Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B
; ; Willems, Luc et al
in Journal of Structural Biology (2016), 194
DNA methylation is an important epigenetic modification involved in chromatin organization and gene expression. The function of DNA methylation depends on cell context and is correlated with histone ... [more ▼]
DNA methylation is an important epigenetic modification involved in chromatin organization and gene expression. The function of DNA methylation depends on cell context and is correlated with histone modification patterns. In particular, trimethylation of Lys36 on histone H3 tail (H3K36me3) is associated with DNA methylation and elongation phase of transcription. PWWP domains of the de novo DNA methyltransferases DNMT3A and DNMT3B read this epigenetic mark to guide DNA methylation. Here we report the first crystal structure of the DNMT3B PWWP domain–H3K36me3 complex. Based on this structure, we propose a model of the DNMT3A PWWP domain–H3K36me3 complex and build a model of DNMT3A (PWWP-ADD-CD) in a nucleosomal context. The trimethylated side chain of Lys36 (H3K36me3) is inserted into an aromatic cage similar to the ‘‘Royal” superfamily domains known to bind methylated histones. A key interaction between trimethylated Lys36 and a conserved water molecule stabilized by Ser270 explains the lack of affinity of mutated DNMT3B (S270P) for the H3K36me3 epigenetic mark in the ICF (Immunodeficiency, Centromeric instability and Facial abnormalities) syndrome. The model of the DNMT3A-DNMT3L heterotetramer in complex with a dinucleosome highlights the mechanism for recognition of nucleosome by DNMT3s and explains the periodicity of de novo DNA methylation. [less ▲]Detailed reference viewed: 19 (4 ULg)
The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools.
Figueroa Yévenes, Maximiliano ; ; Vandevenne, Marylène et al
in Journal of structural biology (2016)
Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the ... [more ▼]
Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (alphabetaalpha) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of them predicted a TIM-barrel fold, i.e. the structure we set out to design more than 10years ago. In addition, local software runs that are human operated can sample a structure similar to the experimental one but fail in selecting it, suggesting that the scoring and ranking functions should be improved. We propose that artificial proteins could be used as tools to test the accuracy of protein structure prediction algorithms, because their lack of evolutionary pressure and unique sequences features. [less ▲]Detailed reference viewed: 21 (5 ULg)
Nucleolar structure across evolution: the transition between bi- and tri-compartmentalized nucleoli lies within the class Reptilia.
; ; et al
in Journal of Structural Biology (2011), 174(2), 352-9
Two types of nucleolus can be distinguished among eukaryotic cells: a tri-compartmentalized nucleolus in amniotes and a bi-compartmentalized nucleolus in all the others. However, though the nucleolus ... [more ▼]
Two types of nucleolus can be distinguished among eukaryotic cells: a tri-compartmentalized nucleolus in amniotes and a bi-compartmentalized nucleolus in all the others. However, though the nucleolus' ultrastructure is well characterized in mammals and birds, it has been so far much less studied in reptiles. In this work, we examined the ultrastructural organization of the nucleolus in various tissues from different reptilian species (three turtles, three lizards, two crocodiles, and three snakes). Using cytochemical and immunocytological methods, we showed that in reptiles both types of nucleolus are present: a bi-compartmentalized nucleolus in turtles and a tri-compartmentalized nucleolus in the other species examined in this study. Furthermore, in a given species, the same type of nucleolus is present in all the tissues, however, the importance and the repartition of those nucleolar components could vary from one tissue to another. We also reveal that, contrary to the mammalian nucleolus, the reptilian fibrillar centers contain small clumps of condensed chromatin and that their surrounding dense fibrillar component is thicker. Finally, we also report that Cajal bodies are detected in reptiles. Altogether, we believe that these results have profound evolutionarily implications since they indicate that the point of transition between bipartite and tripartite nucleoli lies at the emergence of the amniotes within the class Reptilia. [less ▲]Detailed reference viewed: 33 (4 ULg)
Structure composition and mechanical relations to function in sea urchin spine
; ; Compère, Philippe et al
in Journal of Structural Biology (2010), 170Detailed reference viewed: 32 (7 ULg)
Ultrastructural detection of nucleic acids within heat shock-induced perichromatin granules of HeLa cells by cytochemical and immunocytological methods.
; Lamaye, Françoise ; Thelen, Nicolas et al
in Journal of Structural Biology (2009), 166(3), 329-36
The perichromatin granules (PGs) are enigmatic structures of the cell nucleus. The major drawbacks for a biological study are their rare occurrence and their small size in normal conditions. As heat shock ... [more ▼]
The perichromatin granules (PGs) are enigmatic structures of the cell nucleus. The major drawbacks for a biological study are their rare occurrence and their small size in normal conditions. As heat shock has been shown to increase their number, we applied a hyperthermal shock on HeLa cells to investigate the nucleic acid content of PGs by means of cytochemical and immunocytological approaches. These heat shock-induced PGs (hsiPGs) appeared as clusters organized in the form of honeycomb structures and were always associated with some blocks of condensed chromatin, such as the perinucleolar chromatin shell. A stalk connecting the hsiPG to the chromatin could be observed. For the detection of RNA, we applied an immunocytological method involving two anti-RNA antibodies and quantified the gold labelling obtained. The results clearly revealed that hsiPGs contained RNA. Regarding to the detection of DNA, we used three different methods followed by quantitative analyses. The results seemed to indicate that a small amount of DNA was present in hsiPGs. Together, these findings suggest that hsiPGs might be RNP structures associated with particular regions of DNA. [less ▲]Detailed reference viewed: 42 (5 ULg)
Otolith crystals (in Carapidae): Growth and habit
Parmentier, Eric ; Cloots, Rudi ; et al
in Journal of Structural Biology (2007), 159(3), 462-473
The biomineralization of otoliths results mainly from the release of soluble Ca(2+), which is in turn precipitated as CaCO(3) crystals. In some Carapidae, sagittae sections have been shown to reveal a ... [more ▼]
The biomineralization of otoliths results mainly from the release of soluble Ca(2+), which is in turn precipitated as CaCO(3) crystals. In some Carapidae, sagittae sections have been shown to reveal a three-dimensional asymmetry with a nucleus close to the sulcal side, an unusual position. This study seeks to understand otolith formation in Carapus boraborensis. The unusual shape of the otolith is partly explained by the distribution of the epithelium cells, and particularly the sensory epithelium. Experimental evidence shows for the first time that aragonite growth takes place along the c-axis. These aragonite needles present two different habits. On the sulcal side is found the acicular form resulting from rapid growth during a short period of time. On the anti-sulcal side, the prismatic form seen there is due to a slower growth speed over longer periods. The otolith surface was observed each hour during a period of 24h in fishes reared in similar conditions. This allowed for the first time the direct observation on the otolith surface of the deposition of the two layers (L-zone and D-zone). In C. boraborensis, the organic-rich layer (D-zone) develops during the day, whereas the CaCO(3) layer (L-zone) seems to be deposited during the night. [less ▲]Detailed reference viewed: 65 (7 ULg)
Crystal structure of the actin-binding domain of alpha-actinin 1: evaluating two competing actin-binding models.
; Kerff, Frédéric ; et al
in Journal of Structural Biology (2006), 155(2), 230-8
Alpha-actinin belongs to the spectrin family of actin crosslinking and bundling proteins that function as key regulators of cell motility, morphology and adhesion. The actin-binding domain (ABD) of these ... [more ▼]
Alpha-actinin belongs to the spectrin family of actin crosslinking and bundling proteins that function as key regulators of cell motility, morphology and adhesion. The actin-binding domain (ABD) of these proteins consists of two consecutive calponin homology (CH) domains. Electron microscopy studies on ABDs appear to support two competing actin-binding models, extended and compact, whereas the crystal structures typically display a compact conformation. We have determined the 1.7A resolution structure of the ABD of alpha-actinin 1, a ubiquitously expressed isoform. The structure displays the classical compact conformation. We evaluated the two binding models by surface conservation analysis. The results show a conserved surface that spans both domains and corresponds to two previously identified actin-binding sites (ABS2 and ABS3). A third, and probably less important site, ABS1, is mostly buried in the compact conformation. However, a thorough examination of existing structures suggests a weak and semi-polar binding interface between the two CHs, leaving open the possibility of domain reorientation or opening. Our results are consistent with a two-step binding mechanism in which the ABD interacts first in the compact form observed in the structures, and then transitions toward a higher affinity state, possibly through minor rearrangement of the domains. [less ▲]Detailed reference viewed: 42 (1 ULg)
Morphological changes of the nucleolus during oogenesis in oviparous teleost fish, Barbus barbus (L.).
Thiry, Marc ; Poncin, Pascal
in Journal of Structural Biology (2005), 152(1), 1-13
In fishes, like in amphibians, it is well established that variations in rRNA activity occur during oogenesis. Contrary to amphibians, however, little is known about the ultrastructural changes of the ... [more ▼]
In fishes, like in amphibians, it is well established that variations in rRNA activity occur during oogenesis. Contrary to amphibians, however, little is known about the ultrastructural changes of the nucleolus during fish oogenesis. Evolution of the nucleolus has been followed during oogenesis in the teleost fish Barbus barbus (L.) using light and transmission electron microscopies. We show that the behaviour of the nucleolus during B. barbus oogenesis resembles that reported in amphibians but also presents several peculiarities. The most striking feature is the marked vacuolization of nucleoli occurs at the beginning of the growth during previtellogenesis. The results obtained by means of the in situ terminal deoxynucleotidyl transferase-immunogold method for detecting DNA seem further to indicate that the chromatin cap becomes integrated into developing nucleoli during previtellogenesis and then segregate at the periphery of nucleoli at the end of glycoproteinic vitellogenesis. Our study also shows that the nucleoli of germ cells, like that of follicle cells, are devoid of fibrillar centre but comprise a fibrillar and a granular component whatever the oogenetic stage. Ultrastructural detection of DNA and nucleolar proteins (AgNOR proteins, fibrillarin, and pp135) supports further the view that the Barbus nucleolus is a bipartite structure. [less ▲]Detailed reference viewed: 61 (7 ULg)
Ultrastructural distribution of DNA within plant meristematic cell nucleoli during activation and the subsequent inactivation by a cold stress.
Mineur, Pierre ; ; Thiry, Marc et al
in Journal of Structural Biology (1998), 123(3), 199-210
We have investigated the precise location of DNA within the meristematic cell nucleolus of Zea mays root cells and Pisum sativum cotyledonary buds, in the course of their activation and induced ... [more ▼]
We have investigated the precise location of DNA within the meristematic cell nucleolus of Zea mays root cells and Pisum sativum cotyledonary buds, in the course of their activation and induced inactivation following a subsequent treatment at low temperature. For this purpose, we combined the acetylation method, providing an excellent distinction between the various nucleolar components, with the in situ terminal deoxynucleotidyl transferase-immunogold technique, a highly sensitive method for detecting DNA at the ultrastructural level. In addition to the presence of DNA in the condensed chromatin associated with the nucleolus, we demonstrated that a significant label was detected in the nucleolus of quiescent cells in both plant models. Evident labels were also found in the dense fibrillar component of actived nucleoli. Whereas in inactivated nucleoli no significant label was observed within the dense fibrillar component, an intense label was seen over the large heterogeneous fibrillar centres only during inactivation. The granular component was never significantly labelled. These results appear to indicate that the DNA present in the dense fibrillar component of activated nucleoli withdraws from this structure during its inactivation and becomes incorporated in the large fibrillar centres. These observations suggest that in plant cells inactivation of rRNA genes is clearly accompanied by changes in the conformation of ribosomal chromatin. [less ▲]Detailed reference viewed: 82 (2 ULg)
"Exolysosomes", Enzyme-Containing Vesicles in the Ecdysial Space of Molting Crabs
Compère, Philippe ; ; Thiry, Marc et al
in Journal of Structural Biology (1997), 119(3), 247-59
Free vesicle-like bodies (VLBs) present in the ecdysial space of cuticle regions undergoing degradation during preecdysis of the Atlantic shore crab Carcinus maenas have been interpreted either as ... [more ▼]
Free vesicle-like bodies (VLBs) present in the ecdysial space of cuticle regions undergoing degradation during preecdysis of the Atlantic shore crab Carcinus maenas have been interpreted either as infectious organisms or as secretion structures associated with degradation of the old cuticle. Ultrastructural, cytochemical, and immunocytological investigations were performed to test these hypotheses and to see whether VLBs are peculiar to this crab species. Similar VLBs were systematically found in two other preecdysial crabs, Cancer pagurus and Macropipus puber. In Car, maenas, they originate during early premolt inside Golgi buddings and are often gathered into large vacuoles in epidermal cells. The histochemical azo-dye technique and a cerium-based cytochemical method revealed acid phosphatase activity in both the ecdysial space and the VLBs, while Feulgen's method and immunocytological labeling always failed to reveal any DNA or RNA in either the ecdysial space or the VLBs. We conclude that VLBs are not infectious organisms but "extracellular" cuticle-degrading organelles of lysosomal origin and propose to coin them "exolysosomes." [less ▲]Detailed reference viewed: 42 (4 ULg)