An evolutionary change in telomere sequence motif within the plant section Asparagales had significance for telomere nucleoprotein complexes

2004 ◽  
Vol 107 (1-2) ◽  
pp. 132-138 ◽  
Author(s):  
G. Rotková ◽  
M. Skleničková ◽  
M. Dvořáčková ◽  
E. Sýkorová ◽  
A.R. Leitch ◽  
...  
Keyword(s):  
Evolutionary Change ◽  
Sequence Motif ◽  
Telomere Sequence ◽  
Plant Section ◽  
Nucleoprotein Complexes

scholarly journals Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein

2017 ◽  
Vol 292 (18) ◽  
pp. 7607-7618 ◽  
Author(s):  
Aleksandre Japaridze ◽  
Sylvain Renevey ◽  
Patrick Sobetzko ◽  
Liubov Stoliar ◽  
William Nasser ◽  
...  
Keyword(s):  
Long Range ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Sequence Motif ◽  
Structural Differentiation ◽  
Ample Evidence ◽  
Organizational Principle ◽  
Nucleoprotein Complexes

Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring protein (H-NS) is an abundant DNA-bridging, nucleoid-associated protein that binds to an AT-rich conserved DNA sequence motif and regulates both the shape and the genetic expression of the bacterial chromosome. Although there is ample evidence that the mode of H-NS binding depends on environmental conditions, the role of the spatial organization of H-NS-binding sequences in the assembly of long-range nucleoprotein structures remains unknown. In this study, by using high-resolution atomic force microscopy combined with biochemical assays, we explored the formation of H-NS nucleoprotein complexes on circular DNA molecules having different arrangements of identical sequences containing high-affinity H-NS-binding sites. We provide the first experimental evidence that variable sequence arrangements result in various three-dimensional nucleoprotein structures that differ in their shape and the capacity to constrain supercoils and compact the DNA. We believe that the DNA sequence-directed versatile assembly of periodic higher-order structures reveals a general organizational principle that can be exploited for knowledge-based design of long-range nucleoprotein complexes and purposeful manipulation of the bacterial chromatin architecture.

scholarly journals Coordinated Interactions of Multiple POT1-TPP1 Proteins with Telomere DNA

2013 ◽  
Vol 288 (23) ◽  
pp. 16361-16370 ◽  
Author(s):  
Mark Corriveau ◽  
Michael R. Mullins ◽  
Diane Baus ◽  
Michael E. Harris ◽  
Derek J. Taylor
Keyword(s):  
Dna Damage Response ◽  
High Specificity ◽  
Wild Type ◽  
Telomeric Dna ◽  
Telomere Sequence ◽  
G Quadruplex ◽  
Multiple Binding ◽  
Damage Response ◽  
Nuclease Digestion ◽  
Nucleoprotein Complexes

Telomeres are macromolecular nucleoprotein complexes that protect the ends of eukaryotic chromosomes from degradation, end-to-end fusion events, and from engaging the DNA damage response. However, the assembly of this essential DNA-protein complex is poorly understood. Telomere DNA consists of the repeated double-stranded sequence 5′-TTAGGG-3′ in vertebrates, followed by a single-stranded DNA overhang with the same sequence. Both double- and single-stranded regions are coated with high specificity by telomere end-binding proteins, including POT1 and TPP1, that bind as a heterodimer to single-stranded telomeric DNA. Multiple POT1-TPP1 proteins must fully coat the single-stranded telomere DNA to form a functional telomere. To better understand the mechanism of multiple binding, we mutated or deleted the two guanosine nucleotides residing between adjacent POT1-TPP1 recognition sites in single-stranded telomere DNA that are not required for multiple POT1-TPP1 binding events. Circular dichroism demonstrated that spectra from the native telomere sequence are characteristic of a G-quadruplex secondary structure, whereas the altered telomere sequences were devoid of these signatures. The altered telomere strands, however, facilitated more cooperative loading of multiple POT1-TPP1 proteins compared with the wild-type telomere sequence. Finally, we show that a 48-nucleotide DNA with a telomere sequence is more susceptible to nuclease digestion when coated with POT1-TPP1 proteins than when it is left uncoated. Together, these data suggest that POT1-TPP1 binds telomeric DNA in a coordinated manner to facilitate assembly of the nucleoprotein complexes into a state that is more accessible to enzymatic activity.

Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

1992 ◽  
Vol 50 (1) ◽  
pp. 762-763
Author(s):  
Stephen D. Jett
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Carbon Coated ◽  
Nucleoprotein Complexes ◽  
Mobility Shift Assay ◽  
Protein Nucleic Acid ◽  
Gel Mobility Shift ◽  
Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

From Phenotype to Genotype And Back Again

2019 ◽  
Author(s):  
J. Richtsmeier ◽  
K.M. Lesciotto
Keyword(s):  
Human Evolution ◽  
Evolutionary Change ◽  
Cranial Morphology ◽  
Phenotypic Trait ◽  
Critical Feature ◽  
Developmental Mechanism ◽  
Experimental Approaches ◽  
Physical Forces ◽  
Collaborative Efforts ◽  
Current Emphasis

Traditionally, anthropologists study evolutionary change throughmorphological analysis of fossils and comparative primate data. For the analysis of the genotypephenotype continuum, the current emphasis on genes is misplaced because genes don’t make structure. Developmental processes make structure through the activity of cells that use instructions specified by genes. A critical mechanism underlying any phenotypic trait is the genetically guided change in developmental events that produce the trait. But even when a developmental mechanism is identified, the links between genetically guided instructions and phenotypic outcome are lengthy, complicated, flexible, and sensitive to physical forces of functioning organs. We use the study of craniofacial phenotypes of craniosynostosis (premature closure of sutures) to demonstrate how patterns produced by the covariation of cranial traits cannot always reveal mechanism. Next we turn to encephalization, a critical feature of human evolution that covaries with cranial phenotypes, and show how experimental approaches can be used to analyze mechanism underlying this well-documented pattern in human evolution. With the realization that no single line of evidence can explain the dramatic changes in cranial morphology that characterize human evolution come fundamental changes in the way we conduct anthropological inquiry - collaborative efforts from scientists with diverse expertise will continue to push the field forward.

Formation of nucleoprotein complexes between polyoma empty capsides and DNA.

1975 ◽  
Vol 15 (3) ◽  
pp. 645-653 ◽  
Author(s):  
H V Aposhian ◽  
R E Thayer ◽  
P K Qasba
Keyword(s):  
Nucleoprotein Complexes

scholarly journals The double-stranded DNA-binding proteins TEBP-1 and TEBP-2 form a telomeric complex with POT-1

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sabrina Dietz ◽  
Miguel Vasconcelos Almeida ◽  
Emily Nischwitz ◽  
Jan Schreier ◽  
Nikenza Viceconte ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Wild Type ◽  
C Elegans ◽  
Double Stranded Dna ◽  
Telomere Sequence ◽  
Proteomics Approach ◽  
Telomeric Protein ◽  
Regulate Telomere Length

AbstractTelomeres are bound by dedicated proteins, which protect them from DNA damage and regulate telomere length homeostasis. In the nematode Caenorhabditis elegans, a comprehensive understanding of the proteins interacting with the telomere sequence is lacking. Here, we harnessed a quantitative proteomics approach to identify TEBP-1 and TEBP-2, two paralogs expressed in the germline and embryogenesis that associate to telomeres in vitro and in vivo. tebp-1 and tebp-2 mutants display strikingly distinct phenotypes: tebp-1 mutants have longer telomeres than wild-type animals, while tebp-2 mutants display shorter telomeres and a Mortal Germline. Notably, tebp-1;tebp-2 double mutant animals have synthetic sterility, with germlines showing signs of severe mitotic and meiotic arrest. Furthermore, we show that POT-1 forms a telomeric complex with TEBP-1 and TEBP-2, which bridges TEBP-1/-2 with POT-2/MRT-1. These results provide insights into the composition and organization of a telomeric protein complex in C. elegans.

scholarly journals The human TCF-1 gene encodes a nuclear DNA-binding protein uniquely expressed in normal and neoplastic T-lineage lymphocytes

Blood ◽  
1995 ◽  
Vol 86 (8) ◽  
pp. 3050-3059 ◽  
Author(s):  
J Castrop ◽  
D van Wichen ◽  
M Koomans-Bitter ◽  
M van de Wetering ◽  
R de Weger ◽  
...  
Keyword(s):  
T Cell ◽  
Cell Lines ◽  
Nuclear Dna ◽  
Mouse Cell ◽  
Lymphoid Tissues ◽  
Sequence Motif ◽  
Knock Out ◽  
Putative Transcription Factor ◽  
Knock Out Mice ◽  
T Cell Malignancies

Abstract The TCF-1 gene encodes a putative transcription factor with affinity for a sequence motif occurring in a number of T-cell enhancers. TCF-1 mRNA was originally found to be expressed in a T cell-specific fashion within a set of human and mouse cell lines. In contrast, expression reportedly occurs in multiple nonlymphoid tissues during murine embryogenesis. We have now raised a monoclonal antibody to document expression and biochemistry of the human TCF-1 protein. As expected, the TCF-1 protein was detectable only in cell lines of T lineage. Its expression was always restricted to the nucleus. Immunohistochemistry on a panel of human tissues revealed that the TCF-1 protein was found exclusively in thymocytes and in CD3+ T cells in peripheral lymphoid tissues. Western blotting yielded a set of bands ranging from 25 kD to 55 kD, resulting from extensive alternative splicing. The TCF-1 protein was detectable in all samples of a set of 22 T-cell malignancies of various stages of maturation, but was absent from a large number of other hematologic neoplasms. These observations imply a T cell-specific function for TCF-1, a notion corroborated by recent observations on Tcf-1 knock-out mice. In addition, these results indicate that nuclear TCF-1 expression can serve as a pan-T-lineage marker in the diagnosis of lymphoid malignancies.

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