Investigation of Latent Periodicity Phenomenon in the Genomes of Eukaryotic Organisms

The selectivity of the ubiquitin–26 S proteasome system (UPS) for a particular substrate protein relies on the interaction between a ubiquitin-conjugating enzyme (E2, of which a cell contains relatively few) and a ubiquitin–protein ligase (E3, of which there are possibly hundreds). Post-translational modifications of the protein substrate, such as phosphorylation or hydroxylation, are often required prior to its selection. In this way, the precise spatio-temporal targeting and degradation of a given substrate can be achieved. The E3s are a large, diverse group of proteins, characterized by one of several defining motifs. These include a HECT (homologous to E6-associated protein C-terminus), RING (really interesting new gene) or U-box (a modified RING motif without the full complement of Zn2+-binding ligands) domain. Whereas HECT E3s have a direct role in catalysis during ubiquitination, RING and U-box E3s facilitate protein ubiquitination. These latter two E3 types act as adaptor-like molecules. They bring an E2 and a substrate into sufficiently close proximity to promote the substrate's ubiquitination. Although many RING-type E3s, such as MDM2 (murine double minute clone 2 oncoprotein) and c-Cbl, can apparently act alone, others are found as components of much larger multi-protein complexes, such as the anaphase-promoting complex. Taken together, these multifaceted properties and interactions enable E3s to provide a powerful, and specific, mechanism for protein clearance within all cells of eukaryotic organisms. The importance of E3s is highlighted by the number of normal cellular processes they regulate, and the number of diseases associated with their loss of function or inappropriate targeting.

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ANTICYTOKINE ACTIVITY OF THE PROTOZOA BLASTOCYSTIS SPP

Bulletin Biomedicine and sociology ◽

10.26787/nydha-2618-8783-2020-5-4-44-48 ◽

2020 ◽

pp. 44-48

Author(s):

Bugero N.V. ◽

Ilyina N.A. ◽

Aleksandrova S.M.

Keyword(s):

Gastrointestinal Tract ◽

Gastrointestinal Diseases ◽

Control Group ◽

Ulcer Disease ◽

Cytokine Balance ◽

High Prevalence ◽

Blastocystis Spp ◽

High Level ◽

Eukaryotic Organisms ◽

High Degree

In addition to the classical pathogens, which are well understood and well identified, new pathogens with the potential to spread epidemiologically are being identified. Some of these little-known organisms are the simplest Blastocystis spp. blastocystostosis. The clinical significance of Blastocystis spp. and its pathogenicity are still under discussion. This parasite belongs to a group of single-celled eukaryotic organisms living in the colon of the human intestine. Blastocystis spp. is known to be found both in people with reduced immune status and in individuals without any clinical manifestation. It has been established that a sufficiently high degree of invasiveness is observed in persons with gastrointestinal tract diseases, dermatosis, allergic reactions, in patients with carriers of the human immunodeficiency virus, etc. Possessing persistence factors, protozoa blastocysts contribute to the inactivation of host defensive mechanisms, providing a stable anthogonistic effect. In recent years, many works have been devoted to the characteristics of the persistent properties of Blastocystis spr., however, individual properties of blastocysts, in particular, anticytokine activity (ACA), have not yet been studied. In this regard, the work studied the anticytokine activity of microorganisms isolated from healthy subjects and patients with gastrointestinal tract diseases. A high prevalence of the studied characteristic in the subjects was shown. The expression of anticytokine activity in the obtained isolates of blastocysts was the highest in the group of persons with gastric ulcer disease, which decreased in the order of duodenal ulcer, chronic cholecystitis, chronic gastritis, etc. The data obtained in this work on the high level of ACA expression in blastocyst isolates obtained from individuals with gastrointestinal diseases as compared with the control group enables to conclude that their exometabolites may influence the local cytokine balance [1], which supports the inflammatory process.

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Co-Translational Insertion of Aquaporins into Liposome for Functional Analysis via an E. coli Based Cell-Free Protein Synthesis System

Cells ◽

10.3390/cells8111325 ◽

2019 ◽

Vol 8 (11) ◽

pp. 1325 ◽

Cited By ~ 1

Author(s):

Ke Yue ◽

Tran Nam Trung ◽

Yiyong Zhu ◽

Ralf Kaldenhoff ◽

Lei Kai

Keyword(s):

Functional Analysis ◽

Membrane Proteins ◽

Fluorescent Protein ◽

Water Channel ◽

New Approach ◽

E Coli ◽

Straightforward Method ◽

Lipid Environment ◽

Green Fluorescent ◽

Eukaryotic Organisms

Aquaporins are important and well-studied water channel membrane proteins. However, being membrane proteins, sample preparation for functional analysis is tedious and time-consuming. In this paper, we report a new approach for the co-translational insertion of two aquaporins from Escherichia coli and Nicotiana tabacum using the CFPS system. This was done in the presence of liposomes with a modified procedure to form homogenous proteo-liposomes suitable for functional analysis of water permeability using stopped-flow spectrophotometry. Two model aquaporins, AqpZ and NtPIP2;1, were successfully incorporated into the liposome in their active forms. Shifted green fluorescent protein was fused to the C-terminal part of AqpZ to monitor its insertion and status in the lipid environment. This new fast approach offers a fast and straightforward method for the functional analysis of aquaporins in both prokaryotic and eukaryotic organisms.

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Solvent Exposure and Ionic Condensation Drive Fuzzy Dimerization of Disordered Heterochromatin Protein Sequence

Biomolecules ◽

10.3390/biom11060915 ◽

2021 ◽

Vol 11 (6) ◽

pp. 915

Author(s):

Jazelli Mueterthies ◽

Davit A. Potoyan

Keyword(s):

Phase Separation ◽

Low Complexity ◽

Nuclear Bodies ◽

Disordered Proteins ◽

Solvent Exposure ◽

Ion Release ◽

Dimer Formation ◽

Eukaryotic Organisms

Proteins with low complexity, disordered sequences are receiving increasing attention due to their central roles in the biogenesis and regulation of membraneless organelles. In eukaryotic organisms, a substantial fraction of disordered proteins reside in the nucleus, thereby facilitating the formation of nuclear bodies, nucleolus, and chromatin compartmentalization. The heterochromatin family of proteins (HP1) is an important player in driving the formation of gene silenced mesoscopic heterochromatin B compartments and pericentric regions. Recent experiments have shown that the HP1a sequence of Drosophila melanogaster can undergo liquid-liquid phase separation under both in vitro and in vivo conditions, induced by changes of the monovalent salt concentration. While the phase separation of HP1a is thought to be the mechanism underlying chromatin compartmentalization, the molecular level mechanistic picture of salt-driven phase separation of HP1a has remained poorly understood. The disordered hinge region of HP1a is seen as the driver of salt-induced condensation because of its charge enriched sequence and post-translational modifications. Here, we set out to decipher the mechanisms of salt-induced condensation of HP1a through a systematic study of salt-dependent conformations of single chains and fuzzy dimers of disordered HP1a hinge sequences. Using multiple independent all-atom simulations with and without enhanced sampling, we carry out detailed characterization of conformational ensembles of disordered HP1a chains under different ionic conditions using various polymeric and structural measures. We show that the mobile ion release, enhancement of local transient secondary structural elements, and side-chain exposure to solvent are robust trends that accompany fuzzy dimer formation. Furthermore, we find that salt-induced changes in the ensemble of conformations of HP1a disordered hinge sequence fine-tune the inter-chain vs. self-chain interactions in ways that favor fuzzy dimer formation under low salt conditions in the agreement with condensation trends seen in experiments.

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Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation

Nature Communications ◽

10.1038/s41467-021-24553-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yan Xue ◽

Zhenhui Zhong ◽

C. Jake Harris ◽

Javier Gallego-Bartolomé ◽

Ming Wang ◽

...

Keyword(s):

Dna Methylation ◽

Arabidopsis Thaliana ◽

Transposable Element ◽

Zinc Finger ◽

Protein Function ◽

C Elegans ◽

Eukaryotic Organisms

AbstractThe Microrchidia (MORC) family of ATPases are required for transposable element (TE) silencing and heterochromatin condensation in plants and animals, and C. elegans MORC-1 has been shown to topologically entrap and condense DNA. In Arabidopsis thaliana, mutation of MORCs has been shown to reactivate silent methylated genes and transposons and to decondense heterochromatic chromocenters, despite only minor changes in the maintenance of DNA methylation. Here we provide the first evidence localizing Arabidopsis MORC proteins to specific regions of chromatin and find that MORC4 and MORC7 are closely co-localized with sites of RNA-directed DNA methylation (RdDM). We further show that MORC7, when tethered to DNA by an artificial zinc finger, can facilitate the establishment of RdDM. Finally, we show that MORCs are required for the efficient RdDM mediated establishment of DNA methylation and silencing of a newly integrated FWA transgene, even though morc mutations have no effect on the maintenance of preexisting methylation at the endogenous FWA gene. We propose that MORCs function as a molecular tether in RdDM complexes to reinforce RdDM activity for methylation establishment. These findings have implications for MORC protein function in a variety of other eukaryotic organisms.

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The Schizosaccharomyces pombe cho1+ Gene Encodes a Phospholipid Methyltransferase

Genetics ◽

10.1093/genetics/150.2.553 ◽

1998 ◽

Vol 150 (2) ◽

pp. 553-562

Author(s):

Margaret I Kanipes ◽

John E Hill ◽

Susan A Henry

Keyword(s):

Saccharomyces Cerevisiae ◽

Sequence Analysis ◽

Schizosaccharomyces Pombe ◽

Gene Disruption ◽

Structure And Function ◽

Biosynthetic Enzyme ◽

Gene Encoding ◽

Complementation Groups ◽

Eukaryotic Organisms ◽

And Function

Abstract The isolation of mutants of Schizosaccharomyces pombe defective in the synthesis of phosphatidylcholine via the methylation of phosphatidylethanolamine is reported. These mutants are choline auxotrophs and fall into two unlinked complementation groups, cho1 and cho2. We also report the analysis of the cho1+ gene, the first structural gene encoding a phospholipid biosynthetic enzyme from S. pombe to be cloned and characterized. The cho1+ gene disruption mutant (cho1Δ) is viable if choline is supplied and resembles the cho1 mutants isolated after mutagenesis. Sequence analysis of the cho1+ gene indicates that it encodes a protein closely related to phospholipid methyltransferases from Saccharomyces cerevisiae and rat. Phospholipid methyltransferases encoded by a rat liver cDNA and the S. cerevisiae OPI3 gene are both able to complement the choline auxotrophy of the S. pombe cho1 mutants. These results suggest that both the structure and function of the phospholipid N-methyltransferases are broadly conserved among eukaryotic organisms.

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A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Nature Communications ◽

10.1038/s41467-021-25158-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Omid Oftadeh ◽

Pierre Salvy ◽

Maria Masid ◽

Maxime Curvat ◽

Ljubisa Miskovic ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Expression System ◽

Biomass Composition ◽

Industrial Biotechnology ◽

Overflow Metabolism ◽

Cellular Expression ◽

A Genome ◽

Wide Range ◽

Eukaryotic Organisms ◽

Genome Scale

AbstractEukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of multiple biological networks into a single model for cell analysis and engineering. One of the most accurate models of biological systems include Expression and Thermodynamics FLux (ETFL), which efficiently integrates RNA and protein synthesis with traditional genome-scale metabolic models. However, ETFL is so far only applicable for E. coli. To adapt this model for Saccharomyces cerevisiae, we developed yETFL, in which we augmented the original formulation with additional considerations for biomass composition, the compartmentalized cellular expression system, and the energetic costs of biological processes. We demonstrated the ability of yETFL to predict maximum growth rate, essential genes, and the phenotype of overflow metabolism. We envision that the presented formulation can be extended to a wide range of eukaryotic organisms to the benefit of academic and industrial research.

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Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases

International Journal of Molecular Sciences ◽

10.3390/ijms21041352 ◽

2020 ◽

Vol 21 (4) ◽

pp. 1352 ◽

Cited By ~ 3

Author(s):

János András Mótyán ◽

Márió Miczi ◽

József Tőzsér

Keyword(s):

Structural Characteristics ◽

Limited Proteolysis ◽

Structural Data ◽

Data Bank ◽

Life Cycles ◽

Evolutionary Relationships ◽

Multiple Sequence ◽

Dimer Interface ◽

Viral Proteases ◽

Eukaryotic Organisms

The life cycles of retroviruses rely on the limited proteolysis catalyzed by the viral protease. Numerous eukaryotic organisms also express endogenously such proteases, which originate from retrotransposons or retroviruses, including DNA damage-inducible 1 and 2 (Ddi1 and Ddi2, respectively) proteins. In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. In addition to Ddi1 and Ddi2, at least one member of all seven genera of the Retroviridae family was included in this comparison. We found that the studied retroviral and non-viral proteases show differences in the mode of dimerization and density of intermonomeric contacts, and distribution of the structural characteristics is in agreement with their evolutionary relationships. Multiple sequence and structure alignments revealed that the interactions between the subunits depend mainly on the overall organization of the dimer interface. We think that better understanding of the general and specific features of proteases may support the characterization of retroviral-like proteases.

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Functional Characterization of Spliceosomal Introns and Identification of U2, U4, and U5 snRNAs in the Deep-Branching Eukaryote Entamoeba histolytica

Eukaryotic Cell ◽

10.1128/ec.00059-07 ◽

2007 ◽

Vol 6 (6) ◽

pp. 940-948 ◽

Cited By ~ 16

Author(s):

Carrie A. Davis ◽

Michael P. S. Brown ◽

Upinder Singh

Keyword(s):

Entamoeba Histolytica ◽

Splice Site ◽

Expressed Sequence Tag ◽

Functional Characterization ◽

Molecular Evidence ◽

Spliceosomal Introns ◽

Accurate Expression ◽

Eukaryotic Organisms

ABSTRACT Pre-mRNA splicing is essential to ensure accurate expression of many genes in eukaryotic organisms. In Entamoeba histolytica, a deep-branching eukaryote, approximately 30% of the annotated genes are predicted to contain introns; however, the accuracy of these predictions has not been tested. In this study, we mined an expressed sequence tag (EST) library representing 7% of amoebic genes and found evidence supporting splicing of 60% of the testable intron predictions, the majority of which contain a GUUUGU 5′ splice site and a UAG 3′ splice site. Additionally, we identified several splice site misannotations, evidence for the existence of 30 novel introns in previously annotated genes, and identified novel genes through uncovering their spliced ESTs. Finally, we provided molecular evidence for the E. histolytica U2, U4, and U5 snRNAs. These data lay the foundation for further dissection of the role of RNA processing in E. histolytica gene expression.

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