Relevant bibliographies by topics / Plant U-box

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Plant U-box'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Plant U-box"

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Kim, Dae Yeon, Yong Jin Lee, Min Jeong Hong, Jae Ho Kim, and Yong Weon Seo. "Genome Wide Analysis of U-Box E3 Ubiquitin Ligases in Wheat (Triticum aestivum L.)." International Journal of Molecular Sciences 22, no. 5 (March 7, 2021): 2699. http://dx.doi.org/10.3390/ijms22052699.

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U-box E3 ligase genes play specific roles in protein degradation by post-translational modification in plant signaling pathways, developmental stages, and stress responses; however, little is known about U-box E3 genes in wheat. We identified 213 U-box E3 genes in wheat based on U-box and other functional domains in their genome sequences. The U-box E3 genes were distributed among 21 chromosomes and most showed high sequence homology with homoeologous U-box E3 genes. Synteny analysis of wheat U-box E3 genes was conducted with other plant species such as Brachypodium distachyon, barley, rice, Triricum uratu, and Aegilops tauschii. A total of 209 RNA-seq samples representing 22 tissue types, from grain, root, leaf, and spike samples across multiple time points, were analyzed for clustering of U-box E3 gene expression during developmental stages, and the genes responded differently in various tissues and developmental stages. In addition, expression analysis of U-box E3 genes under abiotic stress, including drought, heat, and both heat and drought, and cold conditions, was conducted to provide information on U-box E3 gene expression under specific stress conditions. This analysis of U-box E3 genes could provide valuable information to elucidate biological functions for a better understanding of U-box E3 genes in wheat.
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Jung, Choonkyun, Pingzhi Zhao, Jun Sung Seo, Nobutaka Mitsuda, Shulin Deng, and Nam-Hai Chua. "PLANT U-BOX PROTEIN10 Regulates MYC2 Stability in Arabidopsis." Plant Cell 27, no. 7 (July 2015): 2016–31. http://dx.doi.org/10.1105/tpc.15.00385.

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Li, Min, Si-qi Shen, Yi-bin Xing, Wan-wan Jiao, Yong-rui Zhan, Ya-dan Sun, Da-long Guo, and Yi-He Yu. "Vitis vinifera VvPUB17 functions as a E3 ubiquitin ligase and enhances powdery mildew resistance via the salicylic acid signaling pathway." Journal of Berry Research 11, no. 3 (August 27, 2021): 419–30. http://dx.doi.org/10.3233/jbr-210709.

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BACKGROUND: Powdery mildew affects grapevine growth and development and reduces grapevine fruit yield and quality. Plant U-box (PUB) E3 ubiquitin ligases play important roles in ubiquitin/proteasome-mediated protein degradation during plant development and in the plant defense response. OBJECTIVE: We cloned the VvPUB17 gene from Vitis vinifera and analyzed that VvPUB17 enhanced the resistance of grapevine to powdery mildew through the SA signal pathway. METHODS: Pathogen inoculation of Arabidopsis thaliana and grapevine plants was carried out by the tableting method. Gene expression was analyzed by quantitative real-time PCR. Sequence analysis and in vitro ubiquitination experiments show the structure and characteristics of VvPUB17. Exogenous salicylic acid, methyl jasmonate, ethylene and powdery mildew induced the expression of VvPUB17 in Arabidopsis leaves to verify the resistance of VvPUB17 to powdery mildew. RESULTS: Sequence analysis and in vitro ubiquitination experiments show that VvPUB17 contains U-box and Armadillo repeats (ARM repeat) and has E3 ubiquitin ligase activity dependent on the conserved U-box motif. Transgenic plants showed elevated levels of key genes related to the SA defense response pathway and high concentrations of salicylic acid. CONCLUSIONS: VvPUB17 functions as an E3 ubiquitin ligase that enhances the resistance of grapes to powdery mildew through the SA signal pathway.
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Connelly, S., and W. Filipowicz. "Activity of chimeric U small nuclear RNA (snRNA)/mRNA genes in transfected protoplasts of Nicotiana plumbaginifolia: U snRNA 3'-end formation and transcription initiation can occur independently in plants." Molecular and Cellular Biology 13, no. 10 (October 1993): 6403–15. http://dx.doi.org/10.1128/mcb.13.10.6403.

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Formation of the 3' ends of RNA polymerase II (Pol II)-specific U small nuclear RNAs (U snRNAs) in vertebrate cells is dependent upon transcription initiation from the U snRNA gene promoter. Moreover, U snRNA promoters are unable to direct the synthesis of functional polyadenylated mRNAs. In this work, we have investigated whether U snRNA 3'-end formation and transcription initiation are also coupled in plants. We have first characterized the requirements for 3'-end formation of an Arabidopsis U2 snRNA expressed in transfected protoplasts of Nicotiana plumbaginifolia. We found that the 3'-end-adjacent sequence CA (N)3-10AGTNNAA, conserved in plant Pol II-specific U snRNA genes, is essential for the 3'-end formation of U2 transcripts and, similar to the vertebrate 3' box, is highly tolerant to mutation. The 3'-flanking regions of an Arabidopsis U5 and a maize U2 snRNA gene can effectively substitute for the Arabidopsis U2 3'-end formation signal, indicating that these signals are functionally equivalent among different Pol II-transcribed snRNA genes. The plant U snRNA 3'-end formation signal can be recognized irrespective of whether transcription initiation occurs at U snRNA or mRNA gene promoters, although efficiency of 3' box utilization is higher when transcription initiation occurs at the U snRNA promoter. Moreover, transcripts initiated from the U2 gene promoter can be spliced and polyadenylated. Transcription from a Pol III-specific plant U snRNA gene promoter is not compatible with polyadenylation. Finally, we reveal that initiation at a Pol II-specific plant U snRNA gene promoter can occur in the absence of the snRNA coding region and a functional snRNA 3'-end formation signal, demonstrating that these sequences play no role in determining the RNA polymerase specificity of plant U snRNA genes.
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Connelly, S., and W. Filipowicz. "Activity of chimeric U small nuclear RNA (snRNA)/mRNA genes in transfected protoplasts of Nicotiana plumbaginifolia: U snRNA 3'-end formation and transcription initiation can occur independently in plants." Molecular and Cellular Biology 13, no. 10 (October 1993): 6403–15. http://dx.doi.org/10.1128/mcb.13.10.6403-6415.1993.

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Formation of the 3' ends of RNA polymerase II (Pol II)-specific U small nuclear RNAs (U snRNAs) in vertebrate cells is dependent upon transcription initiation from the U snRNA gene promoter. Moreover, U snRNA promoters are unable to direct the synthesis of functional polyadenylated mRNAs. In this work, we have investigated whether U snRNA 3'-end formation and transcription initiation are also coupled in plants. We have first characterized the requirements for 3'-end formation of an Arabidopsis U2 snRNA expressed in transfected protoplasts of Nicotiana plumbaginifolia. We found that the 3'-end-adjacent sequence CA (N)3-10AGTNNAA, conserved in plant Pol II-specific U snRNA genes, is essential for the 3'-end formation of U2 transcripts and, similar to the vertebrate 3' box, is highly tolerant to mutation. The 3'-flanking regions of an Arabidopsis U5 and a maize U2 snRNA gene can effectively substitute for the Arabidopsis U2 3'-end formation signal, indicating that these signals are functionally equivalent among different Pol II-transcribed snRNA genes. The plant U snRNA 3'-end formation signal can be recognized irrespective of whether transcription initiation occurs at U snRNA or mRNA gene promoters, although efficiency of 3' box utilization is higher when transcription initiation occurs at the U snRNA promoter. Moreover, transcripts initiated from the U2 gene promoter can be spliced and polyadenylated. Transcription from a Pol III-specific plant U snRNA gene promoter is not compatible with polyadenylation. Finally, we reveal that initiation at a Pol II-specific plant U snRNA gene promoter can occur in the absence of the snRNA coding region and a functional snRNA 3'-end formation signal, demonstrating that these sequences play no role in determining the RNA polymerase specificity of plant U snRNA genes.
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Trujillo, Marco. "News from the PUB: plant U-box type E3 ubiquitin ligases." Journal of Experimental Botany 69, no. 3 (December 10, 2017): 371–84. http://dx.doi.org/10.1093/jxb/erx411.

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Graat, Y., J. O. Rosa, M. P. Nepomuceno, L. B. Carvalho, and P. L. C. A. Alves. "Grass Weeds Interfering with Eucalypt: Effects of the Distance of Coexistence on the Initial Plant Growth." Planta Daninha 33, no. 2 (June 2015): 203–11. http://dx.doi.org/10.1590/0100-83582015000200005.

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Two experiments were carried out to evaluate the initial plant growth of Eucalyptus urograndis growing in coexistence with Urochloa decumbens and U. ruziziensis. In 100-L box, one plant of U. decumbens or U. ruziziensis grew in coexistence with one plant of E. urograndis clones C219H or H15, respectively, in the distances of 0, 5, 10, 15, 20, 25, 30, 35, and 40 cm from the crop. After 30, 60, 90 (both clones), and 150 days (just for H15), growth characteristics were evaluated. Plants of both clones, growing in weed-free situations, showed a better growth and development than plants that grew in weedy situations, independently of the distance, having the highest plant height, stem diameter, dry mass of stem, and dry mass of leaves. As the same way, the number of branches, number of leaves, and leaf area of the clone C219H were similarly affected. Urochloa ruziziensis reduced the dry mass accumulation of stem and leaves by the rate of 0.06 and 0.32 g per plant, respectively, per each centimeter growing nearest to the crop, while U. decumbens reduced by 0.03 and 0.14 g per plant. The interference of U. decumbens and U. ruziziensis with E. urograndis is more intense when weedy plants grow in short distances from the crop.
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Feke, Ann M., Jing Hong, Wei Liu, and Joshua M. Gendron. "A Decoy Library Uncovers U-Box E3 Ubiquitin Ligases That Regulate Flowering Time in Arabidopsis." Genetics 215, no. 3 (May 20, 2020): 699–712. http://dx.doi.org/10.1534/genetics.120.303199.

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Targeted degradation of proteins is mediated by E3 ubiquitin ligases and is important for the execution of many biological processes. Redundancy has prevented the genetic characterization of many E3 ubiquitin ligases in plants. Here, we performed a reverse genetic screen in Arabidopsis using a library of dominant-negative U-box-type E3 ubiquitin ligases to identify their roles in flowering time and reproductive development. We identified five U-box decoy transgenic populations that have defects in flowering time or the floral development program. We used additional genetic and biochemical studies to validate PLANT U-BOX 14 (PUB14), MOS4-ASSOCIATED COMPLEX 3A (MAC3A), and MAC3B as bona fide regulators of flowering time. This work demonstrates the widespread importance of E3 ubiquitin ligases in floral reproductive development. Furthermore, it reinforces the necessity of dominant-negative strategies for uncovering previously unidentified regulators of developmental transitions in an organism with widespread genetic redundancy, and provides a basis on which to model other similar studies.
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Wiborg, Jakob, Charlotte O'Shea, and Karen Skriver. "Biochemical function of typical and variant Arabidopsis thaliana U-box E3 ubiquitin-protein ligases." Biochemical Journal 413, no. 3 (July 15, 2008): 447–57. http://dx.doi.org/10.1042/bj20071568.

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The variance of the U-box domain in 64 Arabidopsis thaliana (thale cress) E3s (ubiquitin-protein ligases) was used to examine the interactions between E3s and E2s (ubiquitin-conjugating enzymes). E2s and E3s are components of the ubiquitin protein degradation pathway. Seven U-box proteins were analysed for their ability to ubiquitinate proteins in vitro in co-operation with different E2s. All U-box domains exhibited ubiquitination activity and interacted productively with UBC4/5-type E2s. Three and four of the U-box domains mediated ubiquitin addition in the presence of UBC13 and UBC7 E2s respectively, but no productive interaction was observed with the UBC15 E2 tested. The activity of AtPUB54 [Arabidopsis thaliana (thale cress) plant U-box 54 protein] was dependent on Trp266 in the E2-binding cleft, and the E2 selectivity was changed by substitution of this position. The function of the distant U-box protein, AtPUB49, representing a large family of eukaryotic proteins containing a U-box linked to a cyclophilin-like peptidyl-prolyl cis–trans isomerase domain, was characterized biochemically. AtPUB49 functioned both as a prolyl isomerase and a chaperone by catalysing cis–trans isomerization of peptidyl-prolyl bonds and dissolving protein aggregates. In conclusion, both typical and atypical Arabidopsis U-box proteins were active E3s. The overlap in the E3/E2 selectivity suggests that in vivo specificity is not determined only by the E3–E2 interactions, but also by other parameters, e.g. co-existence or interactions with additional domains. The biochemical functions of AtPUB49 suggest that the protein can be involved in folding or degradation of protein substrates. Similar functions can also be retained within a protein complex with separate chaperone and U-box proteins.
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Knop, Jan, Tim Lienemann, Haifa El-Kilani, Sven Falke, Catharina Krings, Maria Sindalovskaya, Johannes Bergler, Christian Betzel, and Stefan Hoth. "Structural Features of a Full-Length Ubiquitin Ligase Responsible for the Formation of Patches at the Plasma Membrane." International Journal of Molecular Sciences 22, no. 17 (August 31, 2021): 9455. http://dx.doi.org/10.3390/ijms22179455.

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Plant U-box armadillo repeat (PUB-ARM) ubiquitin (Ub) ligases have important functions in plant defense through the ubiquitination of target proteins. Defense against pathogens involves vesicle trafficking and the formation of extracellular vesicles. The PUB-ARM protein SENESCENCE ASSOCIATED UBIQUITIN E3 LIGASE1 (SAUL1) can form patches at the plasma membrane related to tethering multi-vesicular bodies (MVBs) to the plasma membrane. We uncovered the structure of a full-length plant ubiquitin ligase and the structural requirements of SAUL1, which are crucial for its function in patch formation. We resolved the structure of SAUL1 monomers by small-angle X-ray scattering (SAXS). The SAUL1 model showed that SAUL1 consists of two domains: a domain containing the N-terminal U-box and armadillo (ARM) repeats and the C-terminal ARM repeat domain, which includes a positively charged groove. We showed that all C-terminal ARM repeats are essential for patch formation and that this function requires arginine residue at position 736. By applying SAXS to polydisperse SAUL1 systems, the oligomerization of SAUL1 is detectable, with SAUL1 tetramers being the most prominent oligomers at higher concentrations. The oligomerization domain consists of the N-terminal U-box and some N-terminal ARM repeats. Deleting the U-box resulted in the promotion of the SAUL1 tethering function. Our findings indicate that structural changes in SAUL1 may be fundamental to its function in forming patches at the plasma membrane.
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Dissertations / Theses on the topic "Plant U-box"

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Salt, Jennifer Nicole. "Characterization of members of the Arabidopsis Plant U-Box/ARM repeat gene family." 2008. http://link.library.utoronto.ca/eir/EIRdetail.cfm?Resources__ID=742592&T=F.

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Yee, Donna. "The Expanding Diversity of Plant U-box E3 Ubiquitin Ligases in Arabidopsis: Identifying AtPUB18 and AtPUB19 Function during Abiotic Stress Responses." Thesis, 2010. http://hdl.handle.net/1807/26265.

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The ability of plants to sense and respond to environmental and endogenous signals is essential to their growth and development. As part of these diverse cellular functions, ubiquitin-mediated proteolysis has emerged to be an important process involved in how plant signalling pathways can be regulated in response to such cues. Of the three enzymes involved in linking ubiquitin to protein targets, E3 ubiquitin ligases are of interest as they confer substrate specificity during this ubiquitination process. The overall focal point of this research is on plant U-box (PUB) E3 ubiquitin ligases, a family that has undergone a large gene expansion possibly attributable to the regulation of biological processes unique to the plant life cycle. In Arabidopsis there are 64 predicted PUBs, many for which biological roles have yet to be determined. And as research continues to uncover PUB functions, the functional diversity in the gene family will likely expand. Specifically the focus of this research is on characterizing two ARM repeat-containing PUBs – AtPUB18 and AtPUB19. General analysis of pub18 and pub19 T-DNA insertion lines for growth defects did not yield distinct altered phenotypes. Closer inspection of selected lines showed independent gene assortment phenotypes that, with further inordinately convoluted pursuit, proved to have an AtPUB18/19-unrelated outcome. The availability of Arabidopsis microarray databases provided exploratory expression profiling as a starting point to elucidate PUB function. AtPUB19 and closely related AtPUB18 are notable for their increased expression during abiotic stresses. While condition-directed germination assays showed a decreased sensitivity to salt and ABA for pub18 pub19 double insertion lines, no related change in susceptibility to these or other abiotic stress treatments were seen with condition-directed root growth assays. Thus, this preliminary work has begun to reveal insight into the complex abiotic stress-related roles AtPUB18 and AtPUB19 have during mediation of environmental stress acclimation in Arabidopsis.
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Book chapters on the topic "Plant U-box"

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Conference papers on the topic "Plant U-box"

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Dong, Milton, Hong Ming Lee, and Chii Chern. "A Complete Piping Analysis With Thermal Stratification Loads." In 10th International Conference on Nuclear Engineering. ASMEDC, 2002. http://dx.doi.org/10.1115/icone10-22763.

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The U. S. Nuclear Regulatory Commission (USNRC) had issued Bulletins 88-08, 88-11, 89-90, and 93-38 to address the concerns and problems due to thermal stratification loading during the life span of normal plant operation. The thermal stratification condition typically will cause pipe to bow in on a long horizontal segment. These conditions have not been commonly considered in piping design. However, the additional thermal cyclic stresses and loads due to these conditions could lead to the fatigue damage of the piping components and the failures of pipe supports. Analyzing the effects of thermal stratification loads can be very cumbersome if it is not a built-in functionality of the analysis program. Thus in response to the recent increase in such cases we have incorporated this feature in our piping stress computer program. A stress engineer can now define the thermal stratification conditions easily and the program will compute the pipe stresses and pipe support loads automatically as one of the load cases. The program then combines the thermal stratification load cases with other load cases as required in accordance with the load histogram to determine the cumulative fatigue damage of the piping system. The thermal cyclic stresses are evaluated in accordance with the design rules of Nuclear Class 1 piping components provided in NB-3650 of ASME section III Code. This paper presents the method, modeling and validation for implementing the functionality of analyzing thermal stratification loads in a computer program, as well as an application on an actual piping system as an illustration.
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Martin, David E. "PCLINES, A Parametric Lines Development Program for the Home Computer." In SNAME 18th Chesapeake Sailing Yacht Symposium. SNAME, 2007. http://dx.doi.org/10.5957/csys-2007-011.

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An Excel© spreadsheet lines development program has been written for a home computer and is available to conference attendees. The program utilizes B-Spline parametric formulations for planar curve definition of the traditional hull lines: body, waterlines and buttocks. The user establishes the basic hull outline, in BSpline curves, by inputting bow and stern overhangs, freeboard at selected points, the draft of the canoe body at selected points, the beam on deck at selected points, and the maximum beam at the waterline. By judicious selections the user will see the resulting hull outline in profile and plan views, and can easily adjust these inputs to gain the desired hull outline. The user works with actual points on the hull rather than B-Spline vertices. The hull lines are then developed by the Excel program which establishes the hull form defined by the above outlines and satisfying inputs of the conventional hull form parameters: Center of Buoyancy, (Lcb) Center of Floatation, (Lcf) Prismatic Coefficient, (Cp), Maximum Section Coefficient, (Cm) and the Water-plane Coefficient, (Cwp). The lines development is accomplished in two steps. First, the user employs the Excel Solver to establish a waterline, and Sectional Area curve that satisfy the above parameters. The program accomplishes this by varying the draft at stations two and eight, which adjusts the shape of the center-plane curve without changing the draft, Tc. The solver ensures a “fair” waterline by minimizing the “bending” criterion of the waterline: that is, by minimizing the sum of the squares of d2y/du2 and d2x/du2. Here, y and x are defined by B-Spline formulations in the parameter “u”. The vertices of the B-Spline functions are varied by the Excel Solver to find the minimum bending criterion. Second, with the Section Area and waterline beam established for each station, the program establishes the shape of each station body curve which satisfies the section area, draft, freeboard and beams on deck and waterline. Fairness is again established by minimizing the “bending” criterion. Since there are no section areas for stations 10 and the transom, a scheme for constructing a transomgeometrically similar to station 9.5 is provided. Station 10 is established by fairing to the transom. The program can establish a round bottom hull in about a minute and a half after the input parameters are entered. It is essential however that the hull form parameters be selected judiciously. Clearly Lcb and Lcf must be compatible, and the hull outline must be reasonable in order to gain a fair hull. In this regard the user is provided with automatic input of six different hull shapes that provide good starting points for a design effort. Thus, in a matter of minutes the user can examine an alternate hull shape while keeping selected hull form parameters constant.
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