scholarly journals Identification of evolutionarily conserved nuclear matrix proteins and their prokaryotic origins

2019 ◽  
Author(s):  
Rahul Sureka ◽  
Rakesh Mishra
Keyword(s):  
Nuclear Matrix ◽  
Nuclear Architecture ◽  
Eukaryotic Cell ◽  
Nuclear Matrix Proteins ◽  
Evolutionary Origins ◽  
Structural Framework ◽  
Evolutionarily Conserved ◽  
Core Components ◽  
Membrane Bound ◽  
Protein Components

AbstractCompared to prokaryotic cells, a typical eukaryotic cell is much more complex along with its endomembrane system and membrane-bound organelles. Although the endosymbiosis theories convincingly explain the evolution of membrane-bound organelles such as mitochondria and chloroplasts, very little is understood about the evolutionary origins of the nucleus, the defining feature of eukaryotes. Most studies on nuclear evolution have not been able to take into consideration the underlying structural framework of the nucleus, attributed to the nuclear matrix (NuMat), a ribonucleoproteinaceous structure. This can largely be attributed to the lack of annotation of its core components. Since, NuMat has been shown to provide a structural platform for facilitating a variety of nuclear functions such as replication, transcription, and splicing, it is important to identify its protein components to better understand these processes. In this study, we address this issue using the developing embryos of D. melanogaster and D. rerio and identify 362 core NuMat proteins that are conserved between the two organisms. We find that of them, 132 protein groups have originated from pre-existing proteins in prokaryotes. While 51 were conserved across all eukaryotic supergroups, 17 new proteins evolved before the evolution of the last eukaryotic common ancestor and together these 68 proteins out of the 362 core conserved NuMat proteins are conserved across all eukaryotes indicating their indispensable nature for nuclear function for over 1.5 billion years of eukaryotic history. Our analysis paves the way to understand the evolution of the complex internal nuclear architecture and its functions.

scholarly journals Binding of matrix attachment regions to lamin polymers involves single-stranded regions and the minor groove

1994 ◽  
Vol 14 (9) ◽  
pp. 6297-6305
Author(s):  
M E Ludérus ◽  
J L den Blaauwen ◽  
O J de Smit ◽  
D A Compton ◽  
R van Driel
Keyword(s):  
Dna Sequences ◽  
Nuclear Matrix ◽  
Minor Groove ◽  
Structural Features ◽  
Matrix Attachment Regions ◽  
Nuclear Matrix Proteins ◽  
Evolutionarily Conserved ◽  
Related Proteins ◽  
Loop Domains

Chromatin in eukaryotic nuclei is thought to be partitioned into functional loop domains that are generated by the binding of defined DNA sequences, named MARs (matrix attachment regions), to the nuclear matrix. We have previously identified B-type lamins as MAR-binding matrix components (M. E. E. Ludérus, A. de Graaf, E. Mattia, J. L. den Blaauwen, M. A. Grande, L. de Jong, and R. van Driel, Cell 70:949-959, 1992). Here we show that A-type lamins and the structurally related proteins desmin and NuMA also specifically bind MARs in vitro. We studied the interaction between MARs and lamin polymers in molecular detail and found that the interaction is saturable, of high affinity, and evolutionarily conserved. Competition studies revealed the existence of two different types of interaction related to different structural features of MARs: one involving the minor groove of double-stranded MAR DNA and one involving single-stranded regions. We obtained similar results for the interaction of MARs with intact nuclear matrices from rat liver. A model in which the interaction of nuclear matrix proteins with single-stranded MAR regions serves to stabilize the transcriptionally active state of chromatin is discussed.

scholarly journals Binding of matrix attachment regions to lamin polymers involves single-stranded regions and the minor groove.

1994 ◽  
Vol 14 (9) ◽  
pp. 6297-6305 ◽  
Author(s):  
M E Ludérus ◽  
J L den Blaauwen ◽  
O J de Smit ◽  
D A Compton ◽  
R van Driel
Keyword(s):  
Dna Sequences ◽  
Nuclear Matrix ◽  
Minor Groove ◽  
Structural Features ◽  
Matrix Attachment Regions ◽  
Nuclear Matrix Proteins ◽  
Evolutionarily Conserved ◽  
Related Proteins ◽  
Loop Domains

Chromatin in eukaryotic nuclei is thought to be partitioned into functional loop domains that are generated by the binding of defined DNA sequences, named MARs (matrix attachment regions), to the nuclear matrix. We have previously identified B-type lamins as MAR-binding matrix components (M. E. E. Ludérus, A. de Graaf, E. Mattia, J. L. den Blaauwen, M. A. Grande, L. de Jong, and R. van Driel, Cell 70:949-959, 1992). Here we show that A-type lamins and the structurally related proteins desmin and NuMA also specifically bind MARs in vitro. We studied the interaction between MARs and lamin polymers in molecular detail and found that the interaction is saturable, of high affinity, and evolutionarily conserved. Competition studies revealed the existence of two different types of interaction related to different structural features of MARs: one involving the minor groove of double-stranded MAR DNA and one involving single-stranded regions. We obtained similar results for the interaction of MARs with intact nuclear matrices from rat liver. A model in which the interaction of nuclear matrix proteins with single-stranded MAR regions serves to stabilize the transcriptionally active state of chromatin is discussed.

Nucleoskeltal proteins with bifunctional roles in the nucleus and mitotic apparatus: a paradigm for protein dynamics in the cell cycle

1995 ◽  
Vol 53 ◽  
pp. 770-771
Author(s):  
B. R. Brinkley ◽  
D. He ◽  
C. Zeng ◽  
B. Scott ◽  
D. Turner
Keyword(s):  
Nuclear Matrix ◽  
Hormone Receptors ◽  
Nuclear Lamina ◽  
Eukaryotic Cell ◽  
Matrix Proteins ◽  
Mitotic Apparatus ◽  
Nuclear Compartment ◽  
Nuclear Matrix Proteins ◽  
Intact Nucleus ◽  
Nuclease Digestion

The eukaryotic cell nucleus, once believed to contain structureless nucleoplasm surrounding chromatin and the nucleolus is now thought to contain an extensive nucleoskeletal matrix on which chromatin, RNP and a complex array of transcription factors, hormone receptors and other regulatory factors are spatially arranged. A distinct nucleoskeleton has been difficult to identify in the intact nucleus, due in part to masking by a dense array of chromatin fibers. However, if chromatin is extracted by nuclease digestion and high salt, an underlying anastomosing network of 9-13 nm core filaments can be demonstrated. The nucleoskeleton resembles the cytoplasmic intermediate filament complex but is confined entirely within the nucleus where it connects the nuclear lamina with various nuclear organelles, forming an integral lattice of fibers collectively called the nuclear matrix. Although the molecular composition of the nucleoskeleton remains elusive, its integrity apparently requires RNP and a growing list of nuclear matrix proteins.Although relatively insoluble within the nuclear compartment, the entire nucleoskeletal framework and associated chromatin is efficiently dismantled, packaged, partitioned and reassembled into daughter nuclei during mitosis.

Some Aspects of the Polyhexamethyleneguanidine Salts Effect on Cell Cultures

2014 ◽  
Vol 1 (1) ◽  
pp. 62-67 ◽  
Author(s):  
M. Mandygra ◽  
A. Lysytsia
Keyword(s):  
Proliferative Activity ◽  
Cell Monolayer ◽  
Eukaryotic Cell ◽  
Culture Methods ◽  
Cellular Processes ◽  
Negative Effect ◽  
Membrane Bound ◽  
Membrane Bound Enzymes ◽  
Anion Type ◽  
Cell Culture Methods

Aim. To investigate the effect of polyhexamethyleneguanidine (PHMG) to eukaryotic cell culture. Methods. The passaged bovine tracheal cells culture (TCC) and primary culture of chicken embryo fi broblasts (FCE) were used in the experiments. TCC and FCE monolayers were treated with aqueous solutions of PHMG chloride or succinate. The method of PHMG polycation adsorption to the cells’ plasma membrane together with microscopy were applied. Results. The dependence of PHMG effect on the eukaryotic cells on the agent concentration, duration of exposure and the anion type has been fi xed. The PHMG concentration of 10 –5 per cent (0.1 μg/ml) never causes degradation of the previously formed cell monolayer, while the higher concentrations damage it. The conditions of the PHMG chloride and succinate’s negative effect on cell proliferation and inhibition of monolayer formation were determined. The hypothesis that under certain conditions PHMG stimulates the proliferative activity of the cells has been confi rmed. Stimulation may be associated with non-specifi c stress adaptation of cells. In this case, it is due to modifi cations of the cell membrane after PHMG adsorption to it. Conclusions. PHMG polycation binds with the membrane’s phosphoglycerides fi rmly and irreversibly. A portion of the lipids are removed from participation in the normal cellular processes at that. At the same time, the synthesis of new lipids and membrane-bound enzymes is probably accelerated. The phospholip ids’ neogenesis acceleration can stimulate mitosis under certain conditions. The obtained results can be used in the biotechnologies.

Differentiation-Specific Nuclear Matrix Proteins Cross-linked to DNA bycis-Diammine Dichloroplatinum

1998 ◽  
Vol 238 (1) ◽  
pp. 216-219 ◽  
Author(s):  
Elena Mattia ◽  
Margherita Eufemi ◽  
Silvia Chichiarelli ◽  
Mara Ceridono ◽  
Anna Ferraro
Keyword(s):  
Nuclear Matrix ◽  
Matrix Proteins ◽  
Nuclear Matrix Proteins

Protein composition of nuclear matrix preparations from HeLa cells: an immunochemical approach

1986 ◽  
Vol 80 (1) ◽  
pp. 103-122
Author(s):  
R. Verheijen ◽  
H. Kuijpers ◽  
P. Vooijs ◽  
W. van Venrooij ◽  
F. Ramaekers
Keyword(s):  
Nuclear Matrix ◽  
Connective Tissue Diseases ◽  
Protein Composition ◽  
Cytoskeletal Proteins ◽  
Two Dimensional ◽  
Two Dimensional Gel Electrophoresis ◽  
Core Proteins ◽  
Nuclear Rna ◽  
Hela S3 ◽  
Protein Components

Procedures for the isolation of HeLa S3 nuclear matrices were re-examined with special emphasis on the use of various nucleases and detergents as well as on the ionic strength of the final salt extraction. The protein composition of the resulting nuclear matrix preparations was analysed by one- and two-dimensional gel electrophoresis and found to be extremely reproducible. By means of co-electrophoresis several typical cytoskeletal proteins (actin, vimentin and cytokeratins) and heterogeneous nuclear RNA (hnRNA)-associated core proteins (hnRNP) were shown to be present in such nuclear matrix preparations. The nature of some other protein components was elucidated using two-dimensional immunoblotting and immunofluorescence. For this purpose mouse monoclonal antibodies to cytoskeletal components (vimentin, cytokeratins), small nuclear RNP (70 X 10(3) Mr protein of U1-RNP), hnRNP (C1/C2) and the pore-complex lamina (lamins A, B and C) were used next to human autoimmune sera obtained from patients with connective tissue diseases and directed against the residual nucleoli and the internal fibrillar mass. These antibodies enabled us to identify a number of proteins present specifically in the nuclear matrix and to show that part of the cytoskeletal proteins are still present in the isolated structures.

Heterogeneity of High-molecular-weight Human Salivary Mucins

2000 ◽  
Vol 14 (1) ◽  
pp. 69-75 ◽  
Author(s):  
G.D. Offner ◽  
R.F. Troxler
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Biochemical Properties ◽  
Salivary Proteins ◽  
Molecular Weights ◽  
Structural Framework ◽  
Buccal Epithelial Cells ◽  
Membrane Bound ◽  
Membrane Spanning ◽  
Micro Organisms

The existence of high-molecular-weight glycoproteins in saliva and salivary secretions has been recognized for nearly 30 years. These proteins, called mucins, are essential for oral health and perform many diverse functions in the oral cavity. Mucins have been intensively studied, and much has been learned about their biochemical properties and their interactions with oral micro-organisms and other salivary proteins. In the past several years, the major high-molecular-weight mucin in salivary secretions has been identified as MUC5B, one of a family of 11 human mucin gene products expressed in tissue-specific patterns in the gastrointestinal, respiratory, and reproductive tracts. MUC5B is one of four gel-forming mucins which exist as multimeric proteins with molecular weights greater than 20-40 million daltons. The heavily glycosylated mucin multimers form viscous layers which protect underlying epithelial surfaces from microbial, mechanical, and chemical assault. Another class of mucin molecules, the membrane-bound mucins, is structurally and functionally distinct from the gel-forming mucins. These proteins do not form multimers and can exist as both secreted and membrane-bound forms, with the latter anchored to epithelial cell membranes through a short membrane-spanning domain. In the present work, we show that two of the membrane-bound mucins, MUC1 and MUC4, are expressed in all major human salivary glands as well as in buccal epithelial cells. While the functions of these mucins in the oral environment are not understood, it is possible that they form a structural framework on the cell surface which not only is cytoprotective, but also may serve as a scaffold upon which MUC5B, and possibly other salivary proteins, assemble.

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