scholarly journals A Fast Signal–Induced Activation of Poly(Adp-Ribose) Polymerase

2000 ◽  
Vol 150 (2) ◽  
pp. 293-308 ◽  
Author(s):  
S. Homburg ◽  
L. Visochek ◽  
N. Moran ◽  
F. Dantzer ◽  
E. Priel ◽  
...  
Keyword(s):  
Dna Binding ◽  
Cell Membrane ◽  
Binding Proteins ◽  
Nuclear Protein ◽  
Dna Binding Proteins ◽  
Alternative Mechanism ◽  
Dna Breaks ◽  
Downstream Target ◽  
Inositol 1,4,5 Trisphosphate ◽  
Fast Activation

We present the first evidence for a fast activation of the nuclear protein poly(ADP-ribose) polymerase (PARP) by signals evoked in the cell membrane, constituting a novel mode of signaling to the cell nucleus. PARP, an abundant, highly conserved, chromatin-bound protein found only in eukaryotes, exclusively catalyzes polyADP-ribosylation of DNA-binding proteins, thereby modulating their activity. Activation of PARP, reportedly induced by formation of DNA breaks, is involved in DNA transcription, replication, and repair. Our findings demonstrate an alternative mechanism: a fast activation of PARP, evoked by inositol 1,4,5,-trisphosphate–Ca2+ mobilization, that does not involve DNA breaks. These findings identify PARP as a novel downstream target of phospholipase C, and unveil a novel fast signal–induced modification of DNA-binding proteins by polyADP-ribosylation.

Novel DNA-binding proteins regulate intestine-specific transcription of the sucrase-isomaltase gene

1992 ◽  
Vol 12 (8) ◽  
pp. 3614-3627
Author(s):  
P G Traber ◽  
G D Wu ◽  
W Wang
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Nuclear Protein ◽  
Regulatory Element ◽  
Dna Binding Proteins ◽  
Nuclear Proteins ◽  
Intestinal Cell ◽  
Specific Gene ◽  
In Vitro Mutagenesis ◽  
Primary Mouse

Sucrase-isomaltase (SI) is an enterocyte-specific gene which exhibits a complex pattern of expression during intestinal development and in the adult intestinal mucosa. In the studies described in this report, we demonstrate that enterocyte-specific transcription of the SI gene is regulated by an evolutionarily conserved promoter that extends approximately 180 bp upstream of the transcription start site. DNase I footprint analysis allowed the identification of three nuclear protein-binding sites within the SI promoter (SIF1, SIF2, and SIF3 [SI footprint]), each of which acted as a positive regulatory element for transcription in intestinal cell lines. SIF1 was shown to bind nuclear protein complexes present in primary mouse small intestinal cell and in an intestinal cell line (Caco-2). However, SIF1-binding proteins were absent in a variety of other epithelial and nonepithelial cells. In vitro mutagenesis experiments demonstrated that the SIF1 site is required for high-level promoter activity in intestinal cells. The SIF3 element formed prominent binding complexes with intestinal and liver nuclear extracts, whereas nuclear proteins from other epithelial and nonepithelial cells formed weaker complexes of different mobilities. The SIF2 element bound nuclear proteins in a pattern similar to that of SIF3, and cross-competition studies suggested that SIF2 and SIF3 may bind the same nuclear proteins. Taken together, these data have allowed the identification of novel DNA-binding proteins that play an important role in regulating intestine-specific transcription of the SI gene.

scholarly journals Novel DNA-binding proteins regulate intestine-specific transcription of the sucrase-isomaltase gene.

1992 ◽  
Vol 12 (8) ◽  
pp. 3614-3627 ◽  
Author(s):  
P G Traber ◽  
G D Wu ◽  
W Wang
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Nuclear Protein ◽  
Regulatory Element ◽  
Dna Binding Proteins ◽  
Nuclear Proteins ◽  
Intestinal Cell ◽  
Specific Gene ◽  
In Vitro Mutagenesis ◽  
Primary Mouse

Sucrase-isomaltase (SI) is an enterocyte-specific gene which exhibits a complex pattern of expression during intestinal development and in the adult intestinal mucosa. In the studies described in this report, we demonstrate that enterocyte-specific transcription of the SI gene is regulated by an evolutionarily conserved promoter that extends approximately 180 bp upstream of the transcription start site. DNase I footprint analysis allowed the identification of three nuclear protein-binding sites within the SI promoter (SIF1, SIF2, and SIF3 [SI footprint]), each of which acted as a positive regulatory element for transcription in intestinal cell lines. SIF1 was shown to bind nuclear protein complexes present in primary mouse small intestinal cell and in an intestinal cell line (Caco-2). However, SIF1-binding proteins were absent in a variety of other epithelial and nonepithelial cells. In vitro mutagenesis experiments demonstrated that the SIF1 site is required for high-level promoter activity in intestinal cells. The SIF3 element formed prominent binding complexes with intestinal and liver nuclear extracts, whereas nuclear proteins from other epithelial and nonepithelial cells formed weaker complexes of different mobilities. The SIF2 element bound nuclear proteins in a pattern similar to that of SIF3, and cross-competition studies suggested that SIF2 and SIF3 may bind the same nuclear proteins. Taken together, these data have allowed the identification of novel DNA-binding proteins that play an important role in regulating intestine-specific transcription of the SI gene.

Transcriptional regulation of temperature-induced remodeling of muscle bioenergetics in goldfish

2012 ◽  
Vol 303 (2) ◽  
pp. R150-R158 ◽  
Author(s):  
Katharina Bremer ◽  
Christopher T. Monk ◽  
Brendon J. Gurd ◽  
Christopher D. Moyes
Keyword(s):  
Dna Binding ◽  
Mitochondrial Biogenesis ◽  
Binding Proteins ◽  
Nuclear Protein ◽  
Transcriptional Response ◽  
Dna Binding Proteins ◽  
Peroxisome Proliferator ◽  
Mrna Levels ◽  
Protein Patterns ◽  
Peroxisome Proliferator Activated Receptor

Central to mammalian mitochondrial biogenesis is the transcriptional master regulator peroxisome proliferator-activated receptor (PPAR)-γ coactivator-1α (PGC-1α), and a network of DNA-binding proteins it coactivates. We explored the role of this pathway in muscle mitochondrial biogenesis in response to thermal acclimation in goldfish ( Carassius auratus ). We investigated the transcriptional response of PGC-1α, PGC-1β, and their antagonist the nuclear receptor interacting protein 1 ( RIP140), as well as the mRNA and protein patterns of DNA-binding proteins that bind PGC-1, including nuclear respiratory factors (NRF) 1 and 2, retinoid X receptor α (RXRα), estrogen-related receptor α (ERRα), thyroid receptor α-1 (TRα-1), PPARα, and PPARβ/δ, and the host cell factor 1 (HCF1), which links PGC-1 and NRF-2. Cold-acclimated (4°C) fish had higher COX activities (4.5-fold) and COX4-1 mRNA levels (3.5-fold per total RNA; 6.5-fold per gram tissue) than warm-acclimated (32°C) fish. The transcription factor patterns were profoundly influenced by changes in RNA per gram tissue (2-fold higher in cold fish) and nuclear protein content (2-fold higher in warm fish). In cold-acclimated fish, mRNA per gram tissue was elevated for PGC-1β, RIP140, NRF-1, HCF1, NRF-2α, NRF-2β-2, ERRα, PPAR β/δ, and RXRα, but other transcriptional regulators either did not change ( PGC-1α, PPARα) or even decreased ( TRα-1). Nuclear protein levels in cold-acclimated fish were higher only for NRF-1; other proteins were either unaffected (NRF-2α, ERRα) or decreased (NRF-2β1/2, TRα, RXRα). Collectively, these data support the role for NRF-1 in regulating cold-induced mitochondrial biogenesis in goldfish, with effects mediated by PGC-1β, rather than PGC-1α.

scholarly journals Cloning and sequence of the human nuclear protein cyclin: homology with DNA-binding proteins.

1987 ◽  
Vol 84 (6) ◽  
pp. 1575-1579 ◽  
Author(s):  
J. M. Almendral ◽  
D. Huebsch ◽  
P. A. Blundell ◽  
H. Macdonald-Bravo ◽  
R. Bravo
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Nuclear Protein ◽  
Dna Binding Proteins

scholarly journals Phosphorylation of nuclear and DNA-binding proteins in proliferating and quiescent mammalian cells

1981 ◽  
Vol 194 (1) ◽  
pp. 193-207 ◽  
Author(s):  
E W Gerner ◽  
M Costa ◽  
D K Holmes ◽  
B E Magun
Keyword(s):  
Molecular Weight ◽  
Cell Growth ◽  
Dna Binding ◽  
Cyclic Amp ◽  
Binding Proteins ◽  
Nuclear Protein ◽  
Dna Binding Proteins ◽  
Exponential Phase ◽  
Nuclear Proteins ◽  
Dependent Growth

The dependence of cell proliferation on nuclear protein phosphorylation was studied with exponential-phase and stationary-phase cultures of Chinese-hamster ovary cells. Nuclear proteins were fractionated, according to their DNA-binding affinities, by using sequential extractions of isolated nuclei with increasing concentrations of NaCl. When viable whole cells were labelled with H332PO4, phosphorylation of nuclear proteins was found to be lower in quiescent cells than in proliferating cells. Phosphorylation of nuclear proteins soluble in 0.30M-NaCl (less than 50% of these proteins bind to DNA) was greater than for those proteins soluble in higher salt concentrations (80-100% of these proteins bind to DNA). Cyclic AMP enhanced the phosphorylation of nuclear proteins soluble in 0.3 m-NaCl by 40-50%, and this stimulation was independent of cell growth. Cyclic AMP also increased the phosphorylation of nuclear proteins soluble in 0.6M-NaCl and 2.0M-NaCl by 40-50% in exponential-phase cultures, but not in stationary-phase cultures. Several examples of specific phosphorylation in response to cyclic AMP were observed, including a 35000-mol.wt. protein in the 0.30 M-NaCl-soluble fraction and several proteins larger than 100000 molecular weight within this fraction. A major peptide of molecular weight approx. 31000 extracted with 0.6M-NaCl was also phosphorylated. Its phosphorylation was independent of cyclic AMP in exponential-phase cultures, and it was not phosphorylated in plateau-phase cells. These changes in cell-growth-dependent phosphorylation occurred in the absence of any apparent qualitative changes in the nuclear protein molecular-weight distributions. These data demonstrate that (1) phosphorylation of nuclear proteins is dependent on the culture's proliferative status, (2) both cyclic AMP-dependent and cyclic AMP-independent specific phosphorylation occurs, and (3) the cyclic AMP-dependent growth-independent phosphorylation that occurs does not appear to be a modification of DNA-binding proteins, whereas the cyclic AMP-dependent growth-dependent phosphorylation does involve modification of DNA binding proteins.

DBP-PSSM: Combination of evolutionary profiles with the XGBoost algorithm to improve the identification of DNA-binding proteins

2020 ◽  
Vol 23 ◽  
Author(s):  
Yanping Zhang ◽  
Pengcheng Chen ◽  
Ya Gao ◽  
Jianwei Ni ◽  
Xiaosheng Wang
Keyword(s):  
Logistic Regression ◽  
Protein Structure ◽  
Dna Binding ◽  
Molecular Biology ◽  
Binding Proteins ◽  
Protein Sequences ◽  
Low Complexity ◽  
Dna Binding Proteins ◽  
Position Information ◽  
Position Representation

Aim and Objective:: Given the rapidly increasing number of molecular biology data available, computational methods of low complexity are necessary to infer protein structure, function, and evolution. Method:: In the work, we proposed a novel mthod, FermatS, which based on the global position information and local position representation from the curve and normalized moments of inertia, respectively, to extract features information of protein sequences. Furthermore, we use the generated features by FermatS method to analyze the similarity/dissimilarity of nine ND5 proteins and establish the prediction model of DNA-binding proteins based on logistic regression with 5-fold crossvalidation. Results:: In the similarity/dissimilarity analysis of nine ND5 proteins, the results are consistent with evolutionary theory. Moreover, this method can effectively predict the DNA-binding proteins in realistic situations. Conclusion:: The findings demonstrate that the proposed method is effective for comparing, recognizing and predicting protein sequences. The main code and datasets can download from https://github.com/GaoYa1122/FermatS.

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