Advances in Cell biology, vol. 32, 2005, issue 1

Summary: The nuclear envelope separates the nucleoplasm from the rest of the cell. It includes two lipid bilayers, nuclear pores and the nuclear lamina. Lamins are major protein components of the nuclear lamina and are present in the nuclear interior as well. They are type V intermediate filament proteins. Intensive research on lamins has been conducted since early 1970s. At first lamins were known only as major structural components of the nucleus. As our knowledge progressed, their novel functions and roles were revealed. Currently, it is clear that lamins are responsible not only for mechanical functions but also organization of chromatin, DNA replication, regulation of transcription factors, epigenetics, DNA repair, transcription, cell cycle regulation, cell development and differentiation, nuclear migration and apoptosis. Recent studies have provided evidences in support of lamin function in virus infection, tumorogenesis, mitosis and for linking the nucleoplasm to all major cytoskeletal networks. Mutations in nuclear lamina genes may cause a wide range of heritable human diseases.

Mechanisms of a-Amanitin Hepatotoxicity and Comparative Antidotal Efficacy of Substances Used in Amanita phalloides Intoxication – a Review of Experiments on Primary Hepatocyte Cultures

Key words: a-amanitin, apoptosis, hepatocytes, lipid peroxidation, antidotes

Summary: C-terminals of amino acid sequences that are homological to fibrinogen chains, together belong to family of FRED domains. FRED domains are engaged in protein – protein interactions, like in fibrinogen and angiopoietins or bind carbohydrate, like in mammal ficolins. FRED domain spread between mentioned proteins by gen duplications and exon shuffling during evolution of multicellular animals. There are 24 genes in human DNA in which characteristic for FRED sequence is coded. Functions of many products of 24 genes still are not known. Studied proteins, with FRED domain, play different roles in organism. Fibrinogen is responsible for blood clotting, angiopoietins regulate new blood vessels formation, fibroleukin and ficolins are important in immune system response, and tenascines intermediate in cell and matrix interactions. The common feature, besides FRED domain, is participation in differentiation and migration of neoplastic cells. Many of FRED proteins may be potential markers of neoplasm diagnostics and application in therapies also can not be excluded.

Key words: fibrinogen, tenascin, ficolin, fibroleukin protein, fibrinogen-related domains, neoplastic cells

Summary: Stromal-derived factor-1 (SDF-1) is an important a-chemokine that binds to the G-protein-coupled seven-transmembrane span CXCR4. The SDF-1-CXCR4 axis regulates trafficking of normal and malignant cells. SDF-1 is an important chemoattractant for a variety of cells including hematopoietic stem/progenitor cells. For many years, it was believed that CXCR4 was the only receptor for SDF-1. However, several reports recently provided evidence that SDF-1 also binds to another seven-transmembrane span receptor called CXCR7, sharing this receptor with another chemokine family member called Interferon-inducible T-cell chemoattractant (I-TAC). Thus, with CXCR7 identified as a new receptor for SDF-1, the role of the SDF-1-CXCR4 axis in regulating several biological processes becomes more complex. Based on the available literature, this review addresses the biological significance of SDF-1's interaction with CXCR7, which may act as a kind of decoy or signaling receptor depending on cell type.

Key words: gstromal-derived factor-1(SDF-1), CXCR4, CXCR7, chemokines

Key words: glycans, glycosylation, innate immunity, adaptive immunity, galectins, C-type lectins, Siglecs.

Key words: microRNA, immune system, cell differentiation, viral and bacterial infections, neurologic

Summary: Oligomeric and polymeric protein associations often involve purely secondary chemical forces that is, hydrogen bonds, ionic bonds and van der Waals forces. Protein assembly and disassembly can also be regulated by post-translational modifications, such as phosphorylation or dephosphorylation, even in these cases the subunits are not linked covalently. The first transglutaminase enzyme (TGase, EC 2.3.2.13) was recognised on the basis of its ability to catalyse the covalent incorporation of amine into proteins. In general, TGases are a family of enzymes that catalyse the covalent binding of substrates with primary amine groups to the carboxamide group of protein glutamine residues. These enzymes are called 'biological glues' in that they catalyse the post-translational modification of proteins by forming stable intra- and inter-molecular bridges. Through a similar catalytic process, transglutaminases can carry out acylation, esterification, deamidation and isopeptide cleavage, although the biological relevance of these reactions is characteristic only for animal cell and is less clear. Biological functions of TGases are generally attributed to their protein-modifying activity, in some instances it is due to specialised non-catalytic actions, such as scaffolding of the cytoskeleton to maintain membrane integrity, cell adhesion and possibly signal transduction. Three structurally-characterised families of TGases have been identified. These are the papain-like TGases, members of the superfamily of cysteine proteases. These enzymes have a catalytic triad of Cys-His-Asp/Asn. Second group are the protein disulphide isomerase-like TGases, which have disulphide-bond isomerase activity in addition to their TGase activity, and third group is the bacterial toxin TGases; these proteins have an atypical catalytic triad and show no sequence homology with other two groups. Nine different TGase genes have been identified in the human genome. Eight encode potential Ca²⁺ regulated crosslinking enzymes and one encodes the catalytically inactive homologue. Apparent orthologues of the different human TGases have also been identified in organisms ranging from mammals to invertebrates. TGases are encoded by a family of closely related genes. All of the genes isolated so far seem to be organised in a similar way. Despite marked similarities in the organization of the TGase genes, their 5` flanking sequences and mechanisms of transcriptional regulation are not homologous, and this is consistent with their varied and regulated tissue-specific and developmental expression. High sequence conservation and high degree of preservation of residue of secondary structure indicates that all TGases might share a four-domain tertiary structure. Transglutaminases are Ca²⁺-dependent enzymes, as shown by EGTA inhibition. It has been demonstrated in pea root and leaf that calcium concentration affected the type of linkage that regulated intracellular role of TGases. High concentration of Ca²⁺ activated the formation of the glutamyl-lysyl isodipeptide bonds and inhibited amines conjugation to proteins. Other then Ca²⁺ factors like pH, magnesium and -SH protein groups can also modulate the enzyme activity. In animals transglutaminases are located both: intra- (cytosol, mitochondria, nucleus) and extra-cellularly in the matrix where they are involved in differentiation, transmembrane signalling, cell adhesion and organization of the extracellular matrix. Moreover, the presence and the activity of transglutaminases in dying animal cells are considered markers of apoptosis. Transglutaminases are also widespread in all plant organs and cell compartments. Much less is known about plant transglutaminases compared to their animal counterparts. In plants they are found at several different subcellular compartments, including the cytosol, cell wall, chloroplasts and mitochondria. Most data concern the chloroplast transglutaminase activity, which is regulated by light and known to modify Rubisco and several antenna proteins of photosystems I and II, influencing possibly the catalytic activity of the former and the energy transfer efficiency of the latter. Additional roles specific for plants are related to fertilisation, stresses, senescence and programmed cell death. AtPng1p, the first plant transglutaminase sequenced shows undetectable sequence homology to the animal enzymes, except for the catalytic triad (Cys-His-Asp). Despite that, AtPng1p shares with them immunological and biochemical properties and possibly a similar conformation. This review summarises our current knowledge of the structure, biochemical features, and cell localisation of animal and plant transglutaminases and their biological role in the cell.

Keywords: animal cell, enzyme, plant cell, protein cross-links, transglutaminases

Muscle Cells of Caenorhabditis Elegans as an Experimental Model for New Methods of Therapy of Duchenne Muscular Dystrophy

Summary: Duchenne muscular dystrophy is one of the most frequent and most serious types of muscular dystrophies. Both molecular aspects and efficient methods of DMD therapy are not known yet. C. elegans is a promising experimental model in the research on DMD. The paper demonstrates important similarities between structure and function of C. elegans and human muscle cells, which enable a more precise analysis of the muscle degeneration process. The role of ion channels EGL-19 and BK-SLO in muscle degeneration in C. elegans was indicated. The effects of the dyb-1, dyc-1, stn-1 mutations which are associated with muscle degeneration in C. elegans were also described. The knowledge of these genes can be a promising aspect in the research on their function in human. Moreover, C. elegans was pointed out as a model organism in research on efficiency of potential pharmacological compounds which are used or could be used in the therapy of DMD. The beneficial effect of prednisone, serotonine, methazolamide and dichlorophenamide was described. The significance of synaptic transmission and proper structure of proteins responsible for muscle contraction in C. elegans muscle degeneration were also indicated.

Key words: Caenorhabditis elegans, Duchenne muscular dystrophy, muscle cells, muscle degeneration

Summary: Until recently the kidney has not been considered as an important organ in iron metabolism. However, the investigation of last decade showed that even under physiological conditions significant amounts of iron proteins undergo glomerular filtration and are reabsorbed in the proximal tubule. In the case of hemolytic diseases exposition of the kidney towards iron is increased and dependent on plasma haptoglobin level. Uptake of iron protein in the proximal tubule occurs via endocytosis mediated by a tandem of receptors – megalin and cubilin. A chaperon protein amnionless is essential for proper functioning of the complex. Moreover, it has been shown that proteins important in iron metabolism such as DMT-1, hephaestin and ferroportin are expressed in the epithelial cells of the proximal tubule. The article highlights main achievements in this field, and presents a scheme of molecular mechanism of kidney iron metabolism.

Summary: Lipid droplets are usually spherical organelles. A core of lipid consists of neutral lipids sur-rounded by a phospholipid monolayer. Many proteins bind to lipid droplets. Some of them are involved in lipid metabolism and belong to PAT family. Others are well known from different cell compartments, where they play roles not associated with lipid metabolism. Mechanisms of lipid biogenesis and growth are not clear. Several alternative models of lipid droplet formation in eukaryotic cells have been proposed and all of them agree that endoplasmic reticulum plays a key role in lipid droplet biogenesis. Essential differences among the models pertain to the sites of lipid droplet formation (between two leaflets of endoplasmic reticulum membrane or in close neighborhood with endoplasmic reticulum) as well as the mechanisms of lipid droplet detachment from the endoplasmic reticulum membrane. Growth of lipid droplets may result from homotypic fusion or supply of lipid esters and phospholipids to the existing lipid droplet. Lipid droplets interact with organelles (endoplasmic reticulum, mitochondria, peroxisomes, endosomes and phagosomes) and cytoskeleton elements. They are mobile organelles. Intracellular transport of lipid droplets is based mainly on microtubules and their motor proteins. The major roles of lipid droplets are lipid storage and release. Moreover, they mediate intracellular lipid and phospholipid traffic. The ability to bind proteins is a newly discovered function of lipid droplets. The proteins associated with lipid droplets are inactivated and/or destined for degradation. The presence of ribosomes and RNA binding proteins in lipid droplets indicates that they might be capable of RNA binding. Much interest focuses on the role of lipid droplets in pathological states of the cell caused by inflammatory processes or neoplasia. The diverse contents of lipid droplets, their mobility and interactions with many organelles, suggest that they are dynamic and multifunctional organelles.

Key words: lipid droplet biogenesis, growth of lipid droplets, lipid droplet proteins

Summary: Nucleosomes are the basic structures of chromatin and constitute a general repressor in Eukaryote due to the compaction of DNA which limits its accessibility to DNA-binding factors. The first level of compaction consists in wrapping the DNA 147 bp long fragments around a histone octamer, which makes this DNA less accessible to the DNA binding factors than the linker DNA. The unwrapped linker DNA is 20–50 bp long. Nucleosomes further condense by linker histones H1 to form a 30 nm fiber. Differential compaction of the interphase chromatin is important for proper functioning of the genome. Density of nucleosomes along DNA varies between organisms and depends on the functional properties of chromatin. In transcriptionally active euchromatin the density is 6 nucleosomes/11 nm while in inactive heterochromatin – as much as 12–15 nucleosomes/11 nm. Genomic regions that strongly exclude a nucleosome are often found near gene promoter. Nucleosomes have some DNA sequence preferences. DNA fragments containing poly(dAT:dT) elements are poor in nucleosomes. Several factors control nucleosome positioning they are, among others, structures in DNA and in chromatin which depend on the chromatin remodelers and epigenetic modifications of DNA and histones, such as DNA methylation, histone posttranslational modifications and histone variants. N-terminal tails of core histones perform several independent functions. The precise positioning of nucleosomes plays an important role in the regulation of gene expression. The core histone tail domains are molecular determinants responsible for positioning, as it has been demonstrated by the results of experiments in which the core histone tails were removed. In the condensation of nucleosome arrays into higher order chromatin structures, core histone tails take part. The 30 nm fiber constitutes the first order of folding of a nucleosome array. It represents only a minority of chromatin. In the higher order structures the contact between adjacent nucleosomes depend on core histone N-terminal tails and an interaction between them. The degree of compaction depends on the type of histone modifications. It is well known that core histone acetylation results in the decondensation of chromatin and is characteristic of transcriptionally active chromatin. Trimethylation of some lysine residues, e.g. lysine 20 in H4, marks transcriptionally inactive chromatin, and is typical of highly compacted transcriptionally inactive heterochromatin. Variants of the core histone H2A: H2A.Z, H2A.v, H2A.Bbdb and H2A.Bdb can participate in the chromatin compaction and proper regulation of gene expression. In Saccharomyces cerevisiae loss of H2A.Z is tolerated, but the regulation of gene expression is affected. H2A.Z is excluded from constitutive heterochromatin, but present in so-called facultative heterochromatin. H2A.v is present both in eu- and heterochromatin. Its role in the chromatin stabilization seems to consist in the formation of condensed chromatin. New insight into how the folding process is regulated concerns the role of a cluster of seven amino acid residues (the acidic path) present mainly in H2A. This acidic path can interact with a basic N-terminal tail of histone H4 (residues 14–19) from one nucleosome with an adjacent nucleosome when nucleosomal arrays fold into the 30 nm fiber. The acidic path in H2A can be modified in some H2A variants. H2A.Bbd has three acidic residues within the acidic path. This variant inhibits the formation of 30 nm chromatin fiber. As a result of inhibiting the formation of 30 nm fiber, H2A.Bbd enhances transcription. On the other hand, H2A.Z promotes the formation of 30 nm fiber on account of the presence of two additional amino acid residues which extend acidic path of H2A.Z compared to that of H2A. As H2A.Z is present in the facultative heterochromatin (condensed euchromatin), it is possible that this histone variant participates in the condensation of euchromatin.The compacteness of chromatin is modified by ATP-dependent chromatin-remodeling complex, ATPases. They use the energy of ATP hydrolysis to move nucleosomes to different localizations along the DNA. Chromatin remodelers can act both as chromatin condensing and decondensing factors. Chromatin remodeling ATPases play an important role in physiological and developemental processes in eukaryotes.

Key words: nucleosome, N-terminal tail of core histone, H2A variants, chromatin compaction