The Sac10b homolog from Sulfolobus islandicus is an RNA chaperone

Abstract Nucleic acid-binding proteins of the Sac10b family, also known as Alba, are widely distributed in Archaea. However, the physiological roles of these proteins have yet to be clarified. Here, we show that Sis10b, a member of the Sac10b family from the hyperthermophilic archaeon Sulfolobus islandicus, was active in RNA strand exchange, duplex RNA unwinding in vitro and RNA unfolding in a heterologous host cell. This protein exhibited temperature-dependent binding preference for ssRNA over dsRNA and was more efficient in RNA unwinding and RNA unfolding at elevated temperatures. Notably, alanine substitution of a highly conserved basic residue (K) at position 17 in Sis10b drastically reduced the ability of this protein to catalyse RNA strand exchange and RNA unwinding. Additionally, the preferential binding of Sis10b to ssRNA also depended on the presence of K17 or R17. Furthermore, normal growth was restored to a slow-growing Sis10b knockdown mutant by overproducing wild-type Sis10b but not by overproducing K17A in this mutant strain. Our results indicate that Sis10b is an RNA chaperone that likely functions most efficiently at temperatures optimal for the growth of S. islandicus, and K17 is essential for the chaperone activity of the protein.

Download Full-text

Parameters for effective in vitro production of zinc finger nucleic acid-binding proteins

Biotechnology and Applied Biochemistry ◽

10.1002/bab.24 ◽

2011 ◽

Vol 58 (3) ◽

pp. 166-174 ◽

Cited By ~ 3

Author(s):

Zachery R. Belak ◽

Manoj Nair ◽

Nick Ovsenek

Keyword(s):

Nucleic Acid ◽

Zinc Finger ◽

Binding Proteins ◽

Nucleic Acid Binding ◽

In Vitro Production ◽

Nucleic Acid Binding Proteins ◽

Vitro Production

Download Full-text

The DNA sensors AIM2 and IFI16 are NET-binding SLE autoantigens

10.1101/2021.08.19.456941 ◽

2021 ◽

Author(s):

Brendan Antiochos ◽

Paride Fenaroli ◽

Avi Rosenberg ◽

Alan Baer ◽

Jungsan Sohn ◽

...

Keyword(s):

Lupus Erythematosus ◽

Nucleic Acid Binding ◽

Extracellular Traps ◽

Double Stranded Dna ◽

Nucleic Acid Binding Proteins ◽

Dna Antibodies ◽

Inducible Protein ◽

Clinical Measures ◽

Interferon Inducible Protein

Nucleic acid binding proteins are frequently targeted as autoantigens in systemic lupus erythematosus (SLE) and other interferon (IFN)-linked rheumatic diseases. The AIM-like receptors (ALRs) are IFNinducible innate sensors that form supramolecular assemblies along double-stranded DNA of various origins. Here, we identify the ALR Absent in melanoma 2 (AIM2) as a novel autoantigen in SLE, with similar properties to the established ALR autoantigen interferon-inducible protein 16 (IFI16). Our SLE cohort revealed a frequent co-occurrence of anti-AIM2, anti-IFI16 and anti-DNA antibodies, and higher clinical measures of disease activity in patients positive for antibodies against these ALRs. We examined neutrophil extracellular traps (NETs) as DNA scaffolds on which these antigens might interact in a proimmune context, finding that both ALRs bind NETs in vitro and in SLE renal tissues. We demonstrate that ALR binding causes NETs to resist degradation by DNase I, suggesting a mechanism whereby extracellular ALR-NET interactions may promote sustained IFN signaling. Our work suggests that extracellular ALRs bind NETs, leading to DNase resistant nucleoprotein fibers that are targeted as autoantigens in SLE.

Download Full-text

An Acidic Protein, YBAP1, Mediates the Release of YB-1 from mRNA and Relieves the Translational Repression Activity of YB-1

Molecular and Cellular Biology ◽

10.1128/mcb.25.5.1779-1792.2005 ◽

2005 ◽

Vol 25 (5) ◽

pp. 1779-1792 ◽

Cited By ~ 35

Author(s):

Ken Matsumoto ◽

Kimio J. Tanaka ◽

Masafumi Tsujimoto

Keyword(s):

Nucleic Acid ◽

Cold Shock ◽

Acidic Protein ◽

Translational Repression ◽

Nucleic Acid Binding ◽

Wide Range ◽

Nucleic Acid Binding Proteins ◽

Specific Association ◽

Shock Proteins

ABSTRACT Eukaryotic Y-box proteins are nucleic acid-binding proteins implicated in a wide range of gene regulatory mechanisms. They contain the cold shock domain, which is a nucleic acid-binding structure also found in bacterial cold shock proteins. The Y-box protein YB-1 is known to be a core component of messenger ribonucleoprotein particles (mRNPs) in the cytoplasm. Here we disrupted the YB-1 gene in chicken DT40 cells. Through the immunoprecipitation of an epitope-tagged YB-1 protein, which complemented the slow-growth phenotype of YB-1-depleted cells, we isolated YB-1-associated complexes that likely represented general mRNPs in somatic cells. RNase treatment prior to immunoprecipitation led to the identification of a Y-box protein-associated acidic protein (YBAP1). The specific association of YB-1 with YBAP1 resulted in the release of YB-1 from reconstituted YB-1-mRNA complexes, thereby reducing the translational repression caused by YB-1 in the in vitro system. Our data suggest that YBAP1 induces the remodeling of YB-1-mRNA complexes.

Download Full-text

Effect of Temperature, Velocity Gradient and I.V. Heparin on in Vitro Blood Coagulation and Platelet Aggregation

Thrombosis and Haemostasis ◽

10.1055/s-0038-1654086 ◽

1967 ◽

Vol 17 (01/02) ◽

pp. 112-119 ◽

Cited By ~ 3

Author(s):

L Dintenfass ◽

M. C Rozenberg

Keyword(s):

Blood Coagulation ◽

Velocity Gradient ◽

Elevated Temperatures ◽

Morphological Changes ◽

Effect Of Temperature ◽

Clotting Time ◽

Progressive Change ◽

Aggregation Of Platelets ◽

Microscopic Techniques

SummaryA study of blood coagulation was carried out by observing changes in the blood viscosity of blood coagulating in the cone-in-cone viscometer. The clots were investigated by microscopic techniques.Immediately after blood is obtained by venepuncture, viscosity of blood remains constant for a certain “latent” period. The duration of this period depends not only on the intrinsic properties of the blood sample, but also on temperature and rate of shear used during blood storage. An increase of temperature decreases the clotting time ; also, an increase in the rate of shear decreases the clotting time.It is confirmed that morphological changes take place in blood coagula as a function of the velocity gradient at which such coagulation takes place. There is a progressive change from the red clot to white thrombus as the rates of shear increase. Aggregation of platelets increases as the rate of shear increases.This pattern is maintained with changes of temperature, although aggregation of platelets appears to be increased at elevated temperatures.Intravenously added heparin affects the clotting time and the aggregation of platelets in in vitro coagulation.

Download Full-text

Epothilone D alters normal growth, viability and microtubule dependent intracellular functions of cortical neurons in vitro

Scientific Reports ◽

10.1038/s41598-020-57718-z ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

J. A. Clark ◽

J. A. Chuckowree ◽

M. S. Dyer ◽

T. C. Dickson ◽

C. A. Blizzard

Keyword(s):

Cortical Neurons ◽

Normal Growth ◽

Epothilone D

Download Full-text

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

Applied Sciences ◽

10.3390/app11156865 ◽

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.

Download Full-text