Şerefköy-2, a new Late Miocene mammal locality from the Yatağan Formation,Muğla,SW Turkey

Here we report on a new fossil locality, ?erefköy-2, from the Yata?an Basin of southwestern Turkey that preserves a well-sampled, abundant, and diverse mammal fauna. Indeed, after three field seasons, more than 1200 catalogued specimens representing 26 mammal species belonging to 14 genera make the ?erefköy-2 mammalian assemblage one of the richest Late Miocene fauna from Anatolia. Five hipparionines, six bovids, including the rare and enigmatic Urmiatherium rugosifrons and the presence of Pliohyrax graecus, strongly support affinities with Late Miocene faunas from Samos Island, Greece. Through a consideration of the identified material and the subsequent comparison with material from well-known Balkan and Anatolian faunas, a Middle Turolian (MN12) age for ?erefköy-2 is indicated.     

Folivory or fruit/seed predation for Mesopithecus, an earliest colobine from the late Miocene of Eurasia?

Here we compare dental microwear textures from specimens of the fossil genus Mesopithecus (Cercopithecidae, Colobinae) from the late Miocene of Eastern Europe with dental microwear textures from four extant primate species with known dietary differences. Results indicate that the dental microwear textures of Mesopithecus differ from those of extant leaf eaters Alouatta palliata and Trachypithecus cristatus and instead resemble more closely those of the occasional hard-object feeders Cebus apella and Lophocebus albigena. Microwear texture data presented here in combination with results from previous analyses suggest that Mesopithecus was a widespread, opportunistic feeder that often consumed hard seeds. These data are consistent with the hypothesis that early colobines may have preferred hard seeds to leaves.     

Feeding preferences of <Emphasis Type="Italic">Gomphotherium subtapiroideum</Emphasis> (Proboscidea,Mammalia) from the Miocene of Sandelzhausen (Northern Alpine Foreland Basin,southern Germany) through life and geological time: evidence from dental microwear analysis

The objective of this study is to estimate changes in feeding preferences of the proboscidean species Gomphotherium subtapiroideum (Schlesinger 1917) by means of dental microwear analyses. The dietary changes are first evaluated through the ontogeny of this species, between juveniles and adults, and are then studied through geological time, from early Middle Miocene (MN5) to middle Late Miocene (MN8–9) localities of the German Molasse Basin. The microwear patterns of juvenile and adult individuals of G. subtapiroideum from Sandelzhausen (MN5) differ merely by the variable “length of scratches”, emphasizing longer jaw movements during mastication in adults. The microwear signatures of G. subtapiroideum do not vary significantly between the two geological time periods studied, but reflect mixed feeding preferences in both cases. These results imply that, despite an important environmental change at that time (drying and opening), the ecology of G. subtapiroideum and, especially, its feeding habits were not affected. Its dental microwear pattern is then compared with those of other species of Proboscidea from the Middle-Late Miocene of Germany, namely Deinotherium giganteum and Gomphotherium steinheimense.     

Protein Repair l-Isoaspartyl Methyltransferase1 Is Involved in Both Seed Longevity and Germination Vigor in Arabidopsis

The formation of abnormal amino acid residues is a major source of spontaneous age-related protein damage in cells. The protein l-isoaspartyl methyltransferase (PIMT) combats protein misfolding resulting from l-isoaspartyl formation by catalyzing the conversion of abnormal l-isoaspartyl residues to their normal l-aspartyl forms. In this way, the PIMT repair enzyme system contributes to longevity and survival in bacterial and animal kingdoms. Despite the discovery of PIMT activity in plants two decades ago, the role of this enzyme during plant stress adaptation and in seed longevity remains undefined. In this work, we have isolated Arabidopsis thaliana lines exhibiting altered expression of PIMT1, one of the two genes encoding the PIMT enzyme in Arabidopsis. PIMT1 overaccumulation reduced the accumulation of l-isoaspartyl residues in seed proteins and increased both seed longevity and germination vigor. Conversely, reduced PIMT1 accumulation was associated with an increase in the accumulation of l-isoaspartyl residues in the proteome of freshly harvested dry mature seeds, thus leading to heightened sensitivity to aging treatments and loss of seed vigor under stressful germination conditions. These data implicate PIMT1 as a major endogenous factor that limits abnormal l-isoaspartyl accumulation in seed proteins, thereby improving seed traits such as longevity and vigor. The PIMT repair pathway likely works in concert with other anti-aging pathways to actively eliminate deleterious protein products, thus enabling successful seedling establishment and strengthening plant proliferation in natural environments.     

Transfer-NMR and docking studies identify the binding of the peptide derived from activating transcription factor 4 to protein ubiquitin ligase beta-TrCP. Competition STD-NMR with beta-catenin

ATF4 plays a crucial role in the cellular response to stress. The E3 ubiquitin ligase, SCF beta-TrCP protein responsible for ATF4 degradation by the proteasome, binds to ATF4 through a DpSGXXXpS phosphorylation motif, which is similar but not identical to the DpSGXXpS motif found in most other substrates of beta-TrCP. NMR studies were performed on the free and bound forms of a peptide derived from this ATF4 motif that enabled the elucidation of the conformation of the ligand complexed to the beta-TrCP protein and its binding mode. Saturation transfer difference (STD) NMR allowed the study of competition for binding to beta-TrCP, between the phosphorylation motifs of ATF4 and beta-catenin, to characterize the ATF4 binding epitope. Docking protocols were performed using the crystal structure of the beta-catenin-beta-TrCP complex as a template and NMR results of the ATF4-beta-TrCP complex. In agreement with the STD results, in order to bind to beta-TrCP, the ATF4 DpSGIXXpSXE motif required the association of two negatively charged areas, in addition to the hydrophobic interaction in the beta-TrCP central channel. Docking studies showed that the ATF4 DpSGIXXpSXE motif fits the binding pocket of beta-TrCP through an S-turning conformation. The distance between the two phosphate groups is 17.8 A, which matched the corresponding distance 17.1 A for the other extended DpSGXXpS motif in the beta-TrCP receptor model. This study identifies the residues of the beta-TrCP receptor involved in ligand recognition. Using a new concept of STD competition experiment, we show that ATF4 competes and inhibits binding of beta-catenin to beta-TrCP.     

Seed aging and survival mechanisms

Aging and death are universal to living systems. In temperate climate latitudes the mature seeds of higher plants are exposed to aging and have developed resistance mechanisms allowing survival and plant propagation. In addition to the physicochemical properties of the seed that confer stress resistance, the protein metabolism contributes importantly to longevity mechanisms. Recently, genetic studies have demonstrated the occurrence of the Protein L-isoaspartyl methyltransferase repair enzyme in controlling age-related protein damages and seed survival. These protective mechanisms by protein repair are widespread in all kingdoms, so that the use of seeds as models to study these controlling processes offers the prospect of understanding longevity mechanisms better.     

The key-role of tyrosine 155 in the mechanism of prion transconformation as highlighted by a study of sheep mutant peptides

Prion protein is a strongly conserved and ubiquitous glycoprotein. The conformational conversion of the non-pathogenic cellular prion isoform (PrP(C)) into a pathogenic scrapie isoform (PrP(Sc)) is a fundamental event in the onset of transmissible spongiform encephalopathies (TSE). During this conversion, helix H1 and its two flanking loops are known to undergo a conformational transition into a beta-like structure. In order to understand mechanisms which trigger this transconformation, sheep prion protein synthetic peptides spanning helix 1 and beta-strand 2 (residues 142-166) were studied: (1) the N3 peptide, studied earlier, is known to fold into beta-hairpin-like conformation in phosphate buffer at neutral pH and to adopt a helix H1 conformation when dissolved in trifluoroethanol/phosphate buffer mixture, (2) The R156A mutant (peptide R15) and (3) the Y155A mutant (peptide Y14) of the N3 peptide are studied by circular dichroism and NMR spectroscopy in this article. Structural characterization of these peptides highlights the key role of tyrosine 155 in the stabilization of the beta-hairpin-like conformation of the sheep peptide in phosphate buffer. We propose a model where tyrosine 155 could stabilize the beta-hairpin structure by creating a hydrophobic core in phosphate buffer, necessary to initiate the beta-type structure formation. In the turn, the side chain ionic interaction, E152-R156 described before, seems to play a minor role relative to the hydrophobic packing, as observed with the R156A mutation (peptide R15). Interestingly, homology at amino acid residue 155 could be responsible for the species barrier in TSE.     

First evidence that cytochrome P450 may catalyze both S-oxidation and epoxidation of thiophene derivatives

Oxidation of 2-phenylthiophene (2PT) by rat liver microsomes, in the presence of NADPH and glutathione (GSH), led to three kinds of metabolites whose structures were established by 1H NMR and mass spectrometry. The first ones were 2PT-S-oxide dimers formed by Diels-Alder type dimerization of 2PT-S-oxide, while the second ones were GSH adducts derived from the 1,4-Micha?l-type addition of GSH to 2PT-S-oxide. The third metabolites were GSH adducts resulting from a nucleophilic attack of GSH to the 4,5-epoxide of 2PT. Oxidation of 2PT by recombinant, human cytochrome P4501A1, in the presence of NADPH and GSH, also led to these three kinds of metabolites. These results provide the first evidence that cytochrome P450 may catalyze the oxidation of thiophene compounds with the simultaneous formation of two reactive intermediates, a thiophene-S-oxide and a thiophene epoxide.