Higher-order structure of the 5.8 S rRNA sequence within the yeast 35 S precursor ribosomal RNA synthesized in vitro

Despite the effectiveness of cisplatin as an anticancer agent, its trans-isomer, transplatin, is clinically ineffective. Although both isomers target nuclear DNA, there is a large difference in the magnitude of their biological effects. Here, we compared their effects on gene expression in an in vitro luciferase assay and quantified their effects on the higher-order structure of DNA using fluorescence microscopy (FM) and atomic force microscopy (AFM). The inhibitory effect of cisplatin on gene expression was about 7 times that of transplatin. Analysis of the fluctuation autocorrelation function of the intrachain Brownian motion of individual DNA molecules showed that cisplatin increases the spring and damping constants of DNA by one order of magnitude and these visco-elastic characteristics tend to increase gradually over several hours. Transplatin had a weaker effect, which tended to decrease with time. These results agree with a stronger inhibitory effect of cisplatin on gene expression. We discussed the characteristic effects of the two compounds on the higher-order DNA structure and gene expression in terms of the differences in their binding to DNA.

Download Full-text

Higher order structure of chloroplastic 5S ribosomal RNA from spinach

Biochemistry ◽

10.1021/bi00413a021 ◽

1988 ◽

Vol 27 (13) ◽

pp. 4721-4730 ◽

Cited By ~ 42

Author(s):

Pascale Romby ◽

Eric Westhof ◽

Remy Toukifimpa ◽

Regis Mache ◽

Jean Pierre Ebel ◽

...

Keyword(s):

Ribosomal Rna ◽

Higher Order ◽

Order Structure ◽

5S Ribosomal Rna

Download Full-text

Natural chromatin is heterogeneous and self-associates in vitro

Molecular Biology of the Cell ◽

10.1091/mbc.e17-07-0449 ◽

2018 ◽

Vol 29 (13) ◽

pp. 1652-1663 ◽

Cited By ~ 12

Author(s):

Shujun Cai ◽

Yajiao Song ◽

Chen Chen ◽

Jian Shi ◽

Lu Gan

Keyword(s):

Divalent Cations ◽

Large Mass ◽

Higher Order ◽

Linker Histone ◽

Order Structure ◽

Face To Face ◽

Chromatin Packing ◽

Electron Cryotomography

The 30-nm fiber is commonly formed by oligonucleosome arrays in vitro but rarely found inside cells. To determine how chromatin higher-order structure is controlled, we used electron cryotomography (cryo-ET) to study the undigested natural chromatin released from two single-celled organisms in which 30-nm fibers have not been observed in vivo: picoplankton and yeast. In the presence of divalent cations, most of the chromatin from both organisms is condensed into a large mass in vitro. Rare irregular 30-nm fibers, some of which include face-to-face nucleosome interactions, do form at the periphery of this mass. In the absence of divalent cations, picoplankton chromatin decondenses into open zigzags. By contrast, yeast chromatin mostly remains condensed, with very few open motifs. Yeast chromatin packing is largely unchanged in the absence of linker histone and mildly decondensed when histones are more acetylated. Natural chromatin is therefore generally nonpermissive of regular motifs, even at the level of oligonucleosomes.

Download Full-text

Erythromycin Resistance Mutations in Ribosomal Proteins L22 and L4 Perturb the Higher Order Structure of 23 S Ribosomal RNA

Journal of Molecular Biology ◽

10.1006/jmbi.1999.2839 ◽

1999 ◽

Vol 289 (4) ◽

pp. 827-834 ◽

Cited By ~ 93

Author(s):

Steven T. Gregory ◽

Albert E. Dahlberg

Keyword(s):

Ribosomal Rna ◽

Ribosomal Proteins ◽

Higher Order ◽

Order Structure ◽

Resistance Mutations ◽

Erythromycin Resistance

Download Full-text

Higher order structure in ribosomal RNA.

The EMBO Journal ◽

10.1002/j.1460-2075.1986.tb04330.x ◽

1986 ◽

Vol 5 (5) ◽

pp. 1111-1113 ◽

Cited By ~ 66

Author(s):

R.R. Gutell ◽

H.F. Noller ◽

C.R. Woese

Keyword(s):

Ribosomal Rna ◽

Higher Order ◽

Order Structure

Download Full-text

The role of Bni5 in the regulation of septin higher-order structure formation

Biological Chemistry ◽

10.1515/hsz-2015-0165 ◽

2015 ◽

Vol 396 (12) ◽

pp. 1325-1337 ◽

Cited By ~ 9

Author(s):

Csilla Patasi ◽

Jana Godočíková ◽

Soňa Michlíková ◽

Yan Nie ◽

Radka Káčeriková ◽

...

Keyword(s):

Cell Cycle ◽

Structural Changes ◽

Higher Order ◽

Cytoskeletal Proteins ◽

Order Structure ◽

Division Plane ◽

Cellular Processes ◽

Order Structures

Abstract Septins are a family of conserved cytoskeletal proteins playing an essential role in cytokinesis and in many other cellular processes in fungi and animals. In budding yeast Saccharomyces cerevisiae, septins form filaments and higher-order structures at the mother-bud neck depending on the particular stage of the cell cycle. Septin structures at the division plane serve as a scaffold to recruit the proteins required for particular cellular processes. The formation and localization of septin structures at particular stages of the cell cycle also determine functionality of these proteins. Many different proteins participate in regulating septin assembly. Despite recent developments, we are only beginning to understand how specific protein-protein interactions lead to changes in the polymerization of septin filaments or assembly of higher-order structures. Here, using fluorescence and electron microscopy, we found that Bni5 crosslinks septin filaments into networks by bridging pairs or multiple filaments, forming structures that resemble railways. Furthermore, Bni5 appears to be a substrate of the Elm1 protein kinase in vitro. Moreover, Elm1 induces in the presence of Bni5 disassembly of long septin filaments, suggesting that these proteins may participate in the hourglass to double ring transition. This work gives new insight into the regulatory role of Bni5 in the structural changes of septins.

Download Full-text

Higher order structure in ribosomal RNA

The EMBO Journal ◽

10.1002/j.1460-2075.1986.tb04512.x ◽

1986 ◽

Vol 5 (9) ◽

pp. 2417-2417

Keyword(s):

Ribosomal Rna ◽

Higher Order ◽

Order Structure

Download Full-text

Formation of membrane ridges and scallops by the F-BAR protein Nervous Wreck

Molecular Biology of the Cell ◽

10.1091/mbc.e13-05-0271 ◽

2013 ◽

Vol 24 (15) ◽

pp. 2406-2418 ◽

Cited By ~ 24

Author(s):

Agata N. Becalska ◽

Charlotte F. Kelley ◽

Cristina Berciu ◽

Tatiana B. Stanishneva-Konovalova ◽

Xiaofeng Fu ◽

...

Keyword(s):

Electrostatic Interactions ◽

Higher Order ◽

Order Structure ◽

Structural Determinants ◽

Dynamic Membrane ◽

Bar Domain ◽

Neuronal Protein ◽

Positively Curved

Eukaryotic cells are defined by extensive intracellular compartmentalization, which requires dynamic membrane remodeling. FER/Cip4 homology-Bin/amphiphysin/Rvs (F-BAR) domain family proteins form crescent-shaped dimers, which can bend membranes into buds and tubules of defined geometry and lipid composition. However, these proteins exhibit an unexplained wide diversity of membrane-deforming activities in vitro and functions in vivo. We find that the F-BAR domain of the neuronal protein Nervous Wreck (Nwk) has a novel higher-order structure and membrane-deforming activity that distinguishes it from previously described F-BAR proteins. The Nwk F-BAR domain assembles into zigzags, creating ridges and periodic scallops on membranes in vitro. This activity depends on structural determinants at the tips of the F-BAR dimer and on electrostatic interactions of the membrane with the F-BAR concave surface. In cells, Nwk-induced scallops can be extended by cytoskeletal forces to produce protrusions at the plasma membrane. Our results define a new F-BAR membrane-deforming activity and illustrate a molecular mechanism by which positively curved F-BAR domains can produce a variety of membrane curvatures. These findings expand the repertoire of F-BAR domain mediated membrane deformation and suggest that unique modes of higher-order assembly can define how these proteins sculpt the membrane.

Download Full-text