scholarly journals Electrophoretic pattern of the polypeptide component in the tight DNA-protein complexes in rat and chicken tissues and its partial characterisation in rat liver

2010 ◽  
Vol 64 (5-6) ◽  
pp. 188-193
Author(s):  
Normunds Legzdiņš ◽  
Danute Labeikytė ◽  
Nikolajs Sjakste
Keyword(s):  
Rat Liver ◽  
Protein Complexes ◽  
Regulation Of Gene Expression ◽  
Electrophoretic Pattern ◽  
Covalent Bonds ◽  
Chicken Tissues ◽  
Repair Enzymes ◽  
Protein Group ◽  
Ubiquitin Proteasome ◽  
Partial Characterisation

Electrophoretic pattern of the polypeptide component in the tight DNA-protein complexes in rat and chicken tissues and its partial characterisation in rat liverTightly bound to DNA proteins (TBP) are a protein group that remain attached to DNA with covalent or non-covalent bonds after its deproteinisation. The distribution of TBP in genes reflects the type of cell differentiation. It has been hypothesised that TBP binding is involved in regulation of gene expression. Early studies reported uniformity of the TBPs from different sources. Later it was shown that TBPs obtained from DNA, isolated in mild conditions from evolutionary distant species, are different. Application of chloroform DNA extraction without use of externally added enzymes enabled us to reveal differences in the TBP spectrum in plant organs and changes of this spectrum in the course of plant development. The goal of this work was to study the electrophoretic pattern of the polypeptide component in the tight DNA-protein complexes in organs of animals: a mammal (rat) and a bird (chicken). Rat thymus TBPs were represented by 70 and 60 kDa proteins, and the same polypeptides were observed also in brain and skeletal muscles. Kidney TBPs were represented by 85, 70, 65, 60 and 37 kDa polypeptides; 85, 77, 70, 60, 50 and 37 kDa TBPs were characteristic of liver. Numerous minor peptides were observed in all samples studied. The spectrum of chicken liver and blood TBPs differed in distribution of proteins of 25-35 kDa. Mass-spectrometry of 14 bands from rat liver TBP gel revealed 43 different proteins. Chromatin modifying proteins and repair enzymes, transcription factors, serpins, ATPase, kinases and enzymes of ubiquitin-proteasome pathway were found among the TBPs. Thus, TBPs appear to be a vast protein group involved in several intranuclear processes. It is hypothesised that numerous functions ascribed to the nuclear matrix are performed in the TBP complexes.

scholarly journals Current Understanding of Circular RNAs in Systemic Lupus Erythematosus

2021 ◽  
Vol 12 ◽  
Author(s):  
Hongjiang Liu ◽  
Yundong Zou ◽  
Chen Chen ◽  
Yundi Tang ◽  
Jianping Guo
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Lupus Erythematosus ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Current Understanding ◽  
Circular Rnas ◽  
Systemic Lupus

Systemic lupus erythematosus (SLE) is a common and potentially fatal autoimmune disease that affects multiple organs. To date, its etiology and pathogenesis remains elusive. Circular RNAs (circRNAs) are a novel class of endogenous non-coding RNAs with covalently closed loop structure. Growing evidence has demonstrated that circRNAs may play an essential role in regulation of gene expression and transcription by acting as microRNA (miRNA) sponges, impacting cell survival and proliferation by interacting with RNA binding proteins (RBPs), and strengthening mRNA stability by forming RNA-protein complexes duplex structures. The expression patterns of circRNAs exhibit tissue-specific and pathogenesis-related manner. CircRNAs have implicated in the development of multiple autoimmune diseases, including SLE. In this review, we summarize the characteristics, biogenesis, and potential functions of circRNAs, its impact on immune responses and highlight current understanding of circRNAs in the pathogenesis of SLE.

scholarly journals Characterization of major chromatin assembly proteins in tetrahymena thermophile using proeomic and molecular evolutionary analyses

2021 ◽  
Author(s):  
Syed N Shah
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Affinity Purification ◽  
Regulation Of Gene Expression ◽  
Chromatin Assembly ◽  
Histone Chaperones ◽  
Protein Protein Interactions ◽  
Selective Forces ◽  
Assembly Proteins

Histones H3/H4 are deposited onto DNA in a replication-dependent or independent fashion by the CAF1 and HIRA protein complexes. Despite the identification of these protein complexes, mechanistic details remain unclear. Recently, we showed that in T. thermophila histone chaperones Nrp1, Asf1 and the Impβ6 importin function together to transport newly synthesized H3/H4 from the cytoplasm to the nucleus. To characterize chromatin assembly proteins in T.thermophila, I used affinity purification combined with mass spectrometry to identify protein-protein interactions of Nrp1, Cac2 subunit of CAF1, HIRA and histone modifying Hat1-complex in T. thermophila. I found that the three-subunit T.thermophila CAF1 complex interacts with Casein Kinase 2 (CKII), possibly accounting for previously reported human CAF1phosphorylation. I also found that Hat2 subunit of HAT1 complex is also shared by CAF1 complex as its Cac3 subunit. This suggests that Hat2/Cac3 might exist in two separate pools of protein complexes. Remarkably, proteomic analysis of Hat2/Cac3 in turn revealed that it forms several complexes with other proteins including SIN3, RXT3, LIN9 and TESMIN, all of which have known roles in the regulation of gene expression. Finally, I asked how selective forces might have impacted on the function of proteins involved in H3/H4 transport. Focusing on NASP which possesses several TPR motifs, I showed that its protein-protein interactions are conserved in T. thermophila. Using molecular evolutionary methods I show that different TPRs in NASP evolve at different rates possibly accounting for the functional diversity observed among different family members.

scholarly journals p97 Negatively Regulates NRF2 by Extracting Ubiquitylated NRF2 from the KEAP1-CUL3 E3 Complex

2017 ◽  
Vol 37 (8) ◽  
Author(s):  
Shasha Tao ◽  
Pengfei Liu ◽  
Gang Luo ◽  
Montserrat Rojo de la Vega ◽  
Heping Chen ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Protein Complexes ◽  
E3 Ubiquitin Ligase ◽  
Ubiquitin Proteasome System ◽  
Proteasomal Degradation ◽  
Ubiquitin Ligase Complex ◽  
Ubiquitin Proteasome ◽  
Client Proteins

ABSTRACT Activation of the stress-responsive transcription factor NRF2 is the major line of defense to combat oxidative or electrophilic insults. Under basal conditions, NRF2 is continuously ubiquitylated by the KEAP1-CUL3-RBX1 E3 ubiquitin ligase complex and is targeted to the proteasome for degradation (the canonical mechanism). However, the path from the CUL3 complex to ultimate proteasomal degradation was previously unknown. p97 is a ubiquitin-targeted ATP-dependent segregase that extracts ubiquitylated client proteins from membranes, protein complexes, or chromatin and has an essential role in autophagy and the ubiquitin proteasome system (UPS). In this study, we show that p97 negatively regulates NRF2 through the canonical pathway by extracting ubiquitylated NRF2 from the KEAP1-CUL3 E3 complex, with the aid of the heterodimeric cofactor UFD1/NPL4 and the UBA-UBX-containing protein UBXN7, for efficient proteasomal degradation. Given the role of NRF2 in chemoresistance and the surging interest in p97 inhibitors to treat cancers, our results indicate that dual p97/NRF2 inhibitors may offer a more potent and long-term avenue of p97-targeted treatment.

scholarly journals ETO-2 Associates with SCL in Erythroid Cells and Megakaryocytes and Provides Repressor Functions in Erythropoiesis

2005 ◽  
Vol 25 (23) ◽  
pp. 10235-10250 ◽  
Author(s):  
Anna H. Schuh ◽  
Alex J. Tipping ◽  
Allison J. Clark ◽  
Isla Hamlett ◽  
Boris Guyot ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Protein Complexes ◽  
Fetal Liver ◽  
Regulation Of Gene Expression ◽  
Erythroid Differentiation ◽  
Cell Types ◽  
Erythroid Cells ◽  
Proteomic Approach ◽  
Endogenous Proteins

ABSTRACT Lineage specification and cellular maturation require coordinated regulation of gene expression programs. In large part, this is dependent on the activator and repressor functions of protein complexes associated with tissue-specific transcriptional regulators. In this study, we have used a proteomic approach to characterize multiprotein complexes containing the key hematopoietic regulator SCL in erythroid and megakaryocytic cell lines. One of the novel SCL-interacting proteins identified in both cell types is the transcriptional corepressor ETO-2. Interaction between endogenous proteins was confirmed in primary cells. We then showed that SCL complexes are shared but also significantly differ in the two cell types. Importantly, SCL/ETO-2 interacts with another corepressor, Gfi-1b, in red cells but not megakaryocytes. The SCL/ETO-2/Gfi-1b association is lost during erythroid differentiation of primary fetal liver cells. Genetic studies of erythroid cells show that ETO-2 exerts a repressor effect on SCL target genes. We suggest that, through its association with SCL, ETO-2 represses gene expression in the early stages of erythroid differentiation and that alleviation/modulation of the repressive state is then required for expression of genes necessary for terminal erythroid maturation to proceed.

scholarly journals Recognition of the bcd mRNA Localization Signal in Drosophila Embryos and Ovaries

2005 ◽  
Vol 25 (4) ◽  
pp. 1501-1510 ◽  
Author(s):  
Mark J. Snee ◽  
Eric A. Arn ◽  
Simon L. Bullock ◽  
Paul M. Macdonald
Keyword(s):  
Protein Complexes ◽  
Regulation Of Gene Expression ◽  
Mrna Localization ◽  
Signal Recognition ◽  
Recognition Mechanism ◽  
Stem Loop ◽  
Multiple Contexts ◽  
Polarized Cells ◽  
Localization Signal ◽  
Drosophila Embryos

ABSTRACT The process of mRNA localization, often used for regulation of gene expression in polarized cells, requires recognition of cis-acting signals by components of the localization machinery. Many known RNA signals are active in the contexts of both the Drosophila ovary and the blastoderm embryo, suggesting a conserved recognition mechanism. We used variants of the bicoid mRNA localization signal to explore recognition requirements in the embryo. We found that bicoid stem-loop IV/V, which is sufficient for ovarian localization, was necessary but not sufficient for full embryonic localization. RNAs containing bicoid stem-loops III/IV/V did localize within the embryo, demonstrating a requirement for dimerization and other activities supplied by stem-loop III. Protein complexes that bound specifically to III/IV/V and fushi tarazu localization signals copurified through multiple fractionation steps, suggesting that they are related. Binding to these two signals was competitive but not equivalent. Thus, the binding complexes are not identical but appear to have some components in common. We have proposed a model for a conserved mechanism of localization signal recognition in multiple contexts.

scholarly journals The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression

2021 ◽  
Vol 12 ◽  
Author(s):  
Marios Agelopoulos ◽  
Spyros Foutadakis ◽  
Dimitris Thanos
Keyword(s):  
Gene Expression ◽  
Spatial Organization ◽  
Protein Complexes ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Current View ◽  
Regulation Of Expression ◽  
Time Space ◽  
Transcriptional Regulatory ◽  
Immune Related Genes

Regulation of gene expression in time, space and quantity is orchestrated by the functional interplay of cis-acting elements and trans-acting factors. Our current view postulates that transcription factors recognize enhancer DNA and read the transcriptional regulatory code by cooperative DNA binding to specific DNA motifs, thus instructing the recruitment of transcriptional regulatory complexes forming a plethora of higher-ordered multi-protein-DNA and protein-protein complexes. Here, we reviewed the formation of multi-dimensional chromatin assemblies implicated in gene expression with emphasis on the regulatory role of enhancer hubs as coordinators of stochastic gene expression. Enhancer hubs contain many interacting regulatory elements and represent a remarkably dynamic and heterogeneous network of multivalent interactions. A functional consequence of such complex interaction networks could be that individual enhancers function synergistically to ensure coordination, tight control and robustness in regulation of expression of spatially connected genes. In this review, we discuss fundamental paradigms of such inter- and intra- chromosomal associations both in the context of immune-related genes and beyond.

scholarly journals Mitochondrial сomplexome of etiolated pea shoots

2022 ◽  
Vol 11 (4) ◽  
pp. 570-580
Author(s):  
I. V. Ukolova ◽  
I. G. Kondratov ◽  
M. A. Kondakova ◽  
I. V. Lyubushkina ◽  
O. I. Grabelnykh ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Pyruvate Dehydrogenase Complex ◽  
Energy System ◽  
Physiological Status ◽  
Major Protein ◽  
Functional Categories ◽  
Sds Page ◽  
Acid Processing ◽  
Oxphos System ◽  
Protein Group

Studies into mitochondrial сomplexomes in various organisms provide an insight into the native organization of proteins and metabolic pathways in the organelles of the subject under study. “Complexome” is a relatively recent concept describing the proteome of protein complexes, supercomplexes, and oligomeric proteins. Complexome analysis is performed using current electrophoretic and mass spectrometric techniques, in particular, by two-dimensional electrophoresis (2D BN/SDS-PAGE) in combination with mass spectrometry (MS). Unlike 2D IEF/SDS-PAGE, this method enables analysis of not only hydrophilic proteins of the mitochondrial matrix, but also membrane proteins and their associations, thus expanding the possibilities of studying the organelle proteome. In the present work, the complexome of etiolated pea shoots was studied for the first time using 2D BN/SDS-PAGE followed by MALDI-TOF MS. To this end, 145 protein spots excised from the gel were analyzed; 110 polypeptides were identified and assigned to different functional groups. A densitometric analysis revealed that the major protein group comprised the enzymes of the mitochondrial energy system (1), accounting for an average of 43% of the total polypeptide content. The remaining 57% was primarily distributed among the following functional categories: pyruvate dehydrogenase complex and citric acid cycle (2); amino acid metabolism (3); nucleic acid processing (4); protein folding (5); antioxidant protection (6); carrier proteins (7); other proteins (8); proteins having unknown functions (9). The obtained data indicate the complex organization of the pea proteome. In addition to the enzymes of the OXPHOS system, the proteins of other functional categories are found to form supramolecular structures. It is suggested that the presence of proteins from other cellular compartments may indicate the interaction of mitochondria with the enzymes or structures of corresponding organelles. In general, the obtained data on the pea complexome represent a kind of a mitochondrial “passport” that reflects the native state of the proteome of organelles corresponding to their physiological status.

scholarly journals Fungal Secondary Metabolites as Inhibitors of the Ubiquitin–Proteasome System

2021 ◽  
Vol 22 (24) ◽  
pp. 13309
Author(s):  
Magdalena Staszczak
Keyword(s):  
Secondary Metabolites ◽  
Control Function ◽  
Cell Cycle Control ◽  
Regulation Of Gene Expression ◽  
Proteasome Inhibitors ◽  
Ubiquitin Proteasome System ◽  
Regulatory Function ◽  
Deubiquitinating Enzymes ◽  
Ubiquitin Proteasome ◽  
Fungal Secondary Metabolites

The ubiquitin–proteasome system (UPS) is the major non-lysosomal pathway responsible for regulated degradation of intracellular proteins in eukaryotes. As the principal proteolytic pathway in the cytosol and the nucleus, the UPS serves two main functions: the quality control function (i.e., removal of damaged, misfolded, and functionally incompetent proteins) and a major regulatory function (i.e., targeted degradation of a variety of short-lived regulatory proteins involved in cell cycle control, signal transduction cascades, and regulation of gene expression and metabolic pathways). Aberrations in the UPS are implicated in numerous human pathologies such as cancer, neurodegenerative disorders, autoimmunity, inflammation, or infectious diseases. Therefore, the UPS has become an attractive target for drug discovery and development. For the past two decades, much research has been focused on identifying and developing compounds that target specific components of the UPS. Considerable effort has been devoted to the development of both second-generation proteasome inhibitors and inhibitors of ubiquitinating/deubiquitinating enzymes. With the feature of unique structure and bioactivity, secondary metabolites (natural products) serve as the lead compounds in the development of new therapeutic drugs. This review, for the first time, summarizes fungal secondary metabolites found to act as inhibitors of the UPS components.

scholarly journals bromodomain-containing protein Ibd1 links multiple chromatin-related protein complexes to highly expressed genes in Tetrahymena thermophila

2021 ◽  
Author(s):  
Alejandro Saettone ◽  
Jyoti Garg ◽  
Jean-Philippe Lambert ◽  
Syed Nabeel-Shah ◽  
Marcelo Ponce ◽  
...  
Keyword(s):  
Tetrahymena Thermophila ◽  
Protein Complexes ◽  
Affinity Purification ◽  
Regulation Of Gene Expression ◽  
Methyl Transferase ◽  
Chromatin Remodelers ◽  
Highly Expressed Genes ◽  
Chromatin Remodeling Complexes ◽  
Additional Protein ◽  
Active Transcription

Background The chromatin remodelers of the SWI/SNF family are critical transcriptional regulators. Recognition of lysine acetylation through a bromodomain (BRD) component is key to SWI/SNF function; in most eukaryotes, this function is attributed to SNF2/Brg1. Results Using affinity purification coupled to mass spectrometry (AP–MS) we identified members of a SWI/SNF complex (SWI/SNFTt) in Tetrahymena thermophila. SWI/SNFTt is composed of 11 proteins, Snf5Tt, Swi1Tt, Swi3Tt, Snf12Tt, Brg1Tt, two proteins with potential chromatin-interacting domains and four proteins without orthologs to SWI/SNF proteins in yeast or mammals. SWI/SNFTt subunits localize exclusively to the transcriptionally active macronucleus during growth and development, consistent with a role in transcription. While Tetrahymena Brg1 does not contain a BRD, our AP–MS results identified a BRD-containing SWI/SNFTt component, Ibd1 that associates with SWI/SNFTt during growth but not development. AP–MS analysis of epitope-tagged Ibd1 revealed it to be a subunit of several additional protein complexes, including putative SWRTt, and SAGATt complexes as well as a putative H3K4-specific histone methyl transferase complex. Recombinant Ibd1 recognizes acetyl-lysine marks on histones correlated with active transcription. Consistent with our AP–MS and histone array data suggesting a role in regulation of gene expression, ChIP-Seq analysis of Ibd1 indicated that it primarily binds near promoters and within gene bodies of highly expressed genes during growth. Conclusions Our results suggest that through recognizing specific histones marks, Ibd1 targets active chromatin regions of highly expressed genes in Tetrahymena where it subsequently might coordinate the recruitment of several chromatin-remodeling complexes to regulate the transcriptional landscape of vegetatively growing Tetrahymena cells.

scholarly journals Chromatin-associated protein complexes link DNA base J and transcription termination in Leishmania

2020 ◽  
Author(s):  
Bryan C Jensen ◽  
Isabelle Q. Phan ◽  
Jacquelyn R. McDonald ◽  
Aakash Sur ◽  
Mark A. Gillespie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Protein Complexes ◽  
Transcription Termination ◽  
Critical Role ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Control Of Gene Expression ◽  
Polycistronic Transcription ◽  
Post Transcriptional Regulation

AbstractUnlike most other eukaryotes, Leishmania and other trypanosomatid protozoa have largely eschewed transcriptional control of gene expression; relying instead on post-transcriptional regulation of mRNAs derived from polycistronic transcription units (PTUs). In these parasites, a novel modified nucleotide base (β-D-glucopyranosyloxymethyluracil) known as J plays a critical role in ensuring that transcription termination occurs only at the end of each PTU, rather than at the polyadenylation sites of individual genes. To further understand the biology of J-associated processes, we used tandem affinity purification (TAP-tagging) and mass spectrometry to reveal proteins that interact with the glucosyltransferase performing the final step in J synthesis. These studies identified four proteins reminiscent of subunits in the PTW/PP1 complex that controls transcription termination in higher eukaryotes. Moreover, bioinformatic analyses identified the DNA-binding subunit of Leishmania PTW/PP1 as a novel J-binding protein (JBP3). Down-regulation of JBP3 expression levels in Leishmania resulted in a substantial increase in transcriptional read-through at the 3’ end of most PTUs. Additional TAP-tagging experiments showed that JBP3 also associates with two other protein complexes. One consists of subunits with domains suggestive of a role in chromatin modification/remodeling; while the other contains subunits with similarity to those found in the PAF1 complex involved in regulation of transcription in other eukaryotes. Thus, trypanosomatids utilize protein complexes similar to those used to control transcription termination in other eukaryotes and JBP3 appears to function as a hub linking these modules to base J, thereby enabling the parasites’ unique reliance on polycistronic transcription and post-transcriptional regulation of gene expression.

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