scholarly journals The Rice miR396-GRF-GIF-SWI/SNF Module: A Player in GA Signaling

2022 ◽  
Vol 12 ◽  
Author(s):  
Yuzhu Lu ◽  
Jia Zeng ◽  
Qiaoquan Liu
Keyword(s):  
Environmental Factors ◽  
Chromatin Remodeling ◽  
Essential Role ◽  
Dna Binding Domain ◽  
Dual Roles ◽  
Ga Signaling ◽  
Target Dna ◽  
Original Question ◽  
Growth Promoting ◽  
Dna Translocase

Rice Growth-Regulating Factors (GRFs) were originally identified to be gibberellin (GA)-induced, but the nature of GA induction has remained unknown because most reports thereafter focused on revealing their roles in growth-promoting activities. GRFs have the WRC (Trp, Arg, Cys) domain to target DNA and contain the QLQ (Gln, Leu, Gln) domain to interact with GRF-Interacting Factor (GIF), which recruits ATP-dependent DNA translocase Switch/Sucrose Non-fermenting (SWI/SNF) for chromatin remodeling. Both GRFs and GIFs exhibit transcriptional activities but GIFs lack a DNA-binding domain. So, GRFs act like a navigator in the GRF-GIF-SWI/SNF complex, determining when and where the complex should work on. The levels of most rice GRFs can be sensitively regulated by miR396, which responds to many developmental and environmental factors. Recent clues from several studies highlight the original question of how GRFs participate in GA signaling. DELLA (contain DELLA motif) protein plays dual roles in controlling the level of GRFs by regulating the level of miR396 and interacting with GRFs. Here we address the question of why this complex plays an essential role in controlling plant growth focusing on the action of GA signaling pivot, DELLA.

The trithorax group gene osa encodes an ARID-domain protein that genetically interacts with the brahma chromatin-remodeling factor to regulate transcription

Development ◽  
1999 ◽  
Vol 126 (4) ◽  
pp. 733-742 ◽  
Author(s):  
M. Vazquez ◽  
L. Moore ◽  
J.A. Kennison
Keyword(s):  
Gene Regulation ◽  
Chromatin Remodeling ◽  
Homeotic Gene ◽  
Dna Binding Domain ◽  
Atpase Subunit ◽  
Trithorax Group ◽  
Chromatin Remodeling Complex ◽  
P2 Promoter ◽  
Domain Protein ◽  
Arid Domain

The trithorax group gene brahma (brm) encodes the ATPase subunit of a chromatin-remodeling complex involved in homeotic gene regulation. We report here that brm interacts with another trithorax group gene, osa, to regulate the expression of the Antennapedia P2 promoter. Regulation of Antennapedia by BRM and OSA proteins requires sequences 5′ to the P2 promoter. Loss of maternal osa function causes severe segmentation defects, indicating that the function of osa is not limited to homeotic gene regulation. The OSA protein contains an ARID domain, a DNA-binding domain also present in the yeast SWI1 and Drosophila DRI proteins. We propose that the OSA protein may target the BRM complex to Antennapedia and other regulated genes.

scholarly journals Comparative Analysis of SWIRM Domain-Containing Proteins in Plants

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Yan Gao ◽  
Songguang Yang ◽  
Lianyu Yuan ◽  
Yuhai Cui ◽  
Keqiang Wu
Keyword(s):  
Chromatin Remodeling ◽  
Essential Role ◽  
Atp Hydrolysis ◽  
Chromatin Modification ◽  
Dna Binding Proteins ◽  
Plant Responses ◽  
Chromosomal Proteins ◽  
Genes Encoding ◽  
Chromatin Remodeling Complexes ◽  
Affect Gene Expression

Chromatin-remodeling complexes affect gene expression by using the energy of ATP hydrolysis to locally disrupt or alter the association of histones with DNA. SWIRM (Swi3p, Rsc8p, and Moira) domain is an alpha-helical domain of about 85 residues in chromosomal proteins. SWIRM domain-containing proteins make up large multisubunit complexes by interacting with other chromatin modification factors and may have an important function in plants. However, little is known about SWIRM domain-containing proteins in plants. In this study, 67 SWIRM domain-containing proteins from 6 plant species were identified and analyzed. Plant SWIRM domain proteins can be divided into three distinct types: Swi-type, LSD1-type, and Ada2-type. Generally, the SWIRM domain forms a helix-turn-helix motif commonly found in DNA-binding proteins. The genes encoding SWIRM domain proteins inOryza sativaare widely expressed, especially in pistils. In addition,OsCHB701andOsHDMA701were downregulated by cold stress, whereasOsHDMA701andOsHDMA702were significantly induced by heat stress. These observations indicate that SWIRM domain proteins may play an essential role in plant development and plant responses to environmental stress.

Niko Tinbergen's life and work: a new approach to biology

2007 ◽  
Vol 46 (3) ◽  
pp. 543-553
Author(s):  
Iver Mysterud
Keyword(s):  
Fatty Acid ◽  
Environmental Factors ◽  
Essential Role ◽  
Adult Life ◽  
Nobel Laureate ◽  
New Approach ◽  
Acid Deficiency ◽  
Facteurs Environnementaux ◽  
Fatty Acid Deficiency ◽  
Protein Intolerance

English The life and work of the eminent ethologist and Nobel laureate Nikolaas Tinbergen (1907—1988) played an essential role in the introduction of a new approach that is transforming the scientific understanding of animal behaviour, human nature and evolution. This article focuses on an extremely well-written biography of him, Niko's Nature, by Hans Kruuk, one of Tinbergen's former students. Niko's Nature is more than a biography: it is a presentation and an evaluation of the main lines of European ethology and behaviour research in the 20th century up to the 1980s. Tinbergen suffered from depression most of his adult life, and if he had been a child today, he probably would have been diagnosed as hyperactive (ADHD). Tinbergen fits into a pattern of lifelong fatty-acid deficiency. I also discuss other possible causes of his problems (like protein intolerance, vitamin deficiency, genetics and novel environmental factors) and speculate how Tinbergen would have approached such issues if he were alive today. French La vie et l’oeuvre de Nikolaas Tinbergen (1907–1988), éthologue éminent et Prix Nobel, ont été essentielles pour l’apparition d’une approche nouvelle dans la compréhension scientifique du comportement animal, de la nature humaine et de l’évolution. Ce texte commente une biographie de Tinbergen écrite par l’un de ses anciens étudiants Hans Kruuk, Niko’s Nature. Niko’s Nature est plus qu’une simple biographie, il s’agit en fait d’une présentation et d’une évaluation des principaux courants de l’éthologie et de la recherche comportementale en Europe au 20ème siècle, jusqu’aux années 1980. Durant toute sa vie d’adulte, Tinbergen a souffert de dépression et s’il avait été enfant de nos jours, il aurait probablement été diagnostiqué comme enfant hyperactif (THADA). Tinbergen semble correspondre à un schéma de déficience durable en acides gras. L’auteur évoque aussi d’autres pistes explicatives (comme l’intolérance aux protéines, la déficience en vitamines, la génétique, l’apparition de nouveaux facteurs environnementaux) et s’interroge sur la façon dont Tinbergen aurait approché l’étude de ces questions s’il était encore vivant.

scholarly journals Evidence for DNA Translocation by the ISWI Chromatin-Remodeling Enzyme

2003 ◽  
Vol 23 (6) ◽  
pp. 1935-1945 ◽  
Author(s):  
Iestyn Whitehouse ◽  
Chris Stockdale ◽  
Andrew Flaus ◽  
Mark D. Szczelkun ◽  
Tom Owen-Hughes
Keyword(s):  
Nucleic Acids ◽  
Atpase Activity ◽  
Chromatin Remodeling ◽  
Dna Translocation ◽  
Catalytic Core ◽  
Dna Translocase

ABSTRACT The ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin-remodeling activities. Here, we studied the interaction of the ISWI protein with nucleosomal substrates. We found that the ability of nucleic acids to bind and stimulate the ATPase activity of ISWI depends on length. We also found that ISWI is able to displace triplex-forming oligonucleotides efficiently when they are introduced at sites close to a nucleosome but successively less efficiently 30 to 60 bp from its edge. The ability of ISWI to direct triplex displacement was specifically impeded by the introduction of 5- or 10-bp gaps in the 3′-5′ strand between the triplex and the nucleosome. In combination, these observations suggest that ISWI is a 3′-5′-strand-specific, ATP-dependent DNA translocase that may be capable of forcing DNA over the surface of nucleosomes.

scholarly journals Doa1 targets ubiquitinated substrates for mitochondria-associated degradation

2016 ◽  
Vol 213 (1) ◽  
pp. 49-63 ◽  
Author(s):  
Xi Wu ◽  
Lanlan Li ◽  
Hui Jiang
Keyword(s):  
Essential Role ◽  
Outer Membrane Proteins ◽  
Genetic Screen ◽  
Mitochondrial Outer Membrane ◽  
Processing Factor ◽  
Dual Roles ◽  
Mitochondrial Oxidative Stress ◽  
Functional Complex ◽  
Substrate Processing

Mitochondria-associated degradation (MAD) mediated by the Cdc48 complex and proteasome degrades ubiquitinated mitochondrial outer-membrane proteins. MAD is critical for mitochondrial proteostasis, but it remains poorly characterized. We identified several mitochondrial Cdc48 substrates and developed a genetic screen assay to uncover regulators of the Cdc48-dependent MAD pathway. Surprisingly, we identified Doa1, a substrate-processing factor of Cdc48 that inhibits the degradation of some Cdc48 substrates, as a critical mediator of the turnover of mitochondrial Cdc48 substrates. Deletion of DOA1 causes the accumulation and mislocalization of substrates on mitochondria. Profiling of Cdc48 cofactors shows that Doa1 and Cdc48-Ufd1-Npl4 form a functional complex mediating MAD. Biochemically, Doa1 interacts with ubiquitinated substrates and facilitates substrate recruitment to the Cdc48-Ufd1-Npl4 complex. Functionally, Doa1 is critical for cell survival under mitochondrial oxidative stress, but not ER stress, conditions. Collectively, our results demonstrate the essential role of the Doa1–Cdc48-Ufd1-Npl4 complex in mitochondrial proteostasis and suggest that Doa1 plays dual roles on the Cdc48 complex.

scholarly journals Essential Role of p400/mDomino Chromatin-remodeling ATPase in Bone Marrow Hematopoiesis and Cell-cycle Progression

2010 ◽  
Vol 285 (39) ◽  
pp. 30214-30223 ◽  
Author(s):  
Toshihiro Fujii ◽  
Takeshi Ueda ◽  
Shigekazu Nagata ◽  
Rikiro Fukunaga
Keyword(s):  
Cell Cycle ◽  
Bone Marrow ◽  
Chromatin Remodeling ◽  
Cell Cycle Progression ◽  
Essential Role ◽  
Cycle Progression

scholarly journals Tension-dependent nucleosome remodeling at the pericentromere in yeast

2012 ◽  
Vol 23 (13) ◽  
pp. 2560-2570 ◽  
Author(s):  
Jolien S. Verdaasdonk ◽  
Ryan Gardner ◽  
Andrew D. Stephens ◽  
Elaine Yeh ◽  
Kerry Bloom
Keyword(s):  
Chromatin Remodeling ◽  
Mitotic Spindle ◽  
Structural Integrity ◽  
Physical Force ◽  
Yeast Saccharomyces Cerevisiae ◽  
Nucleosome Remodeling ◽  
Nucleosome Dynamics ◽  
Chromosome Arm ◽  
Dna Translocase ◽  
Kinetochore Function

Nucleosome positioning is important for the structural integrity of chromosomes. During metaphase the mitotic spindle exerts physical force on pericentromeric chromatin. The cell must adjust the pericentromeric chromatin to accommodate the changing tension resulting from microtubule dynamics to maintain a stable metaphase spindle. Here we examine the effects of spindle-based tension on nucleosome dynamics by measuring the histone turnover of the chromosome arm and the pericentromere during metaphase in the budding yeast Saccharomyces cerevisiae. We find that both histones H2B and H4 exhibit greater turnover in the pericentromere during metaphase. Loss of spindle-based tension by treatment with the microtubule-depolymerizing drug nocodazole or compromising kinetochore function results in reduced histone turnover in the pericentromere. Pericentromeric histone dynamics are influenced by the chromatin-remodeling activities of STH1/NPS1 and ISW2. Sth1p is the ATPase component of the Remodels the Structure of Chromatin (RSC) complex, and Isw2p is an ATP-dependent DNA translocase member of the Imitation Switch (ISWI) subfamily of chromatin-remodeling factors. The balance between displacement and insertion of pericentromeric histones provides a mechanism to accommodate spindle-based tension while maintaining proper chromatin packaging during mitosis.

scholarly journals Transcriptome analysis reveals the GRAS family in Salvia miltiorrhiza hairy roots in response to gibberellin

2020 ◽  
Author(s):  
Wenrui Li ◽  
Chuangfeng Liu ◽  
Jingling Liu ◽  
Zhenqing Bai ◽  
Zongsuo Liang
Keyword(s):  
Secondary Metabolism ◽  
Signaling Pathway ◽  
Hairy Roots ◽  
Salvia Miltiorrhiza ◽  
Metabolism Pathway ◽  
Ga Signaling ◽  
Medicinal Value ◽  
Chinese Medicinal Plants ◽  
Growth Promoting ◽  
Gene Structures

Abstract Background: Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants with high medicinal value. Gibberellins are growth-promoting phytohormones that regulate numerous growth and developmental processes. However, their role in regulating secondary metabolism has not been investigated. Results: In this study, we found that GA can promote hairy roots growth and increase the content of tanshinones and phenolic acids. Transcriptome sequencing revealed that secondary metabolism pathway genes were enriched in the GA-responded. After further analysis of the changes of GA signaling pathway genes, it was found that the GRAS transcription factors family had a significant response to GA. We identified 35 SmGRAS genes in S. miltiorrhiza. SmGRAS genes can be divided into ten subfamilies in which members of the same subfamily showed similar conserved motifs and gene structures, suggesting the possible conserved functions.Conclusions: Most SmGRAS genes are significantly responsive to GA, indicating that they may play an important role in the GA signaling pathway and participate in GA regulation of root growth and secondary metabolism in S. miltiorrhiza.

scholarly journals Dual roles of chromatin remodeling protein BRG1 in angiotensin II-induced endothelial–mesenchymal transition

2020 ◽  
Vol 11 (7) ◽  
Author(s):  
Zilong Li ◽  
Xiaochen Kong ◽  
Yuanyuan Zhang ◽  
Yangxi Zhang ◽  
Liming Yu ◽  
...  
Keyword(s):  
Angiotensin Ii ◽  
Chromatin Remodeling ◽  
Cardiac Fibrosis ◽  
Vascular Endothelial Cells ◽  
Epigenetic Mechanism ◽  
Ang Ii ◽  
Dual Roles ◽  
Mesenchymal Transition ◽  
The One ◽  
Endothelial Mesenchymal Transition

Abstract Endothelial–mesenchymal transition (EndMT) is considered one of the processes underlying tissue fibrosis by contributing to the pool of myofibroblasts. In the present study, we investigated the epigenetic mechanism whereby angiotensin II (Ang II) regulates EndMT to promote cardiac fibrosis focusing on the role of chromatin remodeling protein BRG1. BRG1 knockdown or inhibition attenuated Ang II-induced EndMT, as evidenced by down-regulation of CDH5, an endothelial marker, and up-regulation of COL1A2, a mesenchymal marker, in cultured vascular endothelial cells. On the one hand, BRG1 interacted with and was recruited by Sp1 to the SNAI2 (encoding SLUG) promoter to activate SNAI2 transcription in response to Ang II stimulation. Once activated, SLUG bound to the CDH5 promoter to repress CDH5 transcription. On the other hand, BRG1 interacted with and was recruited by SRF to the COL1A2 promoter to activate COL1A2 transcription. Mechanistically, BRG1 evicted histones from the target promoters to facilitate the bindings of Sp1 and SRF. Finally, endothelial conditional BRG1 knockout mice (CKO) exhibited a reduction in cardiac fibrosis, compared to the wild type (WT) littermates, in response to chronic Ang II infusion. In conclusion, our data demonstrate that BRG1 is a key transcriptional coordinator programming Ang II-induced EndMT to contribute to cardiac fibrosis.

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