Dinoflagellates have a eukaryotic nuclear matrix with lamin-like proteins and topoisomerase II

1994 ◽  
Vol 107 (10) ◽  
pp. 2861-2873
Author(s):  
A. Minguez ◽  
S. Franca ◽  
S. Moreno Diaz de la Espina
Keyword(s):  
Nuclear Matrix ◽  
Topoisomerase Ii ◽  
Higher Plants ◽  
Supramolecular Organization ◽  
Free Living ◽  
Eukaryotic Nucleus ◽  
Nucleosomal Dna ◽  
Eukaryotic Chromatin ◽  
Early Acquisition ◽  
Loop Domains

Unicellular Dinoflagellates represent the only eukaryotic Phylum lacking histones and nucleosomes. To investigate whether Dinoflagellates do have a nuclear matrix that would modulate the supramolecular organization of their non-nucleosomal DNA and chromosomes, cells of the free-living unarmored Dinoflagellate Amphidinium carterae were encapsulated in agarose microbeads and submitted to sequential extraction with non-ionic detergents, nucleases and 2 M NaCl. Our results demonstrate that this species has a residual nuclear matrix similar to that of vertebrates and higher plants. The cytoskeleton-nuclear matrix complex of A. carterae shows a relatively intricate polypeptide pattern. Immunoblots with different antibodies reveal several intermediate filament types of proteins, one of which is immunologically related to vertebrate lamins, confirming that these proteins are ancestral members of the IF family, which is highly conserved in eukaryotes. A topoisomerase II homologue has also been identified in the nuclear matrix, suggesting that these structures could play a role in organizing the Dinoflagellate DNA in loop domains. Taken together our results demonstrate that the nuclear matrix is an early acquisition of the eukaryotic nucleus, independent of histones and nucleosomes in such a way that the mechanisms controlling the two levels of organization in eukaryotic chromatin would be molecularly and evolutionarily independent.

scholarly journals The SWI/SNF Complex Creates Loop Domains in DNA and Polynucleosome Arrays and Can Disrupt DNA-Histone Contacts within These Domains

1999 ◽  
Vol 19 (2) ◽  
pp. 1470-1478 ◽  
Author(s):  
David P. Bazett-Jones ◽  
Jacques Côté ◽  
Carolyn C. Landel ◽  
Craig L. Peterson ◽  
Jerry L. Workman
Keyword(s):  
Chromatin Remodeling ◽  
Dna Content ◽  
Naked Dna ◽  
Nucleosome Organization ◽  
Nucleosomal Dna ◽  
Close Proximity ◽  
Loop Domains

ABSTRACT To understand the mechanisms by which the chromatin-remodeling SWI/SNF complex interacts with DNA and alters nucleosome organization, we have imaged the SWI/SNF complex with both naked DNA and nucleosomal arrays by using energy-filtered microscopy. By making ATP-independent contacts with DNA at multiple sites on its surface, SWI/SNF creates loops, bringing otherwise-distant sites into close proximity. In the presence of ATP, SWI/SNF action leads to the disruption of nucleosomes within domains that appear to be topologically constrained by the complex. The data indicate that the action of one SWI/SNF complex on an array of nucleosomes can lead to the formation of a region where multiple nucleosomes are disrupted. Importantly, nucleosome disruption by SWI/SNF results in a loss of DNA content from the nucleosomes. This indicates a mechanism by which SWI/SNF unwraps part of the nucleosomal DNA.

scholarly journals The PsbW protein stabilizes the supramolecular organization of photosystem II in higher plants

2010 ◽  
Vol 65 (3) ◽  
pp. 368-381 ◽  
Author(s):  
José G. García-Cerdán ◽  
Laszlo Kovács ◽  
Tünde Tóth ◽  
Sami Kereïche ◽  
Elena Aseeva ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Higher Plants ◽  
Supramolecular Organization

scholarly journals Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA

2006 ◽  
Vol 25 (11) ◽  
pp. 2575-2583 ◽  
Author(s):  
Javier Salceda ◽  
Xavier Fernández ◽  
Joaquim Roca
Keyword(s):  
Topoisomerase I ◽  
Topoisomerase Ii ◽  
Nucleosomal Dna

scholarly journals Localization of topoisomerase II in mitotic chromosomes.

1985 ◽  
Vol 100 (5) ◽  
pp. 1716-1725 ◽  
Author(s):  
W C Earnshaw ◽  
M M Heck
Keyword(s):  
Present Article ◽  
Immunoelectron Microscopy ◽  
Polyclonal Antibody ◽  
Topoisomerase Ii ◽  
Mitotic Chromosome ◽  
Experimental Protocol ◽  
Mitotic Chromosomes ◽  
Restricted Domains ◽  
Loop Domains ◽  
Chromosome Scaffold

In the preceding article we described a polyclonal antibody that recognizes cSc-1, a major polypeptide component of the chicken mitotic chromosome scaffold. This polypeptide was shown to be chicken topoisomerase II. In the experiments described in the present article we use indirect immunofluorescence and immunoelectron microscopy to examine the distribution of topoisomerase II within intact chromosomes. We also describe a simple experimental protocol that differentiates antigens that are interspersed along the chromatin fiber from those that occupy restricted domains within the chromosome. These experiments indicate that the distribution of the enzyme appears to be independent of the bulk chromatin. Our data suggest that topoisomerase II is bound to the bases of the radial loop domains of mitotic chromosomes.

Protein:DNA interactions at chromosomal loop attachment sites

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 503-509 ◽  
Author(s):  
Veronica C. Blasquez ◽  
Ann O. Sperry ◽  
Peter N. Cockerill ◽  
William T. Garrard
Keyword(s):  
Nuclear Matrix ◽  
Binding Sites ◽  
Topoisomerase Ii ◽  
Regulatory Sequences ◽  
Immunoglobulin Gene ◽  
Sequence Motifs ◽  
Cis Acting ◽  
Consensus Sequences ◽  
Dna And Rna ◽  
Multiple Binding Sites

We have recently identified an evolutionarily conserved class of sequences that organize chromosomal loops in the interphase nucleus, which we have termed "matrix association regions" (MARs). MARs are about 200 bp long, AT-rich, contain topoisomerase II consensus sequences and other AT-rich sequence motifs, often reside near cis-acting regulatory sequences, and their binding sites are abundant (> 10 000 per mammalian nucleus). Here we demonstrate that the interactions between the mouse κ immunoglobulin gene MAR and topoisomerase II or the "nuclear matrix" occur between multiple and sometimes overlapping binding sites. Interestingly, the sites most susceptible to topoisomerase II cleavage are localized near the breakpoints of a previously described illegitimate recombination event. The presence of multiple binding sites within single MARs may allow DNA and RNA polymerase passage without disrupting primary loop organization.Key words: MARs, chromatin loops, topoisomerase II, nuclear matrix.

Proteomic approach to characterize the supramolecular organization of photosystems in higher plants

2004 ◽  
Vol 65 (12) ◽  
pp. 1683-1692 ◽  
Author(s):  
Jesco Heinemeyer ◽  
Holger Eubel ◽  
Dirk Wehmhöner ◽  
Lothar Jänsch ◽  
Hans-Peter Braun
Keyword(s):  
Higher Plants ◽  
Supramolecular Organization ◽  
Proteomic Approach

Biological and ecological aspects of nitrogen fixation by free-living micro-organisms

1969 ◽  
Vol 172 (1029) ◽  
pp. 367-388 ◽  
Keyword(s):  
Nitrogen Fixation ◽  
Soil Fertility ◽  
Biological Nitrogen Fixation ◽  
Higher Plants ◽  
Symbiotic Association ◽  
Free Living ◽  
Blue Green Algae ◽  
Ecological Aspects ◽  
Micro Organisms ◽  
Biological Nitrogen

Biological nitrogen fixation is a characteristic of certain micro-organisms, which may be free-living or occur in symbiotic association with higher plants. The purpose of this paper is to summarize some of the biological and ecological aspects of nitrogen-fixation by free-living forms. Biochemical aspects have been reviewed in other contributions to this discussion by Drs Wilson, Burris, and Cox & Fay. Nitrogen fixation by heterotrophic micro-organisms has been considered by Jensen (1965); nitrogen fixation by blue-green algae by Fogg & Stewart (1965), and by Stewart (1966, 1969), while Moore (1966) has evaluated the contribution of nitrogen-fixing micro-organisms to soil fertility.

scholarly journals Fecundity of Aphelenchus Avenae Bastian

1968 ◽  
Vol 21 (1) ◽  
pp. 169 ◽  
Author(s):  
JM Fisher
Keyword(s):  
Life Span ◽  
Egg Production ◽  
Higher Plants ◽  
Egg Laying ◽  
Migratory Species ◽  
Free Living ◽  
Aphelenchus Avenae ◽  
Plant Parasitic

Little is known about the various factors that determine the rate of reproduction of plant parasitic and free-living nematodes. The available data on the life span of females, the number of eggs laid, and the rate of egg-laying are based on total egg counts from single females or rates of egg-laying over short periods. Assessment of egg production in migratory ectoparasitic plant nematodes is also technically difficult because, unlike sedentary endoparasitic nematodes, the eggs are deposited at random in soil. Aphelenchu8 avenae Bastian, 1865, although a parasite of higher plants (Chin and Estey 1966), is easily cultured on many fungi (Townshend 1964) and so offers a ready means of studying fecundity in migratory species.

scholarly journals H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Anand Ranjan ◽  
Feng Wang ◽  
Gaku Mizuguchi ◽  
Debbie Wei ◽  
Yingzi Huang ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Gene Promoters ◽  
Histone H2a ◽  
Chromatin Remodeler ◽  
Histone Fold ◽  
Nucleosomal Dna ◽  
Eukaryotic Chromatin ◽  
Dna Elements ◽  
Key Residues ◽  
Nucleosomal Histone

The histone variant H2A.Z is a universal mark of gene promoters, enhancers, and regulatory elements in eukaryotic chromatin. The chromatin remodeler SWR1 mediates site-specific incorporation of H2A.Z by a multi-step histone replacement reaction, evicting histone H2A-H2B from the canonical nucleosome and depositing the H2A.Z-H2B dimer. Binding of both substrates, the canonical nucleosome and the H2A.Z-H2B dimer, is essential for activation of SWR1. We found that SWR1 primarily recognizes key residues within the α2 helix in the histone-fold of nucleosomal histone H2A, a region not previously known to influence remodeler activity. Moreover, SWR1 interacts preferentially with nucleosomal DNA at superhelix location 2 on the nucleosome face distal to its linker-binding site. Our findings provide new molecular insights on recognition of the canonical nucleosome by a chromatin remodeler and have implications for ATP-driven mechanisms of histone eviction and deposition.

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