scholarly journals Modification of Threonine-825 of SlBRI1 Enlarges Cell Size to Enhance Fruit Yield by Regulating the Cooperation of BR-GA Signaling in Tomato

2021 ◽  
Vol 22 (14) ◽  
pp. 7673
Author(s):  
Shufen Wang ◽  
Siqi Lv ◽  
Tong Zhao ◽  
Meng Jiang ◽  
Dehai Liu ◽  
...  
Keyword(s):  
Cell Size ◽  
Agronomic Traits ◽  
Phosphorylation Site ◽  
Signal Strength ◽  
Fruit Weight ◽  
Fine Tuning ◽  
Phosphorylation Sites ◽  
Phenotypic Analysis ◽  
Ga Signaling ◽  
Agricultural Potential

Brassinosteroids (BRs) are growth-promoting phytohormones that can efficiently function by exogenous application at micromolar concentrations or by endogenous fine-tuning of BR-related gene expression, thus, precisely controlling BR signal strength is a key factor in exploring the agricultural potential of BRs. BRASSINOSTEROID INSENSITIVE1 (BRI1), a BR receptor, is the rate-limiting enzyme in BR signal transduction, and the phosphorylation of each phosphorylation site of SlBRI1 has a distinct effect on BR signal strength and botanic characteristics. We recently demonstrated that modifying the phosphorylation sites of tomato SlBRI1 could improve the agronomic traits of tomato to different extents; however, the associated agronomic potential of SlBRI1 phosphorylation sites in tomato has not been fully exploited. In this research, the biological functions of the phosphorylation site threonine-825 (Thr-825) of SlBRI1 in tomato were investigated. Phenotypic analysis showed that, compared with a tomato line harboring SlBRI1, transgenic tomato lines expressing SlBRI1 with a nonphosphorylated Thr-825 (T825A) exhibited a larger plant size due to a larger cell size and higher yield, including a greater plant height, thicker stems, longer internodal lengths, greater plant expansion, a heavier fruit weight, and larger fruits. Molecular analyses further indicated that the autophosphorylation level of SlBRI1, BR signaling, and gibberellic acid (GA) signaling were elevated when SlBRI1 was dephosphorylated at Thr-825. Taken together, the results demonstrated that dephosphorylation of Thr-825 can enhance the functions of SlBRI1 in BR signaling, which subsequently activates and cooperates with GA signaling to stimulate cell elongation and then leads to larger plants and higher yields per plant. These results also highlight the agricultural potential of SlBRI1 phosphorylation sites for breeding high-yielding tomato varieties through precise control of BR signaling.

scholarly journals Fine-tuning flowering time via genome editing of upstream open reading frames of Heading date 2 in rice

2021 ◽  
Author(s):  
feng xiu Li ◽  
Xinxin Liu ◽  
Yuanye Zhang ◽  
Hualong Liu ◽  
Mingliang He ◽  
...  
Keyword(s):  
Genome Editing ◽  
Flowering Time ◽  
Agronomic Traits ◽  
Oryza Sativa L ◽  
Heading Date ◽  
Transcript Level ◽  
Open Reading Frames ◽  
Fine Tuning ◽  
Phenotypic Analysis ◽  
Mutant Lines

Abstract Flowering time of rice (Oryza sativa L.) is among the most important agronomic traits for region adaptation and grain yield.In the process of rice breeding, efficient and slightly modulating the flowering time of an elite cultivar would be more popular with breeder. Hence, we focus on slightly increasing the expression of flowering repressors by CRISPR/Cas9 genome editing system. It was predicated there were three uORFs in 5' leader sequence of Hd2.By editing Hd2 uORFs, we got four homozygous mutant lines and phenotypic analysis showed their heading date delay by 4.6–11.2 days relative to wide type SJ2.The mutation do not affect transcript level of Hd2, but improve translation of a downstream Hd2 pORF. In summary, we developed a efficient approach for delaying rice heading date based on editing uORF region of flowering repressor, which is time and labor saving compared to traditional breeding. In future, uORF of other flowering time related genes, including flowering promoter and flowering repressor genes, can also be used as targets to fine-tune the flowering time of varieties.

scholarly journals Fine-tuning Flowering Time via Genome Editing of Upstream Open Reading Frames of Heading Date 2 in Rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Xinxin Liu ◽  
Hualong Liu ◽  
Yuanye Zhang ◽  
Mingliang He ◽  
Rongtian Li ◽  
...  
Keyword(s):  
Genome Editing ◽  
Flowering Time ◽  
Agronomic Traits ◽  
Oryza Sativa L ◽  
Heading Date ◽  
Open Reading Frames ◽  
Fine Tuning ◽  
Wild Type ◽  
Phenotypic Analysis ◽  
Mutant Lines

AbstractFlowering time of rice (Oryza sativa L.) is among the most important agronomic traits for region adaptation and grain yield. In the process of rice breeding, efficient and slightly modulating the flowering time of an elite cultivar would be more popular with breeder. Hence, we are interested in slightly increasing the expression of flowering repressors by CRISPR/Cas9 genome editing system. It was predicated there were three uORFs in 5’ leader sequence of Hd2. In this study, through editing Hd2 uORFs, we got four homozygous mutant lines. Phenotypic analysis showed that the hd2 urf edited lines flowered later by 4.6–11.2 days relative to wild type SJ2. Supporting the later flowering phenotype, the expression of Ehd1, Hd3a, and RFT1 is significantly decreased in hd2 urf than that in wild type. Moreover, we found that the transcription level of Hd2 is not affected, whereas the Hd2 protein level was increased in hd2 urf compared with wild type, which indicated that Hd2 uORFs indeed affect the translation of a downstream Hd2 pORF. In summary, we developed a efficient approach for delaying rice heading date based on editing uORF region of flowering repressor, which is time and labor saving compared to traditional breeding. In future, uORF of other flowering time related genes, including flowering promoter and flowering repressor genes, can also be used as targets to fine-tune the flowering time of varieties.

scholarly journals A deep learning based approach for prediction of Chlamydomonas reinhardtii phosphorylation sites

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Niraj Thapa ◽  
Meenal Chaudhari ◽  
Anthony A. Iannetta ◽  
Clarence White ◽  
Kaushik Roy ◽  
...  
Keyword(s):  
Deep Learning ◽  
Chlamydomonas Reinhardtii ◽  
Protein Phosphorylation ◽  
Short Term Memory ◽  
Phosphorylation Site ◽  
Specific Protein ◽  
Training Dataset ◽  
Phosphorylation Sites ◽  
Site Prediction ◽  
Model Combining

AbstractProtein phosphorylation, which is one of the most important post-translational modifications (PTMs), is involved in regulating myriad cellular processes. Herein, we present a novel deep learning based approach for organism-specific protein phosphorylation site prediction in Chlamydomonas reinhardtii, a model algal phototroph. An ensemble model combining convolutional neural networks and long short-term memory (LSTM) achieves the best performance in predicting phosphorylation sites in C. reinhardtii. Deemed Chlamy-EnPhosSite, the measured best AUC and MCC are 0.90 and 0.64 respectively for a combined dataset of serine (S) and threonine (T) in independent testing higher than those measures for other predictors. When applied to the entire C. reinhardtii proteome (totaling 1,809,304 S and T sites), Chlamy-EnPhosSite yielded 499,411 phosphorylated sites with a cut-off value of 0.5 and 237,949 phosphorylated sites with a cut-off value of 0.7. These predictions were compared to an experimental dataset of phosphosites identified by liquid chromatography-tandem mass spectrometry (LC–MS/MS) in a blinded study and approximately 89.69% of 2,663 C. reinhardtii S and T phosphorylation sites were successfully predicted by Chlamy-EnPhosSite at a probability cut-off of 0.5 and 76.83% of sites were successfully identified at a more stringent 0.7 cut-off. Interestingly, Chlamy-EnPhosSite also successfully predicted experimentally confirmed phosphorylation sites in a protein sequence (e.g., RPS6 S245) which did not appear in the training dataset, highlighting prediction accuracy and the power of leveraging predictions to identify biologically relevant PTM sites. These results demonstrate that our method represents a robust and complementary technique for high-throughput phosphorylation site prediction in C. reinhardtii. It has potential to serve as a useful tool to the community. Chlamy-EnPhosSite will contribute to the understanding of how protein phosphorylation influences various biological processes in this important model microalga.

scholarly journals PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor

2007 ◽  
Vol 36 (Database) ◽  
pp. D1015-D1021 ◽  
Author(s):  
J. L. Heazlewood ◽  
P. Durek ◽  
J. Hummel ◽  
J. Selbig ◽  
W. Weckwerth ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Phosphorylation Site ◽  
Phosphorylation Sites

scholarly journals Combining ability and heterosis for agronomic traits in chili pepper

2012 ◽  
Vol 30 (2) ◽  
pp. 226-233 ◽  
Author(s):  
Rosana Rodrigues ◽  
Leandro SA Gonçalves ◽  
Cintia dos S Bento ◽  
Claudia P Sudré ◽  
Renata R Robaina ◽  
...  
Keyword(s):  
Combining Ability ◽  
Agronomic Traits ◽  
Fruit Weight ◽  
Matter Content ◽  
Soluble Solids ◽  
Dry Matter Content ◽  
Additive Effects ◽  
Dry Fruit ◽  
Potential Use ◽  
Janeiro State

The Capsicum breeding has been developed with emphasis in bell pepper (Capsicum annuum) and few studies are available in other species, especially C. baccatum, which has potential use not only as disease resistance source but also in obtaining new genotypes suitable for farmers' production. In the present work, the combining ability of ten C. baccatum hybrids, along with their five parentals, were tested considering 12 agronomic traits. The hybrids were produced from a complete diallel without reciprocals and assessed in greenhouse conditions, in Campos dos Goytacazes, Rio de Janeiro state, Brazil, during the period July to December 2009. The experimental design was a randomized block with three replications and the following agronomic traits evaluated: canopy diameter (CD), plant height (PH), days to fructification (DF), number of fruits per plant (NFP), mean fruit weight (FW), dry fruit matter weight (FDM), dry matter content (DM), fruit length (FL), fruit diameter (FD), pulp thickness (PT), total soluble solids (TSS) and yield per plant (PP). Significant differences were observed only for general combining ability (GCA) in regard to PH, FW, FDM, DM, PT and TSS, indicating that additive effects were involved on the control of these characters. For CD, DF, NFP, FL, FD and PP, there was significance not only for GCA but also for specific combining ability (SCA) indicating that non-additive and additive effects were important in genetic control of these traits. The hybrids UENF 1629 X UENF 1732, UENF 1616 X UENF 1732 and UENF 1624 X UENF 1639 were considered superior because they have favorable agronomic traits.

scholarly journals Engineering a bioluminescent indicator for cyclic AMP-dependent protein kinase

1991 ◽  
Vol 279 (3) ◽  
pp. 727-732 ◽  
Author(s):  
G B Sala-Newby ◽  
A K Campbell
Keyword(s):  
Protein Kinase ◽  
Cyclic Amp ◽  
Specific Activity ◽  
Phosphorylation Site ◽  
Live Cells ◽  
Phosphorylation Sites ◽  
Dependent Protein Kinase ◽  
Ph Optimum ◽  
Dependent Protein

cDNA coding for the luciferase in the firefly Photinus pyralis was amplified in vitro to generate cyclic AMP-dependent protein kinase phosphorylation sites. The DNA was transcribed and translated to generate light-emitting protein. A valine at position 217 was mutated to arginine to generate a site RRFS and the heptapeptide kemptide, the phosphorylation site of the porcine pyruvate kinase, was added at the N- or C-terminus of the luciferase. The proteins carrying phosphorylation sites were characterized for their specific activity, pI, effect of pH on the colour of the light emitted and effect of the catalytic subunit of protein kinase A in the presence of ATP. Only one of the recombinant proteins (RRFS) was significantly different from wild-type luciferase. The RRFS mutant had a lower specific activity, lower pH optimum, emitted greener light at low pH and when phosphorylated it decreased its activity by up to 80%. This latter effect was reversed by phosphatase. This recombinant protein is a good candidate to measure for the first time cyclic AMP-dependent phosphorylation in live cells.

scholarly journals Distinct phosphorylation sites in a prototypical GPCR differently orchestrate β-arrestin interaction, trafficking, and signaling

2020 ◽  
Vol 6 (37) ◽  
pp. eabb8368 ◽  
Author(s):  
Hemlata Dwivedi-Agnihotri ◽  
Madhu Chaturvedi ◽  
Mithu Baidya ◽  
Tomasz Maciej Stepniewski ◽  
Shubhi Pandey ◽  
...  
Keyword(s):  
G Protein ◽  
Phosphorylation Site ◽  
Dynamics Simulation ◽  
Phosphorylation Sites ◽  
Functional Responses ◽  
Biased Signaling ◽  
The Stability ◽  
G Protein Coupled ◽  
Structural Aspects

Agonist-induced phosphorylation of G protein–coupled receptors (GPCRs) is a key determinant for their interaction with β-arrestins (βarrs) and subsequent functional responses. Therefore, it is important to decipher the contribution and interplay of different receptor phosphorylation sites in governing βarr interaction and functional outcomes. Here, we find that several phosphorylation sites in the human vasopressin receptor (V2R), positioned either individually or in clusters, differentially contribute to βarr recruitment, trafficking, and ERK1/2 activation. Even a single phosphorylation site in V2R, suitably positioned to cross-talk with a key residue in βarrs, has a decisive contribution in βarr recruitment, and its mutation results in strong G-protein bias. Molecular dynamics simulation provides mechanistic insights into the pivotal role of this key phosphorylation site in governing the stability of βarr interaction and regulating the interdomain rotation in βarrs. Our findings uncover important structural aspects to better understand the framework of GPCR-βarr interaction and biased signaling.

scholarly journals GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System

2020 ◽  
Vol 21 (21) ◽  
pp. 7891
Author(s):  
Chi-Wei Chen ◽  
Lan-Ying Huang ◽  
Chia-Feng Liao ◽  
Kai-Po Chang ◽  
Yen-Wei Chu
Keyword(s):  
Feature Selection ◽  
Protein Phosphorylation ◽  
Phosphorylation Site ◽  
Path Selection ◽  
Ant Colony ◽  
Ant Colony System ◽  
Phosphorylation Sites ◽  
Selection Approach ◽  
New Feature ◽  
Feature Selection Approach

Protein phosphorylation is one of the most important post-translational modifications, and many biological processes are related to phosphorylation, such as DNA repair, transcriptional regulation and signal transduction and, therefore, abnormal regulation of phosphorylation usually causes diseases. If we can accurately predict human phosphorylation sites, this could help to solve human diseases. Therefore, we developed a kinase-specific phosphorylation prediction system, GasPhos, and proposed a new feature selection approach, called Gas, based on the ant colony system and a genetic algorithm and used performance evaluation strategies focused on different kinases to choose the best learning model. Gas uses the mean decrease Gini index (MDGI) as a heuristic value for path selection and adopts binary transformation strategies and new state transition rules. GasPhos can predict phosphorylation sites for six kinases and showed better performance than other phosphorylation prediction tools. The disease-related phosphorylated proteins that were predicted with GasPhos are also discussed. Finally, Gas can be applied to other issues that require feature selection, which could help to improve prediction performance.

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