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Contains fulltext : 81177.pdf (publisher's version ) (Closed access), Various mammalian small heat-shock proteins (sHSPs) can interact with one another to form large polydisperse assemblies. In muscle cells, HSPB2/MKBP (myotonic dystrophy protein kinase-binding protein) and HSPB3 have been shown to form an independent complex. To date, the biochemical properties of this complex have not been thoroughly characterized. In this study, we show that recombinant HSPB2 and HSPB3 can be successfully purified from Escherichia coli cells co-expressing both proteins. Nanoelectrospray ionization mass spectrometry and sedimentation velocity analytical ultracentrifugation analysis showed that HSPB2/B3 forms a series of well defined hetero-oligomers, consisting of 4, 8, 12, 16, 20 and 24 subunits, each maintaining a strict 3:1 HSPB2/HSPB3 subunit ratio. These complexes are thermally stable up to 40 degrees C, as determined by far-UV circular dichroism spectroscopy. Surprisingly, HSPB2/B3 exerted a poor chaperone-like and thermoprotective activity, which is likely related to the low surface hydrophobicity, as revealed by its interaction with the hydrophobic probe 1-anilino-8-naphthalenesulfonic acid. Co-immunoprecipitation experiments demonstrated that the HSPB2/B3 oligomer cannot interact with HSP20, HSP27 or alphaB-crystallin, whereas the homomeric form of HSPB2, thus not in complex with HSPB3, could associate efficiently with HSP20. Taken altogether, this study provides evidence that, despite the high level of sequence homology within the sHSP family the biochemical properties of the HSPB2/B3 complex are distinctly different from those of other sHSPs, indicating that the HSPB2/B3 assembly is likely to possess cellular functions other than those of its family members.

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Radboud Universiteit Nijmegen, Biomolecular Chemistry, 7 december 2009, Promotor : Jong, W.W.W. de, Contains fulltext : 75266.pdf (publisher's version ) (Open Access)

Radboud Universiteit Nijmegen, 07 januari 2008, Promotor : Jong, W.W.W. de Co-promotores : Boelens, W.C., Schalkwijk, L.T.J.M. van, Grip, W.J. de, Willems, P.H.G.M., Contains fulltext : 72514.pdf (publisher's version ) (Open Access)

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Contains fulltext : 70352.pdf (publisher's version ) (Closed access), The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of intergenic DNA (gene duos). We show here that a lack of head-to-tail (h2t) gene duos is an even more distinctive characteristic of mammalian genomes, with the platypus genome as the only exception. In nonmammalian vertebrate and in nonvertebrate genomes, the frequency of h2h, h2t, and tail-to-tail (t2t) gene duos is close to random. In tetrapod genomes, the h2t and t2t gene duos are more likely to be part of a larger gene cluster of closely spaced genes than h2h gene duos; in fish and urochordate genomes, the reverse is seen. In human and mouse tissues, the expression profiles of gene duos were skewed toward positive coexpression, irrespective of orientation. The organization of orthologs of both members of about 40% of the human gene duos could be traced in other species, enabling a prediction of the organization at the branch points of gnathostomes, tetrapods, amniotes, and euarchontoglires. The accumulation of h2h gene duos started in tetrapods, whereas that of h2t and t2t gene duos only started in amniotes. The apparent lack of evolutionary conservation of h2t and t2t gene duos relative to that of h2h gene duos is thus a result of their relatively late origin in the lineage leading to mammals; we show that once they are formed h2t and t2t gene duos are as stable as h2h gene duos.

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RU, Biochemistry, 17 mei 2006, Promotor : Jong, W.W.W. de Co-promotor : Boelens, W.C., Contains fulltext : 36182.pdf (publisher's version ) (Open Access)

RU, 28 april 2006, Promotor : Jong, W.W.W. de Co-promotor : Lubsen, N.H., Contains fulltext : 27427.pdf (publisher's version ) (Open Access), The general goal of this thesis was to gain insight in what small heat shock proteins (sHsps) do with respect to macromolecular synthesis during a stressful situation in the cell. It is known that after a non-lethal heat shock, cells are better protected against a subsequent more severe heat shock, a phenomenon known as thermotolerance and attributed to the presence of the heat shock proteins. The question we asked first is whether the error rate in macromolecular synthesis (transcription, RNA processing, quality control mechanisms and translation) is increased during or after a heat shock in the cell. To know which of these processes might be failing in a cell during stress we designed different reporter systems and we studied the possible protective effect that the sHsps might have. We have shown that there is molecular misreading of sequence repeats and that this misreading is induced by stress. The sHsps did not prevent this. Concerning splicing, the sHsp Hsp27 provided a faster recovery of splicing after heat shock and a faster rephosphorylation of an inhibitor of splicing, dSRp38. Regarding mRNA quality control mechanisms, no defect in nonsense-mediated decay could be detected after heat shock. Finally we describe a relaxed stringency of AUG selection induced by heat shock. To determine whether the sHsps are able to help in cotranslational protein folding and/or heteromer formation, we examined the folding and assembly of beta-crystallins. In the lens, beta-crystallins are surrounded by a high concentration of the sHsp alpha-crystallin, so these are suitable model proteins to test if sHsps facilitate the folding of other crystallins in the lens, particularly that of heterodimeric crystallins. We described that the folding of betaA4-crystallin is helped by its heterodimeric partner, betaB2-crystallin, but not by sHsps

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RU, Biochemistry, 07 januari 2005, Promotores : Jong, W.W.W. de, Zoelen, E.J.J. van Co-promotor : Lubsen, N.H., Item does not contain fulltext, The DNA sequences of many genomes have been elucidated in the last years. The challenge now is to predict first the genotype and then the phenotype from the genomic sequences. To predict expression patterns of the genes located on the genome, not only regulation at the level of transcription, but also at the level of translation is important. To obtain more information about regulation of transcription, the promoter and its regulatory elements need to be mapped. In this thesis a conventional search for known and active regulatory elements in the B2-crystallin promoter was performed. For the intergenic region between aB-crystallin and HspB2, an alternative approach was taken to determine which elements are likely to be important for gene regulation, and the evolutionary conservation of sequence elements in this region was studied. Alignments of this region of many species lead to the confirmation of importance of known regulatory elements and the finding of new sites. A good example of regulation of gene expression mediated by regulation of translation, is translation after stress. During and after heat shock, cap-dependent translation is inhibited, while cap-independent translation can still take place. After heat shock translation of (s)Hsps is increased, these (s)Hsps are thought to protect cells from stress. We show that two of the sHsps, aB-crystallin and Hsp27 protect cap-dependent, but not cap-independent translation after heat shock. Inhibition of translation is thought to be mediated by a decrease in activity of the translation factors. However, the protection of translation mediated by sHsps does not seem to affect translation factors directly, but overexpression of aB-crystallin seems to increase the dispersal of stress granules that contain the stalled translation initiation complexes. We propose that aB-crystallin, probably together with other Hsps, resolubilizes the stress granule components and that translational thermotolerance is a cooperative effect

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RU Nijmegen, 10 maart 2005, Promotor : Jong, W.W.W. de Co-promotor : Boelens, W.C., Contains fulltext : 33023.pdf (publisher's version ) (Open Access), Small heat shock proteins (sHsps) are molecular chaperones that bind unfolding proteins and confer cellular protection during stress. They form multimeric complexes, with monomers between 12 and 42 kDa, containing a characteristic sequence, the alpha-crystallin domain. The aim of this thesis was to extend our insight in the structural, functional and evolutionary diversity of sHsps. In the first part of this thesis the conserved alpha-crystallin domain was used to screen all available prokaryotic genomes and protein databases for sHsps. Contrary to what was expected, not all genomes contain sHsp genes. Secondary structure predictions demonstrate that unlike the high beta-strand contents of the alpha-crystallin domain, the preceding N-terminal domain mainly comprises alpha-helical structures. A similar screening of the complete human genome and the human EST databases yielded three new sHsps, designated protein kinase-related HspB8, testis-specific HspB9 and spermtail-specific HspB10. This brings the final number of human sHsps to ten. The second part describes the biochemical characterization of Tsp36, a tapeworm sHsp containing two alpha-crystallin domains, and the mammalian alphaB-crystallin and Hsp20. Tsp36 turned out to form reversible disulfides between the single cysteines in the Tsp36 monomers. This disulfide promotes formation of tetramers which have better chaperone activity than the dimers. Mixtures of different alphaB-crystallin to Hsp20 ratios show intermediate complex sizes and chaperone capacities compared to homomeric alphaB-crystallin and Hsp20. Characterization of chimeras of alphaB-crystallin and Hsp20, in which N-terminal domains were swapped, demonstrated that this domain is important for complex sizes and chaperone capacities as well. Both the redox state dependence of complex size in Tsp36 and the ratios of sHsps in heteromeric alphaB-Hsp20 complexes are possible means to regulate the oligomerization and chaperoning properties of these complexe

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Contains fulltext : 57736.pdf (publisher's version ) (Closed access), An unexpected feature of the large mammalian genome is the frequent occurrence of closely linked head-to-head gene pairs. Close apposition of such gene pairs has been suggested to be due to sharing of regulatory elements. We show here that the head-to-head gene pair encoding two small heat shock proteins, alphaB-crystallin and HspB2, is closely linked in all major mammalian clades, suggesting that this close linkage is of selective advantage. Yet alphaB-crystallin is abundantly expressed in lens and muscle and in response to a heat shock, while HspB2 is abundant only in muscle and not upregulated by a heat shock. The intergenic distance between the genes for these two proteins in mammals ranges from 645 bp (platypus) to 1069 bp (opossum), with an average of about 900 bp; in chicken the distance was the same as in duck (1.6 kb). Phylogenetic footprinting and sequence alignment identified a number of conserved sequence elements close to the HspB2 promoter and two farther upstream. All known regulatory elements of the mouse alphaB-crystallin promoter are conserved, except in platypus and birds. The lens-specific region 1 (LSR1) and the heat shock elements (HSEs) lack in birds; in platypus the LSR1 is reduced to a Pax-6 site, while the Pax-6 site in LSR2 and a HSE are absent. Most likely the primordial mammalian alphaB-crystallin promoter had two LSRs and two HSEs. In transfection experiments the platypus alphaB-crystallin promoter retained heat shock responsiveness and lens expression. It also directed lens expression in Xenopus laevis transgenes, as did the HspB2 promoter of rat or blind mole rat. Deletion of the middle of the intergenic region including the upstream enhancer affected the activity of both the rat alphaB-crystallin and the HspB2 promoters, suggesting sharing of the enhancer region by the two promoters.

Contains fulltext : 58487.pdf (publisher's version ) (Closed access), All vertebrates express multiple small heat shock proteins (sHsps), which are important components of the cellular chaperoning machinery and display a spectacular diversity of functions. This ranges from remodeling the cytoskeleton and inhibiting apoptosis to serving as structural proteins in eye lens and sperm tail. Most information is available for the 10 known mammalian sHsps, formally named HspB1-B10. Only three of them (Hsp27/B1, alphaA-crystallin/B4, alphaB-crystallin/B5) have been reported from nonmammalian vertebrates, while an apparent paralog, Hsp30/B11, is found in frogs and teleost fish. To reconstruct the evolutionary diversification of the sHsps in vertebrates, we searched for additional sHsps in genome, protein, and EST databases and sequenced some avian and amphibian sHsps (HspB2, Hsp30/B11). The urochordate Ciona intestinalis was included in the search, as the outgroup of vertebrates. Orthologs of seven mammalian sHsps were now found in other vertebrate classes. Two novel sHsps, named HspB11 and HspB12, were recognized in birds, and four novel sHsps, named HspB12-B15, in teleost fish. Secondary structure predictions of orthologous sHsps from different vertebrate classes indicate conservation of the beta-sandwich structure of the functionally important C-terminal "alpha-crystallin domain," while the N-terminal domains generally have alpha-helical structures, despite their pronounced sequence variation. The constructed chordate sHsp tree is supported by shared introns, indels, and diagnostic sequences. The tree distinguishes putative orthologous and paralogous relationships, which will facilitate the functional and structural comparison of the various vertebrate sHsps. The 15 recognized paralogous vertebrate sHsps reflect the period of extensive gene duplications early in vertebrate evolution. Eleven of these sHsps are grouped in a clade that might be specific for chordates. It is inferred that at least 13 intron insertions have occurred during the ev

RU Radboud Universiteit Nijmegen, 18 mei 2004, Promotor : Jong, W.W.W. de, Contains fulltext : 60643.pdf (publisher's version ) (Open Access), In this thesis, the principles of molecular evolution and phylogeny are introduced in Chapter 1, while the subsequent chapters deal with the three topics mentioned in the title. Part I: Birds, reptiles and mammals are Amniota, organisms that have an amnion during their embryonal development. Even though these organisms have been studied for centuries, their interrelationships remain debated in some cases. In Chapter 2, the molecular phylogenetic position of the egg-laying mammals (Monotremata) is analysed, and Chapter 3 presents an example of rare genomic changes - in this case deletions in protein-coding DNA - that are very useful to distinguish relationships between the orders of placental mammals. Part II: The molecules that constitute the eye lens are stable, transparant proteins termed crystallins. In this part we report some typical examples of the origin and molecular evolution of the vertebrate eye lens crystallins. We present the (-crystallin genes from the platypus (Chapter 4) and the discovery in this species of a novel lens protein, upsilon-crystallin, which turns out to be overexpressed lactate dehydrogenase A (Chapter 5). We further present a paper on the evolution of regulatory sequences of the (B-crystallin gene, which are located in the bidirectional promoter between the head-to-head arranged (B-crystallin and HspB2 genes (Chapter 6). The (-crystallins originated evolutionarily from the family of small heat shock proteins. Some data about the evolution of this protein family in vertebrates and lower chordates are included in General Discussion and Summary (Chapter 8). Part III: Chapter 7 addresses the evolutionary aspects of the mammalian prion protein and touches on the evolution of the prion protein gene family. Specifically, the evolution of a repeat region in the vertebrate prion is discussed. The remarkable finding of a deviating prion gene in the squirrel is presented in General Discussion and Summary (Chapter 8).

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Item does not contain fulltext, Deciphering relationships among the orders of placental mammals remains an important problem in evolutionary biology and has implications for understanding patterns of morphological character evolution, reconstructing the ancestral placental genome, and evaluating the role of plate tectonics and dispersal in the biogeographic history of this group. Until recently, both molecular and morphological studies provided only a limited and questionable resolution of placental relationships. Studies based on larger and more diverse molecular datasets, and using an array of methodological approaches, are now converging on a stable tree topology with four major groups of placental mammals. The emerging tree has revealed numerous instances of convergent evolution and suggests a role for plate tectonics in the early evolutionary history of placental mammals. The reconstruction of mammalian phylogeny illustrates both the pitfalls and the powers of molecular systematics.

Contains fulltext : 59182.pdf (publisher's version ) (Closed access), Small heat shock proteins (sHSPs), which range in monomer size between 12 and 42 kDa, are characterized by a conserved C-terminal alpha-crystallin domain of 80-100 residues. They generally form large homo- or heteromeric complexes, and typically have in vitro chaperone-like activity, keeping unfolding proteins in solution. A special type of sHSP, with a duplicated alpha-crystallin domain, is present in parasitic flatworms (Platyhelminthes). Considering that an alpha-crystallin domain is essential for the oligomerization and chaperone-like properties of sHSPs, we characterized Tsp36 from the tapeworm Taenia saginata. Both wild-type Tsp36 and a mutant (Tsp36C-->R) in which the single cysteine has been replaced by arginine were expressed and purified. Far-UV CD measurements of Tsp36 were in agreement with secondary structure predictions, which indicated alpha-helical structure in the N-terminal region and the expected beta-sandwich structure for the two alpha-crystallin domains. Gel permeation chromatography and nano-ESI-MS showed that wild type Tsp36 forms dimers in a reducing environment, and tetramers in a non-reducing environment. The tetramers are stabilized by disulfide bridges involving a large proportion of the Tsp36 monomers. Tsp36C-->R exclusively occurs as dimers according to gel permeation chromatography, while the nondisulfide bonded fraction of wild type Tsp36 dissociates from tetramers into dimers under nonreducing conditions at increased temperature (43 degrees C). The tetrameric form of Tsp36 has a greater chaperone-like activity than the dimeric form.

Item does not contain fulltext, Searching EST databases for new members of the human small heat shock protein family, we recently identified HSPB9, which is expressed exclusively in testis as determined by Northern blotting (Kappe et al., Biochim. Biophys. Acta 1520, 1-6, 2001). Here we confirm this testis-specific expression pattern by RT-PCR in a larger series of normal tissues. Interestingly, while screening HSPB9 ESTs, we also noted expression in tumours, which could be verified by RT-PCR. Protein expression of HSPB9 was also detected in normal human testis and various tumour samples using immunohistochemical staining. We thus conclude that HSPB9 belongs to the steadily growing number of cancer/testis antigens. To get a better understanding of the function of HSPB9, we performed a yeast two-hybrid screen to search for HSPB9-interacting proteins. TCTEL1, a light chain component of cytoplasmic and flagellar dynein, interacted in both the yeast two-hybrid system and in immunoprecipitation experiments with HSPB9. Additionally, immunohistochemical staining showed co-expression of HSPB9 and TCTEL1 in similar stages of spermatogenesis and in tumour cells. The possible functional significance of this interaction is discussed.

Contains fulltext : 57972.pdf (publisher's version ) (Closed access), The alpha-, beta- and gamma-crystallins are the major protein components of the vertebrate eye lens, alpha-crystallin as a molecular chaperone as well as a structural protein, beta- and gamma-crystallins as structural proteins. For the lens to be able to retain life-long transparency in the absence of protein turnover, the crystallins must meet not only the requirement of solubility associated with high cellular concentration but that of longevity as well. For proteins, longevity is commonly assumed to be correlated with long-term retention of native structure, which in turn can be due to inherent thermodynamic stability, efficient capture and refolding of non-native protein by chaperones, or a combination of both. Understanding how the specific interactions that confer intrinsic stability of the protein fold are combined with the stabilizing effect of protein assembly, and how the non-specific interactions and associations of the assemblies enable the generation of highly concentrated solutions, is thus of importance to understand the loss of transparency of the lens with age. Post-translational modification can have a major effect on protein stability but an emerging theme of the few studies of the effect of post-translational modification of the crystallins is one of solubility and assembly. Here we review the structure, assembly, interactions, stability and post-translational modifications of the crystallins, not only in isolation but also as part of a multi-component system. The available data are discussed in the context of the establishment, the maintenance and finally, with age, the loss of transparency of the lens. Understanding the structural basis of protein stability and interactions in the healthy eye lens is the route to solve the enormous medical and economical problem of cataract.

Contains fulltext : 59210.pdf (publisher's version ) (Closed access), Crosslinking of proteins by tissue transglutaminase (tTG) is enhanced in amyloid (Abeta) deposits characteristic of Alzheimer's disease and sporadic inclusion body myositis. Small heat shock proteins (sHsps) also occur in amyloid deposits. We here report the substrate characteristics for tTG of six sHsps. Hsp27, Hsp20 and HspB8 are both lysine- and glutamine-donors, alphaB-crystallin only is a lysine-donor, HspB2 a glutamine-donor, and HspB3 no substrate at all. Close interaction of proteins stimulates crosslinking efficiency as crosslinking between different sHsps only takes place within the same heteromeric complex. We also observed that alphaB-crystallin, Hsp27 and Hsp20 associate with Abeta in vitro, and can be readily crosslinked by tTG.

Contains fulltext : 252409.pdf (Publisher’s version ) (Closed access), AlphaB-crystallin is a small heat-shock protein in which three serine residues (positions 19, 45, and 59) can be phosphorylated under various conditions. We describe here the interaction of alphaB-crystallin with FBX4, an F-box-containing protein that is a component of the ubiquitin-protein isopeptide ligase SCF (SKP1/CUL1/F-box). The interaction with FBX4 was enhanced by mimicking phosphorylation of alphaB-crystallin at both Ser-19 and Ser-45 (S19D/S45D), but not at other combinations. Ser-19 and Ser-45 are preferentially phosphorylated during the mitotic phase of the cell cycle. Also alphaB-crystallin R120G, a mutant found to co-segregate with a desmin-related myopathy, displayed increased interaction with FBX4. Both alphaB-crystallin S19D/S45D and R120G specifically translocated FBX4 to the detergent-insoluble fraction and stimulated the ubiquitination of one or a few yet unknown proteins. These findings implicate the involvement of alphaB-crystallin in the ubiquitin/proteasome pathway in a phosphorylation- and cell cycle-dependent manner and may provide new insights into the alphaB-crystallin-induced aggregation in desmin-related myopathy.

Contains fulltext : 252427.pdf (Publisher’s version ) (Closed access), Heat shock results in inhibition of general protein synthesis. In thermotolerant cells, protein synthesis is still rapidly inhibited by heat stress, but protein synthesis recovers faster than in naive heat-shocked cells, a phenomenon known as translational thermotolerance. Here we investigate the effect of overexpressing a single heat shock protein on cap-dependent and cap-independent initiation of translation during recovery from a heat shock. When overexpressing alphaB-crystallin or Hsp27, cap-dependent initiation of translation was protected but no effect was seen on cap-independent initiation of translation. When Hsp70 was overexpressed however, both cap-dependent and -independent translation were protected. This finding indicates a difference in the mechanism of protection mediated by small or large heat shock proteins. Phosphorylation of alphaB-crystallin and Hsp27 is known to significantly decrease their chaperone activity; therefore, we tested phosphorylation mutants of these proteins in this system. AlphaB-crystallin needs to be in its non-phosphorylated state to give protection, whereas phosphorylated Hsp27 is more potent in protection than the unphosphorylatable form. This indicates that chaperone activity is not a prerequisite for protection of translation by small heat shock proteins after heat shock. Furthermore, we show that in the presence of 2-aminopurine, an inhibitor of kinases, among which is double-stranded RNA-activated kinase, the protective effect of overexpressing alphaB-crystallin is abolished. The synthesis of the endogenous Hsps induced by the heat shock to test for thermotolerance is also blocked by 2-aminopurine. Most likely the protective effect of alphaB-crystallin requires synthesis of the endogenous heat shock proteins. Translational thermotolerance would then be a co-operative effect of different heat shock proteins.

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Contains fulltext : 252428.pdf (Publisher’s version ) (Closed access), For more than a century, living insectivore-like mammals have been viewed as little removed from the ancestral mammalian stock based on their retention of numerous primitive characteristics. This circumstance has made "insectivores" a group of special interest in the study of mammalian evolution. included hedgehogs, moles, shrews, solenodons, golden moles, tenrecs, flying lemurs, tree shrews, and elephant shrews in Insectivora. Subsequently, morphologists excluded flying lemurs, tree shrews, and elephant shrews from Insectivora and placed these taxa in the orders Dermoptera, Scandentia, and Macroscelidea, respectively. The remaining insectivores constitute Lipotyphla, which is monophyletic based on morphology. In contrast, molecular data suggest that lipotyphlans are polyphyletic, with golden moles and tenrecs placed in their own order (Afrosoricida) in the superordinal group Afrotheria. Studies based on nuclear genes support the monophyly of the remaining lipotyphlans (=Eulipotyphla) whereas mitochondrial genome studies dissociate hedgehogs from moles and place the former as the first offshoot on the placental tree. One shortcoming of previous molecular studies investigating lipotyphlan relationships is limited taxonomic sampling. Here, we evaluate lipotyphlan relationships using the largest and taxonomically most diverse data set yet assembled for Lipotyphla. Our results provide convincing support for both lipotyphlan diphyly and the monophyly of Eulipotyphla. More surprisingly, we find strong evidence for a sister-group relationship between shrews and hedgehogs to the exclusion of moles.

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De Marseille à la frontière espagnole s’étend le long de la Méditerranée une large plaine côtière. En arrière de la côte s’allonge une chaîne d’étangs saumâtres peu profonds, qui avaient autrefois une étendue beaucoup plus grande. Le comblement de ces étangs se poursuit (voir Braun-Blanquet et al., 1958). Autour des étangs, la végétation halophile, qui prend une grande extension, s’ordonne selon la salinité du sol. La succession de la végétation, à partir des étangs jusqu’au Populetum albae, passe par les associations suivantes: Suaedo-Salsoletum, Salicornietum fruticosae, Junco-Triglochinetum, Agropyro-Inuletum, Caricetum divisae, Agropyro-Trifolietum maritimi et Molinietum mediterraneum.