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121.
122.
Eric G. Brown Malcolm J. Edwards Russell P. Newton Christopher J. Smith 《Phytochemistry》1979,18(12):1943-1948
An active cyclic nucleotide phosphodiesterase has been partially purified from the 100 000 g supernatant of a spinach homogenate. It precipitated at 20–40% saturation with (NH4)2SO4 and was separated on a column of Sephadex G-200 into two major peaks of activity (peaks 1 and 2). Peak 1 (MW 5 × 105) was resolved by column chromatography on DEAE-cellulose into 5 protein fractions; two of these (1c and 1m) exhibited cyclic nucleotide phosphodiesterase activity. Subcellular fractionation showed that the phosphodiesterase of highest specific activity is located in the peroxisomes but that an enzyme of relatively high specific activity also occurs in the chloroplast and Golgi fractions. The largest total activity was in the microsomes. Isoelectric focussing of chloroplast phosphodiesterase activity gave two bands corresponding to peaks 1c and 2. Similar examination of the microsomal, peroxisomal and Golgi fractions showed phosphodiesterases corresponding to peaks 1m and 2. Peak 1c activity is greater towards purine 3′,5′-cyclic nucleotides than towards their 2′,3′-isomers; the converse is true of peak 1m. Examination of the properties of 1c and 1m showed a number of other differences. The pH optimum of 1c is 6.1 and that of 1m is 4.9. Theophylline (0.1 mM) inhibited 1c to a greater extent than it did 1m; Ca2+ stimulated 1c activity but had no effect on 1m. Pre-incubation with trypsin inhibited 1m activity whereas similar treatment of 1c gave an initial 5-fold stimulation. Repeated freezing and thawing of preparations 1c and 1m also evoked a difference in response. These results were shown to be attributable to removal of an inhibitor from 1c. Evidence is presented that an endogenous activator is also present. 相似文献
123.
蛋白质亚细胞定位的生物信息学研究 总被引:3,自引:1,他引:3
细胞中蛋白质合成后被转运到特定的细胞器中,只有转运到正确的部位才能参与细胞的各种生命活动,如果定位发生偏差,将会对细胞功能甚至生命产生重大影响.蛋白质的亚细胞定位是蛋白质功能研究的重要方面,也是生物信息学中的热点问题,数据库的构建和亚细胞定位分析及预测加速了蛋白质结构和功能的研究. 相似文献
124.
Shigeki Suzuki Hiroaki Hoshino Kazuma Yoshida Jun Nakanishi Shizu Tsuchiya-Hirata Seiji Kobuke Naoto Haruyama Fusanori Nishimura Hideki Shiba 《Biochemical and biophysical research communications》2018,495(3):2303-2309
Chromatin-enriched noncoding RNAs (ncRNAs) have emerged as key molecules in epigenetic processes by interacting with chromatin-associated proteins. Recently, protein-coding mRNA genes have been reported to be chromatin-tethered, similar with ncRNA. However, very little is known about whether chromatin-enriched mRNA is involved in the chromatin modification process. Here, we comprehensively examined chromatin-enriched RNA in squamous cell carcinoma (SQCC) cells by RNA subcellular localization analysis, which was a combination of RNA fractionation and RNA-seq. We identified 11 mRNAs as highly chromatin-enriched RNAs. Among these, we focused on the dentin matrix protein-1 (DMP-1) gene because its expression in SQCC cells has not been reported. Furthermore, we clarified that DMP-1 mRNA was retained in chromatin in its unspliced form in SQCC in vitro and in vivo. As the inhibition of the unspliced DMP-1 mRNA (unspDMP-1) expression resulted in decreased cellular proliferation in SQCC cells, we performed ChIP-qPCR to identify cell cycle-related genes whose expression was epigenetically modified by unspDMP-1, and found that the CDKN1B promoter became active in SQCC cells by inhibiting unspDMP-1 expression. This result was further validated by the increased CDKN1B gene expression in the cells treated with siRNA for unspDMP-1 and by restoration of the decreased cellular proliferation rate by simultaneously inhibiting CDKN1B expression in SQCC cells. Further, to examine whether unspDMP-1 was able to associate with the CDKN1B promoter region, SQCC cells stably expressing PP7-mCherry fusion protein were transiently transfected with the unspDMP-1 fused to 24 repeats of the PP7 RNA stem loop (unspDMP-1-24xPP7) and we found that unspDMP-1-24xPP7 was efficiently precipitated with the antibody against mCherry and was significantly enriched in the CDKN1B promoter region. Thus, unspDMP-1 is a novel chromatin-enriched RNA that epigenetically regulates cellular proliferation of SQCC. 相似文献
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127.
Tianyi Zhu Xuan Ling Hilary Yong Di Xia Jocelyn Widagdo Victor Anggono 《Journal of molecular biology》2018,430(3):363-371
Genetic polymorphisms in the fat mass and obesity-associated (FTO) gene have been strongly associated with obesity in humans. The cellular level of FTO is tightly regulated, with alterations in its expression influencing energy metabolism, food intake and body weight. Although the proteasome system is involved, the cellular mechanism underlying FTO protein turnover remains unknown. Here, we report that FTO undergoes post-translational ubiquitination on Lys-216. Knock-in HeLa cells harboring the ubiquitin-deficient K216R mutation displayed a slower rate of FTO turnover, resulting in an increase in the level of FTO as well as enhanced phosphorylation of the ribosomal S6 kinase. Surprisingly, we also found that K216R mutation reduced the level of nuclear FTO and completely abolished the nuclear translocation of FTO in response to amino acid starvation. Collectively, our results reveal the functional importance of ubiquitination in controlling FTO expression and localization, which may be crucial for determining body mass and composition. 相似文献
128.
Jia P Qian Z Zeng Z Cai Y Li Y 《Biochemical and biophysical research communications》2007,357(2):366-370
Assigning subcellular localization (SL) to proteins is one of the major tasks of functional proteomics. Despite the impressive technical advances of the past decades, it is still time-consuming and laborious to experimentally determine SL on a high throughput scale. Thus, computational predictions are the preferred method for large-scale assignment of protein SL, and if appropriate, followed up by experimental studies. In this report, using a machine learning approach, the Nearest Neighbor Algorithm (NNA), we developed a prediction system for protein SL in which we incorporated a protein functional domain profile. The overall accuracy achieved by this system is 93.96%. Furthermore, comparisons with other methods have been conducted to demonstrate the validity and efficiency of our prediction system. We also provide an implementation of our Subcellular Location Prediction System (SLPS), which is available at http://pcal.biosino.org. 相似文献
129.
Electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis of the lipid molecular species composition of yeast subcellular membranes reveals acyl chain-based sorting/remodeling of distinct molecular species en route to the plasma membrane. 下载免费PDF全文
R Schneiter B Brügger R Sandhoff G Zellnig A Leber M Lampl K Athenstaedt C Hrastnik S Eder G Daum F Paltauf F T Wieland S D Kohlwein 《The Journal of cell biology》1999,146(4):741-754
Nano-electrospray ionization tandem mass spectrometry (nano-ESI-MS/MS) was employed to determine qualitative differences in the lipid molecular species composition of a comprehensive set of organellar membranes, isolated from a single culture of Saccharomyces cerevisiae cells. Remarkable differences in the acyl chain composition of biosynthetically related phospholipid classes were observed. Acyl chain saturation was lowest in phosphatidylcholine (15.4%) and phosphatidylethanolamine (PE; 16.2%), followed by phosphatidylserine (PS; 29.4%), and highest in phosphatidylinositol (53.1%). The lipid molecular species profiles of the various membranes were generally similar, with a deviation from a calculated average profile of approximately +/- 20%. Nevertheless, clear distinctions between the molecular species profiles of different membranes were observed, suggesting that lipid sorting mechanisms are operating at the level of individual molecular species to maintain the specific lipid composition of a given membrane. Most notably, the plasma membrane is enriched in saturated species of PS and PE. The nature of the sorting mechanism that determines the lipid composition of the plasma membrane was investigated further. The accumulation of monounsaturated species of PS at the expense of diunsaturated species in the plasma membrane of wild-type cells was reversed in elo3Delta mutant cells, which synthesize C24 fatty acid-substituted sphingolipids instead of the normal C26 fatty acid-substituted species. This observation suggests that acyl chain-based sorting and/or remodeling mechanisms are operating to maintain the specific lipid molecular species composition of the yeast plasma membrane. 相似文献
130.
Elisia A. Paiz Jeffre H. Allen John J. Correia Nicholas C. Fitzkee Loren E. Hough Steven T. Whitten 《The Journal of biological chemistry》2021,297(5)
The complex cellular milieu can spontaneously demix, or phase separate, in a process controlled in part by intrinsically disordered (ID) proteins. A protein''s propensity to phase separate is thought to be driven by a preference for protein–protein over protein–solvent interactions. The hydrodynamic size of monomeric proteins, as quantified by the polymer scaling exponent (v), is driven by a similar balance. We hypothesized that mean v, as predicted by protein sequence, would be smaller for proteins with a strong propensity to phase separate. To test this hypothesis, we analyzed protein databases containing subsets of proteins that are folded, disordered, or disordered and known to spontaneously phase separate. We find that the phase-separating disordered proteins, on average, had lower calculated values of v compared with their non-phase-separating counterparts. Moreover, these proteins had a higher sequence-predicted propensity for β-turns. Using a simple, surface area-based model, we propose a physical mechanism for this difference: transient β-turn structures reduce the desolvation penalty of forming a protein-rich phase and increase exposure of atoms involved in π/sp2 valence electron interactions. By this mechanism, β-turns could act as energetically favored nucleation points, which may explain the increased propensity for turns in ID regions (IDRs) utilized biologically for phase separation. Phase-separating IDRs, non-phase-separating IDRs, and folded regions could be distinguished by combining v and β-turn propensity. Finally, we propose a new algorithm, ParSe (partition sequence), for predicting phase-separating protein regions, and which is able to accurately identify folded, disordered, and phase-separating protein regions based on the primary sequence. 相似文献