained unaffected. Long-term responses to red light in PEP6-32 expressing plants, such as repression of flowering time, did not show defects in red light signaling or integration. A synthesized peptide applied exogenously induced the long-hypocotyl phenotype under red light in non-transformed seedlings. The results indicate that the PEP6-32 peptide causes discrete cell expansion defects during early seedling development in red light, mimicking weak phyB alleles in some aspects of seedling photomorphogenesis. The findings demonstrate that new chemistries derived from random peptide expression can modulate specific facets of plant growth and development.One Sentence SummaryA plant line expressing random DNA sequence expresses a synthetic peptide that affects specific red-light responses in a developing seedling.

scholarly journals On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome

2018 ◽  
Vol 293 (21) ◽  
pp. 8161-8172 ◽  
Author(s):  
Heikki Takala ◽  
Heli K. Lehtivuori ◽  
Oskar Berntsson ◽  
Ashley Hughes ◽  
Rahul Nanekar ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Deinococcus Radiodurans ◽  
Red Light ◽  
Light Responses ◽  
Structural Mechanism ◽  
Weakly Coupled ◽  
Activity State ◽  
Conserved Tyrosine

Phytochromes are photoreceptors in plants, fungi, and various microorganisms and cycle between metastable red light–absorbing (Pr) and far-red light–absorbing (Pfr) states. Their light responses are thought to follow a conserved structural mechanism that is triggered by isomerization of the chromophore. Downstream structural changes involve refolding of the so-called tongue extension of the phytochrome-specific GAF-related (PHY) domain of the photoreceptor. The tongue is connected to the chromophore by conserved DIP and PRXSF motifs and a conserved tyrosine, but the role of these residues in signal transduction is not clear. Here, we examine the tongue interactions and their interplay with the chromophore by substituting the conserved tyrosine (Tyr263) in the phytochrome from the extremophile bacterium Deinococcus radiodurans with phenylalanine. Using optical and FTIR spectroscopy, X-ray solution scattering, and crystallography of chromophore-binding domain (CBD) and CBD–PHY fragments, we show that the absence of the Tyr263 hydroxyl destabilizes the β-sheet conformation of the tongue. This allowed the phytochrome to adopt an α-helical tongue conformation regardless of the chromophore state, hence distorting the activity state of the protein. Our crystal structures further revealed that water interactions are missing in the Y263F mutant, correlating with a decrease of the photoconversion yield and underpinning the functional role of Tyr263 in phytochrome conformational changes. We propose a model in which isomerization of the chromophore, refolding of the tongue, and globular conformational changes are represented as weakly coupled equilibria. The results also suggest that the phytochromes have several redundant signaling routes.

scholarly journals FIN5 Positively Regulates Far-red Light Responses in Arabidopsis thaliana

2003 ◽  
Vol 44 (6) ◽  
pp. 565-572 ◽  
Author(s):  
Dae-Shik Cho ◽  
Sung-Hyun Hong ◽  
Hong-Gil Nam ◽  
Moon-Soo Soh
Keyword(s):  
Arabidopsis Thaliana ◽  
Red Light ◽  
Light Responses

scholarly journals Ultra-High-Density QTL Marker Mapping for Seedling Photomorphogenesis Mediating Arabidopsis Establishment in Southern Patagonia

2021 ◽  
Vol 12 ◽  
Author(s):  
Daniel Matsusaka ◽  
Daniele Filiault ◽  
Diego H. Sanchez ◽  
Javier F. Botto
Keyword(s):  
Complex Traits ◽  
Red Light ◽  
High Density ◽  
Potential Candidate ◽  
Hypocotyl Length ◽  
Light Responses ◽  
Wide Range ◽  
Southern Patagonia ◽  
Ril Population ◽  
Wild Accessions

Arabidopsis thaliana shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, Arabidopsis has a high potential for the identification of genes underlying ecologically important complex traits, thus providing new insights on genome evolution. Previous research suggested that distinct light responses were crucial for Arabidopsis establishment in a peculiar ecological niche of southern Patagonia. The aim of this study was to explore the genetic basis of contrasting light-associated physiological traits that may have mediated the rapid adaptation to this new environment. From a biparental cross between the photomorphogenic contrasting accessions Patagonia (Pat) and Columbia (Col-0), we generated a novel recombinant inbred line (RIL) population, which was entirely next-generation sequenced to achieve ultra-high-density saturating molecular markers resulting in supreme mapping sensitivity. We validated the quality of the RIL population by quantitative trait loci (QTL) mapping for seedling de-etiolation, finding seven QTLs for hypocotyl length in the dark and continuous blue light (Bc), continuous red light (Rc), and continuous far-red light (FRc). The most relevant QTLs, Rc1 and Bc1, were mapped close together to chromosome V; the former for Rc and Rc/dark, and the latter for Bc, FRc, and dark treatments. The additive effects of both QTLs were confirmed by independent heterogeneous inbred families (HIFs), and we explored TZP and ABA1 as potential candidate genes for Rc1 and Bc1QTLs, respectively. We conclude that the Pat × Col-0 RIL population is a valuable novel genetic resource to explore other adaptive traits in Arabidopsis.

scholarly journals A Multifaceted Action of Phytochrome B in Plant Environmental Adaptation

2021 ◽  
Vol 12 ◽  
Author(s):  
Jae Young Kim ◽  
June-Hee Lee ◽  
Chung-Mo Park
Keyword(s):  
Red Light ◽  
Environmental Adaptation ◽  
Signaling Cascades ◽  
Adaptive Behaviors ◽  
Environmental Cues ◽  
Plant Responses ◽  
Light Illumination ◽  
Light Responses ◽  
And Performance

Light acts as a vital external cue that conveys surrounding information into plant growth and performance to facilitate plants to coordinate with changing environmental conditions. Upon exposure to light illumination, plants trigger a burst of molecular and physiological signaling cascades that induces not only photomorphogenic responses but also diverse adaptive behaviors. Notably, light responses and photomorphogenic traits are often associated with plant responses to other environmental cues, such as heat, cold, drought, and herbivore and pathogen attack. Growing evidence in recent years demonstrate that the red/far-red light-absorbing phytochrome (phy) photoreceptors, in particular phyB, play an essential role in plant adaptation responses to abiotic and biotic tensions by serving as a key mediator of information flow. It is also remarkable that phyB mediates the plant priming responses to numerous environmental challenges. In this minireview, we highlight recent advances on the multifaceted role of phyB during plant environmental adaptation. We also discuss the biological relevance and efficiency of the phy-mediated adaptive behaviors in potentially reducing fitness costs under unfavorable environments.

Divergence in red light responses associated with thermal reversion of PHYTOCHROME B between high‐ and low‐latitude species

2021 ◽  
Author(s):  
Hajime Ikeda ◽  
Tomomi Suzuki ◽  
Yoshito Oka ◽  
A. Lovisa S. Gustafsson ◽  
Christian Brochmann ◽  
...  
Keyword(s):  
Red Light ◽  
Phytochrome B ◽  
Low Latitude ◽  
Light Responses

scholarly journals Novel light-regulated genes in Trichoderma atroviride: a dissection by cDNA microarrays

Microbiology ◽  
2006 ◽  
Vol 152 (11) ◽  
pp. 3305-3317 ◽  
Author(s):  
T. Rosales-Saavedra ◽  
E. U. Esquivel-Naranjo ◽  
S. Casas-Flores ◽  
P. Martínez-Hernández ◽  
E. Ibarra-Laclette ◽  
...  
Keyword(s):  
Red Light ◽  
Continuous Light ◽  
Soil Fungus ◽  
Light Response ◽  
Trichoderma Atroviride ◽  
Light Responses ◽  
The Common ◽  
Living Organisms ◽  
Regulated Gene Expression

The influence of light on living organisms is critical, not only because of its importance as the main source of energy for the biosphere, but also due to its capacity to induce changes in the behaviour and morphology of nearly all forms of life. The common soil fungus Trichoderma atroviride responds to blue light in a synchronized manner, in time and space, by forming a ring of green conidia at what had been the colony perimeter at the time of exposure (photoconidiation). A putative complex formed by the BLR-1 and BLR-2 proteins in T. atroviride appears to play an essential role as a sensor and transcriptional regulator in photoconidiation. Expression analyses using microarrays containing 1438 unigenes were carried out in order to identify early light response genes. It was found that 2.8 % of the genes were light responsive: 2 % induced and 0.8 % repressed. Expression analysis in blr deletion mutants allowed the demonstration of the occurrence of two types of light responses, a blr-independent response in addition to the expected blr-dependent one, as well as a new role of the BLR proteins in repression of transcription. Exposure of T. atroviride to continuous light helped to establish that the light-responsive genes are subject to photoadaptation. Finally, evidence is provided of red-light-regulated gene expression and a possible crosstalk between the blue and red light signalling pathways.

scholarly journals Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome

2009 ◽  
Vol 106 (37) ◽  
pp. 15639-15644 ◽  
Author(s):  
Xiaojing Yang ◽  
Jane Kuk ◽  
Keith Moffat
Keyword(s):  
Crystal Structure ◽  
Pseudomonas Aeruginosa ◽  
Crystal Packing ◽  
Red Light ◽  
Binding Pocket ◽  
Site Directed Mutagenesis ◽  
Light Responses ◽  
Propionate Group ◽  
Core Module ◽  
Absorbing States

Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria by means of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here, we report the crystal structure of the Q188L mutant of Pseudomonas aeruginosa bacteriophytochrome (PaBphP) photosensory core module, which exhibits altered photoconversion behavior and different crystal packing from wild type. We observe two distinct chromophore conformations in the Q188L crystal structure that we identify with the Pfr and Pr states. The Pr/Pfr compositions, varying from crystal to crystal, seem to correlate with light conditions under which the Q188L crystals are cryoprotected. We also compare all known Pr and Pfr structures. Using site-directed mutagenesis, we identify residues that are involved in stabilizing the 15Ea (Pfr) and 15Za (Pr) configurations of the biliverdin chromophore. Specifically, Ser-261 appears to be essential to form a stable Pr state in PaBphP, possibly by means of its interaction with the propionate group of ring C. We propose a “flip-and-rotate” model that summarizes the major conformational differences between the Pr and Pfr states of the chromophore and its binding pocket.

The Effects of Light and Temperature on Yellow Nutsedge (Cyperus esculentus) Basal-Bulb Formation

Weed Science ◽  
1983 ◽  
Vol 31 (2) ◽  
pp. 148-152 ◽  
Author(s):  
E. W. Stoller ◽  
Joseph T. Woolley
Keyword(s):  
White Light ◽  
Red Light ◽  
Fluorescent Light ◽  
Cyperus Esculentus ◽  
Light Responses ◽  
Yellow Nutsedge ◽  
Bulb Formation ◽  
Basal Bulb ◽  
Alternating Temperature

Investigations were conducted to determine whether light, temperature, or their interaction stimulated primary basal-bulb formation on underground stems of yellow nutsedge (Cyperus esculentusL.) seedlings grown from tubers. Basal-bulb formation results when internodes shorten and leaves lengthen. When seedlings were grown without medium around the underground shoots, a temperature alternation of 10C stimulated basal-bulb formation; light did not affect the process. When seedlings were grown with medium around the underground shoots, either light or alternating temperature stimulated basal-bulb formation. Nine colors of light gave the same stimulus as white (fluorescent) light. Phytochrome did not appear to be the photoreceptor for the stimulus, as both red and far-red light responses were identical to that of white light.

scholarly journals PhyB induces intron retention and uORF-mediated translational inhibition of PIF3

2019 ◽  
Author(s):  
Jie Dong ◽  
Haodong Chen ◽  
Xing Wang Deng ◽  
Vivian F. Irish ◽  
Ning Wei
Keyword(s):  
Alternative Splicing ◽  
Protein Degradation ◽  
Intron Retention ◽  
Red Light ◽  
Light Response ◽  
Protein Translation ◽  
Light Cycle ◽  
Light Responses ◽  
E3 Ligases ◽  
Short Day

AbstractThe phytochrome B (phyB) photoreceptor stimulates light responses in plants in part by inactivating repressors of light responses such as phytochrome-interacting factor 3 (PIF3). It has been established that activated phyB inhibits PIF3 by rapid protein degradation and decreased transcription. PIF3 protein degradation has been shown to be mediated by EIN3-BINDING F-BOX PROTEIN (EBF) and LIGHT-RESPONSE BTB (LRB) E3 ligases, the latter simultaneously targeting phyB for degradation. In this study, we show that PIF3 level is additionally regulated by alternative splicing and protein translation. Overaccumulation of photo-activated phyB, which occur in the mutant defective for LRB genes under continuous red light (Rc), induces a specific alternative splicing of PIF3 that results in retention of an intron in the 5’UTR of PIF3 mRNA. In turn, the upstream opening reading frames (uORF) contained within this intron inhibit PIF3 protein synthesis. The phyB-dependent alternative splicing of PIF3 is diurnally regulated under the short-day light cycle. We hypothesize that this reversible regulatory mechanism may be utilized to fine-tune the level of PIF3 protein in light-grown plants, and may contribute to the oscillation of PIF3 protein abundance under the short-day environment.One Sentence SummaryLight down-regulates PIF3 by multiple mechanisms. We show that phyB induces an alternative splicing event that inhibits PIF3 protein translation, and that is regulated by short-day diurnal cycle.

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