Evaluation of RNA Chaperone Activity In Vivo and In Vitro Using Misfolded Group I Ribozymes

2013 ◽  
pp. 239-254
Author(s):  
Katharina Semrad
Keyword(s):  
Chaperone Activity ◽  
Rna Chaperone ◽  
Group I

Assays for the RNA chaperone activity of proteins

2005 ◽  
Vol 33 (3) ◽  
pp. 450-456 ◽  
Author(s):  
L. Rajkowitsch ◽  
K. Semrad ◽  
O. Mayer ◽  
R. Schroeder
Keyword(s):  
Group I Intron ◽  
Chaperone Activity ◽  
Structural Elements ◽  
Rna Chaperone ◽  
Group I ◽  
Monomolecular Reactions ◽  
Rna Chaperones ◽  
Complementary Rnas

Proteins with RNA chaperone activity promote RNA folding by loosening the structure of misfolded RNAs or by preventing their formation. How these proteins achieve this activity is still unknown, the mechanism is not understood and it is unclear whether this activity is always based on the same mechanism or whether different RNA chaperones use different mechanisms. To address this question, we compare and discuss in this paper a set of assays that have been used to measure RNA chaperone activity. In some assays, this activity is related to the acceleration of monomolecular reactions such as group I intron cis-splicing or anti-termination of transcription. Hereby, it is proposed that the proteins release the RNAs from folding traps, which represent the kinetic barriers during the folding process and involve the loosening of structural elements. In most assays, however, bimolecular reactions are monitored, which include the simple acceleration of annealing of two complementary RNAs, the turnover stimulation of ribozyme cleavage and group I intron trans-splicing. The acceleration of these reactions most probably involves the unfolding of structures that interfere with annealing or folding and may in addition provoke annealing by crowding. Most assays are performed in vitro, where conditions might differ substantially from intracellular conditions, and two assays have been reported that detect RNA chaperone activity in vivo.

scholarly journals Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Katharina Semrad
Keyword(s):  
Structural Diversity ◽  
Chaperone Activity ◽  
Cellular Mechanisms ◽  
Rna Chaperone ◽  
Common Task ◽  
Disordered Regions ◽  
Ubiquitous Proteins

Proteins with RNA chaperone activity are ubiquitous proteins that play important roles in cellular mechanisms. They prevent RNA from misfolding by loosening misfolded structures without ATP consumption. RNA chaperone activity is studiedin vitroandin vivousing oligonucleotide- or ribozyme-based assays. Due to their functional as well as structural diversity, a common chaperoning mechanism or universal motif has not yet been identified. A growing database of proteins with RNA chaperone activity has been established based on evaluation of chaperone activity via the described assays. Although the exact mechanism is not yet understood, it is more and more believed that disordered regions within proteins play an important role. This possible mechanism and which proteins were found to possess RNA chaperone activity are discussed here.

Folding of the td pre-RNA with the help of the RNA chaperone StpA

2002 ◽  
Vol 30 (6) ◽  
pp. 1175-1180 ◽  
Author(s):  
O. Mayer ◽  
C. Waldsich ◽  
R. Grossberger ◽  
R. Schroeder
Keyword(s):  
Conformational Changes ◽  
Three Dimensional ◽  
Group I Intron ◽  
Dimensional Structure ◽  
Rna Chaperone ◽  
Three Dimensional Structure ◽  
Group I ◽  
The Impact

The td group I intron is inserted in the reading frame of the thymidylate synthase gene, which is mainly devoid of structural elements. In vivo, translation of the pre-mRNA is required for efficient folding of the intron into its splicing-competent structure. The ribosome probably resolves exon-intron interactions that interfere with splicing. Uncoupling splicing from translation, by introducing a non-sense codon into the upstream exon, reduces the splicing efficiency of the mutant pre-mRNA. Alternatively to the ribosome, co-expression of genes that encode proteins with RNA chaperone activity promote folding of the td pre-mRNA in vivo. These proteins also efficiently accelerate folding of the td pre-mRNA in vitro. In order to understand the mechanism of action of RNA chaperones, we probed the impact of the RNA chaperone StpA on the structure of the td intron in vivo and compared it with that of the well characterized Cyt-18 protein, which is a group-I-intron-specific splicing factor. We found that the two proteins have opposite effects on the structure of the td intron. While StpA loosens the three-dimensional structure, Cyt-18 tightens it up. Furthermore, mutations that destabilize the intron structure render the mutants sensitive to StpA, whereas splicing of these mutants is rescued by Cyt-18. Our results provide direct evidence for protein-induced conformational changes within a catalytic RNA in vivo. Whereas StpA resolves tertiary contacts enabling the RNA to refold, Cyt-18 contributes to the stabilization of the native three-dimensional structure.

Effects of Rest and Exercise on Cardiac Blood Volume Determinations

1997 ◽  
Vol 36 (08) ◽  
pp. 259-264
Author(s):  
N. Topuzović
Keyword(s):  
Radionuclide Ventriculography ◽  
Left Ventricular ◽  
Peak Exercise ◽  
Volume Determination ◽  
Group I ◽  
Lv Volumes ◽  
Group Ii ◽  
Lv Volume

Summary Aim: The purpose of this study was to investigate the changes in blood activity during rest, exercise and recovery, and to assess its influence on left ventricular (LV) volume determination using the count-based method requiring blood sampling. Methods: Forty-four patients underwent rest-stress radionuclide ventriculography; Tc-99m-human serum albumin was used in 13 patients (Group I), red blood cells was labeled using Tc-99m in 17 patients (Group II) in vivo, and in 14 patients (Group III) by modified in vivo/in vitro method. LV volumes were determined by a count-based method using corrected count rate in blood samples obtained during rest, peak exercise and after recovery. Results: In group I at stress, the blood activity decreased by 12.6 ± 5.4%, p <0.05, as compared to the rest level, and increased by 25.1 ± 6.4%, p <0.001, and 12.8 ± 4.5%, p <0.05, above the resting level in group II and III, respectively. This had profound effects on LV volume determinations if only one rest blood aliquot was used: during exercise, the LV volumes significantly decreased by 22.1 ± 9.6%, p <0.05, in group I, whereas in groups II and III it was significantly overestimated by 32.1 ± 10.3%, p <0.001, and 10.7 ± 6.4%, p <0.05, respectively. The changes in blood activity between stress and recovery were not significantly different for any of the groups. Conclusion: The use of only a single blood sample as volume aliquot at rest in rest-stress studies leads to erroneous estimation of cardiac volumes due to significant changes in blood radioactivity during exercise and recovery.

scholarly journals Arabidopsis Disulfide Reductase, Trx-h2, Functions as an RNA Chaperone under Cold Stress

2021 ◽  
Vol 11 (15) ◽  
pp. 6865
Author(s):  
Eun Seon Lee ◽  
Joung Hun Park ◽  
Seong Dong Wi ◽  
Ho Byoung Chae ◽  
Seol Ki Paeng ◽  
...  
Keyword(s):  
Cold Stress ◽  
Wild Type ◽  
Rna Chaperone ◽  
E Coli ◽  
Cold Sensitive ◽  
Thioredoxin H ◽  
Functional Rnas

The thioredoxin-h (Trx-h) family of Arabidopsis thaliana comprises cytosolic disulfide reductases. However, the physiological function of Trx-h2, which contains an additional 19 amino acids at its N-terminus, remains unclear. In this study, we investigated the molecular function of Trx-h2 both in vitro and in vivo and found that Arabidopsis Trx-h2 overexpression (Trx-h2OE) lines showed significantly longer roots than wild-type plants under cold stress. Therefore, we further investigated the role of Trx-h2 under cold stress. Our results revealed that Trx-h2 functions as an RNA chaperone by melting misfolded and non-functional RNAs, and by facilitating their correct folding into active forms with native conformation. We showed that Trx-h2 binds to and efficiently melts nucleic acids (ssDNA, dsDNA, and RNA), and facilitates the export of mRNAs from the nucleus to the cytoplasm under cold stress. Moreover, overexpression of Trx-h2 increased the survival rate of the cold-sensitive E. coli BX04 cells under low temperature. Thus, our data show that Trx-h2 performs function as an RNA chaperone under cold stress, thus increasing plant cold tolerance.

Evaluation of Annona muricata (Graviola) leaves activity against experimental trichinellosis: in vitro and in vivo studies

2021 ◽  
Vol 95 ◽  
Author(s):  
E.S. El-Wakil ◽  
H.F. Abdelmaksoud ◽  
T.S. AbouShousha ◽  
M.M.I. Ghallab
Keyword(s):  
Culture Media ◽  
Trichinella Spiralis ◽  
Drug Effects ◽  
In Vivo Studies ◽  
Control Group ◽  
Annona Muricata ◽  
Group I ◽  
Small Intestinal

Abstract Our work aimed to evaluate the possible effect of Annona muricata (Graviola) leaf extract on Trichinella spiralis in in vitro and in vivo studies. Trichinella spiralis worms were isolated from infected mice and transferred to three culture media – group I (with no drugs), group II (contained Graviola) and group III (contained albendazole) – then they were examined using the electron microscope. In the in vivo study, mice were divided into five groups: GI (infected untreated), GII (prophylactically treated with Graviola for seven days before infection), GIII (infected and treated with Graviola), GIV (infected and treated with albendazole) and GV (infected and treated with a combination of Graviola plus albendazole in half doses). Drug effects were assessed by adults and larvae load beside the histopathological small intestinal and muscular changes. A significant reduction of adult and larval counts occurred in treated groups in comparison to the control group. Histopathologically, marked improvement in the small intestinal and muscular changes was observed in treated groups. Also, massive destruction of the cultured adults’ cuticle was detected in both drugs. This study revealed that Graviola leaves have potential activity against trichinellosis, especially in combination with albendazole, and could serve as an adjuvant to anti-trichinellosis drug therapy.

Autocatalytic activities of intron 5 of the cob gene of yeast mitochondria

1988 ◽  
Vol 8 (6) ◽  
pp. 2562-2571
Author(s):  
S Partono ◽  
A S Lewin
Keyword(s):  
Group I Introns ◽  
Yeast Mitochondria ◽  
High Concentration ◽  
Functional Protein ◽  
Full Spectrum ◽  
Group I ◽  
Intron Boundary ◽  
Monovalent Ion

The terminal intron of the mitochondrial cob gene of Saccharomyces cerevisiae can undergo autocatalytic splicing in vitro. Efficient splicing of this intron required a high concentration of monovalent ion (1 M). We found that at a high salt concentration this intron was very active and performed many of the reactions described for other group I introns. The rate of the splicing reaction was dependent on the choice of the monovalent ion; the reaction intermediate, the intron-3' exon molecule, accumulated in NH4Cl but not in KCl. In addition, the intron was more reactive in KCl, accumulating in two different circular forms: one cyclized at the 5' intron boundary and the other at 236 nucleotides from the 5' end. These circular forms were able to undergo the opening and recyclization reactions previously described for the Tetrahymena rRNA intron. Cleavage of the 5' exon-intron boundary by the addition of GTP did not require the 3' terminus of the intron and the downstream exon. An anomalous guanosine addition at the 3' exon and at the middle of the intron was also detected. Hence, this intron, which requires a functional protein to splice in vivo, demonstrated a full spectrum of characteristic reactions in the absence of proteins.

scholarly journals RNA chaperone activity of the tombusviral p33 replication protein facilitates initiation of RNA synthesis by the viral RdRp in vitro

Virology ◽  
2011 ◽  
Vol 409 (2) ◽  
pp. 338-347 ◽  
Author(s):  
Jozsef Stork ◽  
Nikolay Kovalev ◽  
Zsuzsanna Sasvari ◽  
Peter D. Nagy
Keyword(s):  
Rna Synthesis ◽  
Chaperone Activity ◽  
Replication Protein ◽  
Rna Chaperone ◽  
Viral Rdrp

scholarly journals Pentoxifylline Attenuates Methionine- and Choline-Deficient-Diet-Induced Steatohepatitis by Suppressing TNF-αExpression and Endoplasmic Reticulum Stress

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Min Kyung Chae ◽  
Sang Gyu Park ◽  
Sun-Ok Song ◽  
Eun Seok Kang ◽  
Bong Soo Cha ◽  
...  
Keyword(s):  
Er Stress ◽  
Deficient Diet ◽  
Group Iii ◽  
Unfolded Protein ◽  
Sd Rats ◽  
Group I ◽  
Hep3b Cells ◽  
Protein Response

Background. Pentoxifylline (PTX) anti-TNF properties are known to exert hepatoprotective effects in various liver injury models. The aim of this study was to investigate whether PTX has beneficial roles in the development of methionine- and choline-deficient-(MCD-) diet-induced NAFLD SD ratsin vivoand TNF-α-induced Hep3B cellsin vitro.Methods. SD Rats were classified according to diet (chow or MCD diet) and treatment (normal saline or PTX injection) over a period of 4 weeks: group I (chow + saline,n=4), group II (chow + PTX), group III (MCD + saline), and group IV (MCD + PTX). Hep3B cells were treated with 100 ng/ml TNF-α(24 h) in the absence or presence of PTX (1 mM).Results. PTX attenuated MCD-diet-induced serum ALT levels and hepatic steatosis. In real-time PCR and western blotting analysis, PTX decreased MCD-diet-induced TNF-alpha mRNA expression and proapoptotic unfolded protein response by ER stress (GRP78, p-eIF2, ATF4, IRE1α, CHOP, and p-JNK activation)in vivo. PTX (1 mM) reduced TNF-α-induced activation of GRP78, p-eIF2, ATF4, IRE1α, and CHOPin vitro.Conclusion. PTX has beneficial roles in the development of MCD-diet-induced steatohepatitis through partial suppression of TNF-αand ER stress.

An Experimental Model for the Study of Venous Thrombosis in Vivo

1975 ◽  
Author(s):  
T. K. Day ◽  
K. G. A. Glark ◽  
V. V. Kakkar
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Experimental Model ◽  
Femoral Vein ◽  
Total Charge ◽  
Small Current ◽  
Group I ◽  
Scanning Electron

The lack of a satisfactory in vivo experimental model has probably been responsible for the delay in the clinical application of recent advances in in vitro research on thrombosis. This paper describes a model in which thrombosis is initiated by an electrical stimulus. The thrombus produced has the histological and biochemical features of human deep vein thrombosis (DVT).The minimum stimulus necessary to induce thrombosis was first determined by passing a fixed current for timed intervals along the femoral veins of 10 rabbits. Thrombi were seen 24 hours later if the total charge passed exceeded a threshold value of 25 millicoulombes. With this small current, no endothelial changes were visible immediately after the passage of the charge on light or scanning electron microscopy. At 24 hours a mural thrombus formed, which had fully cross-linked fibrin and histological features resembling human DVT.In the second series of experiments, the sequence of changes occurring in thrombus production was investigated in 3 groups of 18 rabbits each. After passage of the critical charge along the femoral vein in each animal, veins were removed at fixed intervals, the contralateral vein acting as a control. The veins were examined by scanning electron-microscopy (Group I), transmission electron-microscopy (Group II) and light microscopy (Group III), The earliest changes were detectable at 5 minutes and consisted of the laying down of an organised structure of criss-crossing fibrin strands with small platelet clumps at fibrin intersections. Later the fibrin structure spread towards the lumen; platelet clumps fused and a coralline thrombus was formed by 24 hours. The significance of these changes will be discussed.

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