Étude de la dynamique des interactions des constituants du complexe de biosynthèse et d’insertion de la sélénocystéine dans la traduction des sélénoprotéines in vivo

Les sélénoprotéines sont des protéines auxquelles des sélénocystéines, soit le 21e acide aminé, sont incorporées durant leur traduction. Plus précisément, la sélénocystéine (Sec) est un dérivé métabolique de la sérine, mais structurellement équivalent à une cystéine dont on a remplacé l'atome de soufre par du sélénium. Elle se distingue des autres acides aminés puisqu’elle possède sa propre synthétase qui sert à convertir la sérine en Sec alors que le résidu est déjà fixé à l’ARNt. La position d’une Sec sur l’ARNm est indiquée par le codon UGA étant habituellement un signal STOP introduisant le concept de recoding. Grâce à une machinerie métabolique spécifique à l'ARNtSec et à la présence d’un SecIS (Selenocystein Insertion Sequence) sur l’ARNm, ce codon permet la présence d'une Sec dans la protéine. Il est connu que la synthèse débute avec l’acétylation de l’ARNt[Ser]Sec par la seryl-ARNt synthétase (SerRS) afin de donner la seryl-ARNt[Ser]Sec. Cette dernière est subséquemment phosphorylée par l’O-phosphoséryl-ARNt[Ser]Sec kinase (PSTK) qui donnera l’O-phosphoséryl-ARNt[Ser]Sec. Par la suite, un complexe de plusieurs protéines et cofacteurs, agissant comme machinerie pour l’incorporation des Sec durant la traduction, s’associe avec l’ARNt[Ser]Sec puis l’ARNm et, finalement, les composantes du ribosome. Parmi ces protéines, SepSecS catalyse l’étape finale de la synthèse des Sec en convertissant le O-phosphoseryl-ARNt[Ser]Sec en selenocysteinyl-ARNt[Ser]Sec utilisant le sélénophosphate comme source de sélénium. Des études récentes montrent que l’association avec SECp43 serait nécessaire pour que SepSecS joue son rôle et soit ségrégée au noyau pour s’associer à la machinerie de biosynthèse des sélénoprotéines, soit le complexe moléculaire qui reconnaît le codon UGA. Parmi les protéines de la machinerie de biosynthèse des sélénoprotéines que nous avons analysées, il y a eEFSec, RPL30, SPS2, SPS1, SBP2 et NSEP1. Nos résultats d’analyse de la dynamique de l’interaction entre les constituants de la machinerie de biosynthèse et d’incorporation des Sec, confirment plusieurs données de la littérature, mais remettent en question le modèle jusqu’à maintenant établi. Une meilleure compréhension de la dynamique des interactions entre ses constituants et la régulation de cette dynamique permet d’émettre des hypothèses quant au rôle de la machinerie de biosynthèse des sélénoprotéines et de l’importance de sa complexité. Nous avons analysé les interactions in vivo dans des cellules HEK293T au moyen de la technique de Protein-Fragment Complementation Assay (PCA) en couplant, par un clonage moléculaire, les gènes de chacune des protéines d’intérêt avec des fragments des gènes de la protéine luciférase (hRluc). Nous avons ainsi réalisé une fusion en N-terminal et en C-terminal des fragments de luciférase pour chacune des protéines d’intérêt. Puis, nous avons analysé la dynamique des interactions avec les composantes de la machinerie de biosynthèse des Sec. D’autres travaux seront essentiels afin de bâtir sur les résultats présentés dans cette recherche.

Pro-inflammatory and angiogenic activities of VEGF and angiopoietins in murine sponge/Matrigel model

La dérégulation de la formation et l'intégrité des vaisseaux sanguins peut conduire à un état pathologique tel qu’observé dans de nombreuses maladies ischémiques telles que: la croissance de tumeur solide, l’arthrite rhumatoïde, le psoriasis, les rétinopathies et l'athérosclérose. Par conséquent, la possibilité de moduler l'angiogenèse régionale chez les patients souffrant d'ischémie est cliniquement pertinente. Un élément clé dans l'induction de l'angiogenèse pathologique est une inflammation qui précède et accompagne la formation des nouveaux vaisseaux. Ce phénomène est démontré par l'augmentation de la perméabilité vasculaire et le recrutement de monocytes/ macrophages et cellules polynucléaires (neutrophiles). En collaboration avec d'autres groupes, nous avons montré que différents facteurs de croissance tels que le facteur de croissance endothélial vasculaire et les angiopoïétines peuvent non seulement promouvoir l'angiogenèse mais aussi induire diverses étapes connexes au processus de la réaction inflammatoire, y compris la synthèse et la libération des médiateurs inflammatoires et la migration des neutrophiles. Les objectifs de notre étude étaient d'adresser si le vascular endothelial growth factor (VEGF) et les angiopoïétines (Ang1 et Ang2) sont capables de promouvoir la formation des nouveaux vaisseaux sanguins au fil du temps et d'identifier la présence de différentes cellules inflammatoires dans ce processus. Des éponges d'alcool polyvinylique stérilisées et imbibées de Matrigel appauvri en facteur de croissance (contenant PBS, VEGF, Ang1 ou Ang2 (200 ng/200 μl)) ont été insérées sous la peau de souris C57/Bl6 anesthésiées. Les éponges ont ensuite été retirées aux jours 4, 7, 14 ou 21 après la procédure pour des analyses histologiques, immunohistologiques et cytométriques. La formation des nouveaux vaisseaux a été validée par la coloration au Trichrome de Masson et des analyses histologiques et immunohistologiques contre les cellules endothéliales (anti-CD31). De plus, la maturation des vaisseaux a été démontrée par la coloration séquentielle contre les cellules endothéliales (anti-CD31) et musculaires lisses (anti-alpha-actine). Nous avons effectué la même procédure pour caractériser le recrutement de neutrophiles (anti-MPO), et de macrophages (anti-F4/80). Afin de mieux délimiter la présence de différents sous-ensembles de leucocytes recrutés dans les éponges, nous avons utilisé une technique de cytométrie en flux sur des préparations de cellules isolées à partir de ces éponges. Nous avons observé que le VEGF et les angiopoïétines favorisent le recrutement de cellules endothéliales et la formation de nouveaux vaisseaux plus rapidement qu’en présence de PBS. Une fois formé au jour 7, ces nouveaux vaisseaux restent stables en nombre, et ne subissent pas une réorganisation importante de leur surface. Ces vaisseaux maturent grâce au recrutement et au recouvrement par les cellules musculaires lisses des néovaisseaux. En outre, le microenvironnement angiogénique est composé de cellules inflammatoires, principalement de neutrophiles, macrophages et quelques cellules de type B et T. Donc, le VEGF, l’Ang1 et l’Ang2 induisent séparément la formation et la stabilisation de nouveaux vaisseaux sanguins, ainsi que le recrutement de cellules inflammatoires avec des puissances différentes et une action temps-dépendante dans un modèle d’éponge/Matrigel.

Molecular cloning of alkaline protease gene from marine fungus Engyodontium album

Department of Biotechnology, Cochin University of Science and Technology

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

An alkaline protease gene (Eap) was isolated for the first time from a marine fungus, Engyodontium album. Eap consists of an open reading frame of 1,161 bp encoding a prepropeptide consisting of 387 amino acids with a calculated molecular mass of 40.923 kDa. Homology comparison of the deduced amino acid sequence of Eap with other known proteins indicated that Eap encode an extracellular protease that belongs to the subtilase family of serine protease (Family S8). A comparative homology model of the Engyodontium album protease (EAP) was developed using the crystal structure of proteinase K. The model revealed that EAP has broad substrate specificity similar to Proteinase K with preference for bulky hydrophobic residues at P1 and P4. Also, EAP is suggested to have two disulfide bonds and more than two Ca2? binding sites in its 3D structure; both of which are assumed to contribute to the thermostable nature of the protein.

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

An alkaline protease gene (Eap) was isolated for the first time from a marine fungus, Engyodontium album. Eap consists of an open reading frame of 1,161 bp encoding a prepropeptide consisting of 387 amino acids with a calculated molecular mass of 40.923 kDa. Homology comparison of the deduced amino acid sequence of Eap with other known proteins indicated that Eap encode an extracellular protease that belongs to the subtilase family of serine protease (Family S8). A comparative homology model of the Engyodontium album protease (EAP) was developed using the crystal structure of proteinase K. The model revealed that EAP has broad substrate specificity similar to Proteinase K with preference for bulky hydrophobic residues at P1 and P4. Also, EAP is suggested to have two disulfide bonds and more than two Ca2? binding sites in its 3D structure; both of which are assumed to contribute to the thermostable nature of the protein.

Ecology of sponge assemblages (Porifera) in the Wakatobi region, south-east Sulawesi, Indonesia: richness and abundance

The influence of sedimentation, depth and substratum angle on sponge assemblages in the Wakatobi region, south-eastern Sulawesi, Indonesia was considered. Sponge assemblages were sampled from two reef localities. The first reef (Sampela) was highly impacted by high sedimentation rates with fine sediment particles that settle slowly, while the second (Hoga) experienced only fast settling coarse sediment with lower overall sedimentation rates. Sponge assemblages were sampled (area occupied and numbers) on the reef fiat (0 m) and at 5 (reef crest), 10 and 15 m (15 m at Hoga only). Some significant (P < 0.001) differences were observed in the area occupied and the number of sponge patches between surface angles and sites. Significantly lower (t > 4.61, df = 9, P < 0.001) sponge numbers, percentage cover and richness were associated with the reef flat at both sites compared with all other depths at each site, with the exception of abundance of sponges on the reef flat at Sampela, which was much greater than at any other depth sampled. Species richness increased with depth at both sites but differences between surface angles were only recorded at Sampela, with higher species richness being found on vertical, inclined and horizontal surfaces respectively A total of 100 sponge species (total area sampled 52.5 m(2)) was reported from the two sites, with 58 species found at Sampela and 71 species at Hoga (41% of species shared). Multi-dimensional scaling (MDS) indicated differences in assemblage structure between sites and most depth intervals, but not substratum angles. A number of biological (e.g. competition and predation) and physical (e.g. sedimentation and aerial exposure) factors were considered to control sponge abundance and richness. Unexpectedly a significant (F-1,F-169 = 148.98, P < 0.001) positive linear relationship was found between sponge density and area occupied. In areas of high sponge coverage, the number of patches was also high, possibly due to fragmentation of large sponges produced as a result of predation and physical disturbance. The MDS results were also the same whether sponge numbers or percentage cover estimates were used, suggesting that although these different approaches yield different sorts of information, the same assemblage structure can be identified.

Purification and molecular cloning of antimicrobial peptides from Scots pine seedlings

A novel protocol for rapid and efficient purification of antimicrobial peptides from plant seedlings has been developed. Two peptides with antimicrobial activity, designated p1 and p2, were purified nearly to homogeneity from Scots pine seedlings by a combination of sulfuric acid extraction, ammonium sulfate precipitation, heat-inactivation and ion-exchange chromatography on phosphocellulose. Purified proteins had molecular masses of 11 kDa (p1) and 5.8 kDa (p2) and were identified by mass spectrometry as defensin and lipid-transfer protein, respectively. We demonstrated their growth inhibitory effects against a group of phytopathogenic fungi. Furthermore, we report for the first time molecular cloning and characterization of defensin I cDNA from Scots pine. A cDNA expression library from 7 days Scots pine seedlings was generated and used to isolate a cDNA clone corresponding to Scots pine defensin, termed PsDef1. The full-length coding sequence of PsDef1 is 252 bp in length and has an open reading frame capable to encode a protein of 83 amino residues. The deduced sequence has the typical features of plant defensins, including an endoplasmic reticulum signal sequence of 33 aa, followed by a characteristic defensin domain of 50 amino acids representing its active form. The calculated molecular weight of the mature form of PsDef1 is 5601.6 Da, which correlates well with the results of SDS-PAGE analysis. Finally, the antimicrobial properties of PsDef1 against a panel of fungi and bacteria define it as a member of the morphogenic group of plant defensins. (C) 2009 Elsevier Inc. All rights reserved.

Molecular cloning and comparative analysis of four beta-galactosidase genes from Bifidobacterium bifidum NCIMB41171

Bifidobacterium bifidum NCIMB41171 carries four genes encoding different beta-galactosidases. One of them, named bbgIII, consisted of an open reading frame of 1,935 amino acid (a.a.) residues encoding a protein with a multidomain structure, commonly identified on cell wall bound enzymes, having a signal peptide, a membrane anchor, FIVAR domains, immunoglobulin Ig-like and discoidin-like domains. The other three genes, termed bbgI, bbgII and bbgIV, encoded proteins of 1,291, 689 and 1,052 a.a. residues, respectively, which were most probably intracellularly located. Two cases of protein evolution between strains of the same species were identified when the a.a. sequences of the BbgI and BbgIII were compared with homologous proteins from B. bifidum DSM20215. The homologous proteins were found to be differentiated at the C-terminal a.a. part either due to a single nucleotide insertion or to a whole DNA sequence insertion, respectively. The bbgIV gene was located in a gene organisation surrounded by divergently transcribed genes putatively for sugar transport (galactoside-symporter) and gene regulation (LacI-transcriptional regulator), a structure that was found to be highly conserved in B. longum, B. adolescentis and B. infantis, suggesting optimal organisation shared amongst those species.

A novel alpha-galactosidase from I'ifidobacterium bifidum with transgalactosylating properties: gene molecular cloning and heterologous expression

A genomic library of Bifidobacterium bifidum (NCIMB 41171) DNA was constructed in Escherichia coli RA11r (melA(-)B(+)) and one alpha-galactosidase encoding gene was isolated. Conceptual translation combined with insertional mutagenesis analysis indicated an open reading frame (ORF) of 759 amino acid (aa) residues encoding an alpha-galactosidase (named as MelA) of 82.8 kDa. Partial purification and characterisation showed that the enzyme had an apparent native molecular mass of a parts per thousand 243 kDa and a subunit size of a parts per thousand 85 kDa. The enzyme belongs to glycosyl hydrolases 36 family with high aa sequence similarities (a parts per thousand 73%) to other known alpha-galactosidases of bifidobacterial origin. Under optimum pH conditions for activity (pH 6.0) and high melibiose concentration (40% w/v), the enzyme was able to form oligosaccharides with degree of polymerisation (DP) a parts per thousand yen3 at higher concentration than DP = 2, with a total yield of 20.5% (w/w).

Cloning, expression, and characterization of human cytosolic aminopeptidase P: a single manganese(II)-dependent enzyme

The mammalian bradykinin-degrading enzyme aminopeptidase P (AP-P; E. C. 3.4.11.9) is a metal-dependent enzyme and is a member of the peptidase clan MG. AP-P exists as membrane-bound and cytosolic forms, which represent distinct gene products. A partially truncated clone encoding the cytosolic form was obtained from a human pancreatic cDNA library and the 5' region containing the initiating Met was obtained by 5' rapid accumulation of cDNA ends (RACE). The open reading frame encodes a protein of 623 amino acids with a calculated molecular mass of 69,886 Da. The full-length cDNA with a C-terminal hexahistidine tag was expressed in Escherichia coli and COS-1 cells and migrated on SDS-PAGE with a molecular mass of 71 kDa. The expressed cytosolic AP-P hydrolyzed the X-Pro bond of bradykinin and substance P but did not hydrolyze Gly-Pro-hydroxyPro. Hydrolysis of bradykinin was inhibited by 1,10-phenanthroline and by the specific inhibitor of the membrane-bound form of mammalian AP-P, apstatin. Inductively coupled plasma atomic emission spectroscopy of AP-P expressed in E. coli revealed the presence of 1 mol of manganese/mol of protein and insignificant amounts of cobalt, iron, and zinc. The enzymatic activity of AP-P was promoted in the presence of Mn(II), and this activation was increased further by the addition of glutathione. The only other metal ion to cause slight activation of the enzyme was Co(II), with Ca(II), Cu(II), Mg(II), Ni(II), and Zn(II) all being inhibitory. Removal of the metal ion from the protein was achieved by treatment with 1,10-phenanthroline. The metal-free enzyme was reactivated by the addition of Mn(II) and, partially, by Fe(II). Neither Co(II) nor Zn(II) reactivated the metal-free enzyme. On the basis of these data we propose that human cytosolic AP-P is a single metal ion-dependent enzyme and that manganese is most likely the metal ion used in vivo.

Construction of a Festuca pratensis BAC library for map-based cloning in Festulolium substitution lines

Introgression in Festulolium is a potentially powerful tool to isolate genes for a large number of traits which differ between Festuca pratensis Huds. and Lolium perenne L. Not only are hybrids between the two species fertile, but the two genomes can be distinguished by genomic in situ hybridisation and a high frequency of recombination occurs between homoeologous chromosomes and chromosome segments. By a programme of introgression and a series of backcrosses, L. perenne lines have been produced which contain small F. pratensis substitutions. This material is a rich source of polymorphic markers targeted towards any trait carried on the F. pratensis substitution not observed in the L. perenne background. We describe here the construction of an F. pratensis BAC library, which establishes the basis of a map-based cloning strategy in L. perenne. The library contains 49,152 clones, with an average insert size of 112 kbp, providing coverage of 2.5 haploid genome equivalents. We have screened the library for eight amplified fragment length polymorphism (AFLP) derived markers known to be linked to an F. pratensis gene introgressed into L. perenne and conferring a staygreen phenotype as a consequence of a mutation in primary chlorophyll catabolism. While for four of the markers it was possible to identify bacterial artificial chromosome (BAC) clones, the other four AFLPs were too repetitive to enable reliable identification of locus-specific BACs. Moreover, when the four BACs were partially sequenced, no obvious coding regions could be identified. This contrasted to BACs identified using cDNA sequences, when multiple genes were identified on the same BAC.

Sponge layer feedbacks in middle-atmosphere models

Middle-atmosphere models commonly employ a sponge layer in the upper portion of their domain. It is shown that the relaxational nature of the sponge allows it to couple to the dynamics at lower levels in an artificial manner. In particular, the long-term zonally symmetric response to an imposed extratropical local force or diabatic heating is shown to induce a drag force in the sponge that modifies the response expected from the “downward control” arguments of Haynes et al. [1991]. In the case of an imposed local force the sponge acts to divert a fraction of the mean meridional mass flux upward, which for realistic parameter values is approximately equal to exp(−Δz/H), where Δz is the distance between the forcing region and the sponge layer and H is the density scale height. This sponge-induced upper cell causes temperature changes that, just below the sponge layer, are of comparable magnitude to those just below the forcing region. In the case of an imposed local diabatic heating, the sponge induces a meridional circulation extending through the entire depth of the atmosphere. This circulation causes temperature changes that, just below the sponge layer, are of opposite sign and comparable in magnitude to those at the heating region. In both cases, the sponge-induced temperature changes are essentially independent of the height of the imposed force or diabatic heating, provided the latter is located outside the sponge, but decrease exponentially as one moves down from the sponge. Thus the effect of the sponge can be made arbitrarily small at a given altitude by placing the sponge sufficiently high; e.g., its effect on temperatures two scale heights below is roughly at the 10% level, provided the imposed force or diabatic heating is located outside the sponge. When, however, an imposed force is applied within the sponge layer (a highly plausible situation for parameterized mesospheric gravity-wave drag), its effect is almost entirely nullified by the sponge-layer feedback and its expected impact on temperatures below largely fails to materialize. Simulations using a middle-atmosphere general circulation model are described, which demonstrate that this sponge-layer feedback can be a significant effect in parameter regimes of physical interest. Zonally symmetric (two dimensional) middle-atmosphere models commonly employ a Rayleigh drag throughout the model domain. It is shown that the long-term zonally symmetric response to an imposed extratropical local force or diabatic heating, in this case, is noticeably modified from that expected from downward control, even for a very weak drag coefficient

Optimization of a sponge cake formulation with inulin as fat replacer: structure, physicochemical, and sensory properties

The effects of several fat replacement levels (0%, 35%, 50%, 70%, and 100%) by inulin in sponge cake microstructure and physicochemical properties were studied. Oil substitution for inulin decreased significantly (P < 0.05) batter viscosity, giving heterogeneous bubbles size distributions as it was observed by light microscopy. Using confocal laser scanning microscopy the fat was observed to be located at the bubbles’ interface, enabling an optimum crumb cake structure development during baking. Cryo-SEM micrographs of cake crumbs showed a continuous matrix with embedded starch granules and coated with oil; when fat replacement levels increased, starch granules appeared as detached structures. Cakes with fat replacement up to 70% had a high crumb air cell values; they were softer and rated as acceptable by an untrained sensory panel (n = 51). So, the reformulation of a standard sponge cake recipe to obtain a new product with additional health benefits and accepted by consumers is achieved.