Palaeoenvironments and hominin evolutionary dynamics in southeast Asia

Secure environmental contexts are crucial for hominin interpretation and comparison. The discovery of a Denisovan individual and associated fauna at Tam Ngu Hao 2 (Cobra) Cave, Laos, dating back to 164-131 ka, allows for environmental comparisons between this (sub)tropical site and the Palearctic Denisovan sites of Denisova Cave (Russia) and Baishiya Karst Cave (China). Denisovans from northern latitudes foraged in a mix of forested and open landscapes, including tundra and steppe. Using stable isotope values from the Cobra Cave assemblage, we demonstrate that, despite the presence of nearby canopy forests, the Denisovan individual from Cobra Cave primarily consumed plants and/or animals from open forests and savannah. Using faunal evidence and proxy indicators of climates, results herein highlight a local expansion of rainforest at ~ 130 ka, raising questions about how Denisovans responded to this local climate change. Comparing the diet and habitat of the archaic hominin from Cobra Cave with those of early Homo sapiens from Tam Pà Ling Cave (46-43 ka), Laos, it appears that only our species was able to exploit rainforest resources.

Trophic ecology of a Late Pleistocene early modern human from tropical Southeast Asia inferred from zinc isotopes

Tam Pà Ling, a cave site in northeastern Laos, has yielded the earliest skeletal evidence of Homo sapiens in mainland Southeast Asia. The reliance of Pleistocene humans in rainforest settings on plant or animal resources is still largely unstudied, mainly due to poor collagen preservation in fossils from tropical environments precluding stable nitrogen isotope analysis, the classical trophic level proxy. However, isotopic ratios of zinc (Zn) in bioapatite constitute a promising proxy to infer trophic and dietary information from fossil vertebrates, even under adverse tropical taphonomic conditions. Here, we analyzed the zinc isotope composition (⁶⁶Zn/⁶⁴Zn expressed as δ⁶⁶Zn value) in the enamel of two teeth of the Late Pleistocene (63-46 ka) H. sapiens individual (TPL1) from Tam Pà Ling, as well as 76 mammal teeth from the same site and the nearby Nam Lot cave. The human individual exhibits relatively low enamel δ⁶⁶Zn values (+0.24‰) consistent with an omnivorous diet, suggesting a dietary reliance on both plant and animal matter. These findings offer direct evidence of the broad utilization of resources from tropical rainforests by one of the earliest known anatomically modern humans in Southeast Asia.

Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking

The proteomic analysis of hairs, yarns or textiles has emerged as a powerful method to determine species of origin, mainly used in archaeozoological research and fraud control. Differentiation between the South American camelid (SAC) species (the wild guanaco and vicuña and their respective domesticates the llama and alpaca) is particularly challenging due to poor database information and significant hybridization between species. In this study, we analysed 41 modern and 4 archaeological samples from the four SACs species. Despite strong similarities with Old World Camelidae, we identified 7 peptides specific to SACs assigned to keratin K86 and the keratin-associated proteins KAP13-1 and KAP11-1. Untargeted multivariate analysis of the LC-MS data permitted to distinguish SAC species and propose discriminant features. MS/MS-based molecular networking combined with database-assisted de novo sequencing permitted to identify 5 new taxonomic peptides assigned to K33a, K81 and/or K83 keratins and KAP19-1. These peptides differentiate the two wild species, guanaco and vicuña. These results show the value of combining database search and untargeted metabolomic approaches for paleoproteomics, and reveal for the first time the potential of molecular networks to highlight deamidation related to diagenesis and cluster highly similar peptides related to interchain homologies or intra- or inter-specific polymorphism. SIGNIFICANCE: This study used an innovative approach combining multivariate analysis of LC-MS data together with molecular networking and database-assisted de novo sequencing to identify taxonomic peptides in palaeoproteomics. It constitutes the first attempt to differentiate between hair fibres from the four South American camelids (SACs) based on proteomic analysis of modern and archaeological samples. It provides different proteomic signatures for each of the four SAC species and proposes new SAC taxonomic peptides of interest in archaeozoology and fraud control. SACs have been extensively exploited since human colonization of South America but have not been studied to the extent of their economic, cultural and heritage importance. Applied to the analysis of ancient Andean textiles, our results should permit a better understanding of cultural and pastoral practices in South America. The wild SACs are endangered by poaching and black-market sale of their fibre. For the first time, our results provide discriminant features for the determination of species of origin of contraband fibre.

Seasonal oxygen isotope variations in freshwater bivalve shells as recorders of Amazonian rivers hydrogeochemistry

Freshwater bivalve shell oxygen isotope values (δ¹⁸O_S) may act as a recorder of river δ¹⁸O variations that can then be interpreted in terms of hydrology (e.g. precipitation-evaporation balance, precipitation and river discharge patterns). We investigated the potential of this proxy measured across the hinge of South American unionid shells: Anodontites elongatus collected in Peru and A. trapesialis in Brazil. The isotopic signatures were reproducible between individuals of the same species. A. trapesialis clearly showed a strong δ¹⁸O_S cyclicity in accordance with its growth patterns while A. elongatus presented less clear δ¹⁸O_S with lower amplitude. We confirm that the deposition of successive growth lines and increments is annual, with growth line corresponding to the wet season. Also, we suggest that low amplitude of δ¹⁸O_S in the A. elongatus shells indicates a habitat close to the river while large amplitude of δ¹⁸O_S cycles observed in A. trapesialis shells would reflect a floodplain lake habitat, seasonally disconnected from the river and thus subjected to higher seasonal fluctuations in water δ¹⁸O. Considering these promising first results, future studies could be directed towards the use of fossil shells to reconstruct the past and present hydrological and geochemical conditions of the Amazon.

Pastoralism in northern Peru during pre-Hispanic times: insights from the Mochica Period (100-800 AD) based on stable isotopic analysis of domestic camelids

Llama (Lama glama) and alpaca (Vicugna pacos) are the only large domesticated animals indigenous to the Americas. Pastoralism occupies a fundamental economic, social and religious role in Andean life. Today, camelid livestock are confined to the ecozone of the puna (above 3,500 masl), while their presence on the Pacific coast during pre-Hispanic times is attested by archaeological skeletal remains. This study aims to document herding practices on the northern Peruvian coast during the Early Intermediate Period (200 BC-600 AD) by gaining insights into diet, location of breeding and mobility of archaeological camelids from the funerary and ritual contexts of two Mochica sites, Uhle Platform in Huacas de Moche and El Brujo. The three first early years and the long-term life histories of the animals were documented by the combined bulk analysis of bone collagen (δ¹³C_col and δ¹⁵N_col) and bone structural carbonate (δ¹³C_bone and δ¹⁸O_bone) and the serial analysis of structural carbonate of molar tooth enamel (δ¹³C_enamel and δ¹⁸O_enamel). Mochica camelids were bred in the low and/or middle valleys, unlike their modern counterparts, who are restricted to highland puna C₃ pastures. Archaeological camelids had diverse and complex life histories, usually with substantial maize foddering. An ontogenetic switch in diet and possible residential mobility during the course of life were identified for some specimens. Although the inference of geographic origin from δ¹⁸O_bone and δ¹⁸O_enamel values was limited because of the lack of understanding of the influence of environmental and biological factors, tooth enamel analysis has great potential for exploring camelid herding practices and Andean pastoralism. Our study suggested that Mochica herders adapted their practices to the difficult lowland environment and that herding practices were varied and not restricted to breeding at higher altitudes. The role of maize in different aspects of the economic life of the Mochicas is also underlined.

‘Clickable’ 2,5-diketopiperazines as scaffolds for ligation of biomolecules: their use in Aβ inhibitor assembly

The synthesis of 1,3,6-trisubstituted-2,5-diketopiperazine scaffolds bearing up to three ‘clickable’ sites for further oxime bond or alkyne–azide cycloaddition ligations is described.

Inferring occurrence of growth checks in pike (Esox lucius) scales by using sequential isotopic analysis of otoliths

RATIONALE

Sequential analysis of otolith oxygen isotope (δ(18) O(oto) ) values was performed by classical mechanical microdrilling and dual inlet mass spectrometry to infer the timing of growth checks in pike (Esox lucius) scales from Lake Annecy (France). It indicated that the first check on scales occurs before the first winter of life of the fish.

METHODS

Eleven fish caught in February and June 2008 were studied. Intra-individual isotopic profiles exhibit cyclic variations that are consistent with that of modeled δ(18) O(oto) values using variations in epilimnion temperature and otolith-specific isotope fractionation equations. The positions of growth checks on scales were compared with the periodic variations of δ(18) O(oto) values on otolith radii using an allometric relationship.

RESULTS

All individuals presented at least one check deposited before the first winter. Deposition of some checks might be linked to a shift in fish diet or habitat or to catch-and-release induced stress.

CONCLUSIONS

Although coupling between sequential analysis of δ(18) O(oto) values and observation of scale growth features has been shown to be useful, there are limitations in the methodology, especially for the growth-attenuated region of otoliths associated with older ages.

Application of the threshold of toxicological concern approach for the safety evaluation of calendula flower (Calendula officinalis) petals and extracts used in cosmetic and personal care products

Calendula flower (Calendula officinalis) (CF) has been used in herbal medicine because of its anti-inflammatory activity. CF and C. officinalis extracts (CFE) are used as skin conditioning agents in cosmetics. Although data on dermal irritation and sensitization of CF and CFE's are available, the risk of subchronic systemic toxicity following dermal application has not been evaluated. The threshold of toxicological concern (TTC) is a pragmatic, risk assessment based approach that has gained regulatory acceptance for food and has been recently adapted to address cosmetic ingredient safety. The purpose of this paper is to determine if the safe use of CF and CFE can be established based upon the TTC class for each of its known constituents. For each constituent, the concentration in the plant, the molecular weight, and the estimated skin penetration potential were used to calculate a maximal daily systemic exposure which was then compared to its corresponding TTC class value. Since the composition of plant extracts are variable, back calculation was used to determine the maximum acceptable concentration of a given constituent in an extract of CF. This paper demonstrates the utility and practical application of the TTC concept when used as a tool in the safety evaluation of botanical extracts.

The effect of raw milk microbial flora on the sensory characteristics of Salers-type cheeses

The sensory characteristics of Salers Protected Denomination of Origin raw-milk cheeses are linked to the biochemical composition of the raw material (milk) and to the resultant microbial community. To evaluate the influence of the microbial community on sensory characteristics, Salers-type cheeses were manufactured with the same pasteurized milk, reinoculated with 3 different microbial communities from 3 different filtrates from microfiltered milks. Each cheese was subjected to microbial counts (on selective media), biochemical tests, and volatile and sensory component analyses at different times of ripening. Adding different microbial communities to specimens of the same (biochemically identical) pasteurized milk lead to different sensory characteristics of the cheeses. Cheeses with fresh cream, hazelnut, and caramel attributes were opposed to those with fermented cream, chemical, and garlic flavors. The aromatic compounds identified (esters, acids, alcohols, and aldehydes) in these cheeses were quite similar. Nevertheless, one milk was distinguished by a higher content of acetoin, and lower 2-butanone and 3-methylpentanone concentrations. Over the production period of 1 mo, the different cheeses were characterized by the same balance of the microbial population assessed by microbial counts on different media. This was associated with the stability of some sensory attributes describing these cheeses. Nevertheless, there was no linear correlation between microbial flora data and sensory characteristics as measured in this study.

Composition and properties of the soluble organic matrix of the otolith of a marine fish: Gadus morhua Linne, 1758 (Teleostei, Gadidae)

The soluble matrix of the sagittal otolith of the cod Gadus morhua was analyzed using UV and IR spectroscopy, liquid chromatography and electrophoresis. This matrix is a complex mixture of proteins and glycoproteins, with a large range of molecular weights. High weights (>1000 kDa) are shown for the first time in water-soluble matrix of otolith. However, the 2D denaturing electrophoresis and large range of sorting used in high performance liquid chromatography columns do not separate the soluble matrix to well-defined molecular weights. The IR data indicate that several conformations are present and the main part of the sugars is not sulfated. Additionally, electrophoresis data show that the acidity of the sugar components is higher than that of the proteins. Despite the relative scarcity of literature data, our study of G. morhua suggests that the chemical composition of otolith soluble organic matrix may differ among species.

Evaluation of standardized tasks for primary care physicians using the MOXXI electronic prescribing and integrated drug management system

The Medical Office for the Twenty First Century (MOXXI) is a research project testing the potential benefits of an electronic prescription and drug management system for primary care physicians. This system includes a dynamic electronic pad for prescription entry with fields for treatment indications; a drug profiler with a graphic representation of the list of prescription medications purchased in the last year; a refill compliance calculator; dates of emergency room visits and hospital admissions; cost of drugs dispensed; and an alert system that detects interactions among drugs, treatment duplications, and contraindications with certain allergies or specific diseases. One concern expressed by physicians that could influence uptake and acceptability is the increased time that may be required to use the system. User abilities are a factor in this process, as well as user interface, user training and system speed.

Overexpression of the alternative oxidase restores senescence and fertility in a long-lived respiration-deficient mutant of Podospora anserina

Several lines of evidence have implicated reactive oxygen species (ROS) in the pathogenesis of various degenerative diseases and in organismal ageing. Furthermore, it has been shown recently that the alternative pathway respiration present in plants lowers ROS mitochondrial production. An alternative oxidase (AOXp) also occurs in the filamentous fungus Podospora anserina. We show here that overexpression of this oxidase does not decrease ROS production and has no effect on longevity, mitochondrial stability or ageing in this fungus. In the same way, inactivation of the gene has no effect on these parameters. In contrast, overexpression of the alternative oxidase in the long-lived cox5::BLE mutant, deficient in cytochrome c oxidase, considerably increases ROS production of the mutant. It rescues slow growth rate and female sterility, indicating an improved energy level. This overexpression also restores senescence and mitochondrial DNA instability, demonstrating that these parameters are controlled by the energy level and not by the expression level of the alternative oxidase. We also suggest that expression of this oxidase in organisms naturally devoid of it could rescue respiratory defects resulting from cytochrome pathway dysfunctions.

Experimental discovery of charge-exchange-caused dips in spectral lines from laser-produced plasmas

We report the first experimental observation of charge-exchange-caused dips (also called x dips) in spectral lines of multicharged ions in laser-produced plasmas. Specifically, in the process of a laser irradiation of targets made out of aluminum carbide, we observed two x dips in the Ly(gamma) line of Al XIII perturbed by fully stripped carbon. From the practical point of view, this opens up a way to experimentally produce not-yet-available fundamental data on charge exchange between multicharged ions, virtually inaccessible by other experimental methods. From the theoretical viewpoint, the results are important because the x dips are the only one signature of charge exchange in profiles of spectral lines emitted by plasmas and they are the only one quasimolecular phenomenon that could be observed at relatively "low" densities of laser-produced plasmas.

The Composition of the Milk Fat Globule Surface Alters the Structural Characteristics of the Coagulum

The effects of the composition of a fat globule surface in reconstituted milks on the properties of rennet-induced coagulums were studied by rheological measurements and by front-face fluorescence spectroscopy in combination with a multivariate statistical method to investigate, at a molecular level, the evolution of the structure during the milk coagulation process. Reconstituted milks used in this study were prepared from different fat-in-water emulsions stabilized by whole skim-milk proteins, beta-casein, or beta-lactoglobulin. Coagulation of milk reconstituted with natural fat globules was also investigated. The study showed that the fat droplet/water interface influences the rheological properties (G' modulus) of the reconstituted milks during the coagulation process. The tryptophan fluorescence emission spectra of proteins were recorded during the kinetics of coagulation. The results of the principal component analysis performed on the spectral data showed a discrimination in the different systems investigated. It was shown that the fluorescence properties of protein tryptophans and, consequently, the structures of the protein networks were different for the investigated systems. The development of fluorescence transfer between protein tryptophans and fat-globule vitamin A during the coagulation kinetics agreed with the interactions between the protein network and fat globules. Copyright 2001 Academic Press.

Assessment of the contaminant concentration variability among Lake Geneva Arctic char using stable isotopic composition (delta15N and delta13C)

Measurements of organochlorine [polychlorinated biphenyls (PCBs) and dichloro-diphenyl-dichloroethylene (DDE)] and Hg concentrations and nitrogen and carbon stable isotopic compositions (delta15N and delta13C) were performed on 63 Arctic char (Salvelinus alpinus) from Lake Geneva. Fish exhibited a high interindividual variablity in pollutant concentrations. Since the accumulation of such persistent contaminants is obtained from food, the co-occurrence of dietary differentiation leading to the contaminant interindividual variability was suspected. delta15N and delta13C were used for assessing trophic position and food source differences among Arctic char. The low ranges of delta15N and delta13C could not explain the interindividual variability in pollutant concentrations. The lack of relation between delta15N and contaminant concentration did not suggest a trophic level biomagnification of PCB, DDE, and Hg. Lake Geneva spatial variability in pollutants may be an important factor of variability within the Arctic char population. The bioaccumulation pattern occurring for Hg was not apparent for PCB and DDE. Organochlorines are hydrophobic contaminants, and their bioaccumulation pattern may be masked by seasonal variations in fish lipid content.

An aspartic acid residue in TPR-1, a specific region of protein-priming DNA polymerases, is required for the functional interaction with primer terminal protein

A multiple sequence alignment of eukaryotic-type DNA polymerases led to the identification of two regions of amino acid residues that are only present in the group of DNA polymerases that make use of terminal proteins. (TPs) as primers to initiate DNA replication of linear genomes. These amino acid regions (named terminal region (TPR protein-1 and TPR-2) are inserted between the generally conserved motifs Dx(2)SLYP and Kx(3)NSxYG (TPR-1) and motifs Kx(3)NSxYG and YxDTDS (TPR-2) of the eukaryotic-type family of DNA polymerases. We carried out site-directed mutagenesis in two of the most conserved residues of phi29 DNA polymerase TPR-1 to study the possible role of this specific region. Two mutant DNA polymerases, in conserved residues AsP332 and Leu342, were purified and subjected to a detailed biochemical analysis of their enzymatic activities. Both mutant DNA polymerases were essentially normal when assayed for synthetic activities in DNA-primed reactions. However, mutant D332Y was drastically affected in phi29 TP-DNA replication as a consequence of a large reduction in the catalytic efficiency of the protein-primed reactions. The molecular basis of this defect is a non-functional interaction with TP that strongly reduces the activity of the DNA polymerase/TP heterodimer.

La diagenese des otolithes par la comparaison des donnees microstructurales, mineralogiques et geochimiques; application aux fossiles du Pliocene du Sud-Est de la France

Microstructure, mineralogy and elemental and isotopic compositions of recent and fossil otoliths have been investigated. Fossil otoliths come from marine Pliocene localities of southeastern France. The study of the different parameters show that diagenetic changes are weak. Microstructural features specific to otoliths, such as needle-like crystals and growth increments, are usually well preserved. When present, the microstructural modifications remain limited inside each otolith. Except a few pyritic specimens, the only mineral found is aragonite like in recent specimens. The chemical compositions of fossil and recent otoliths are not significantly different, and any element is preferentially changed by diagenesis. The isotopic composition does not show strong alterations. However, the difference in 18 O content between recent fishes having different ecological habits is not found with the same magnitude in fossil specimens. Finally, when elemental and isotopic compositions are compared, the specimens are sorted according to taxonomy and not according to their geologic age. This suggests that biogenic signals have been preserved.

Gelation by phase separation in a whey protein system: in-situ kinetics of aggregation

The aggregation and gelation properties of beta-lactoglobulin (BLG), a globular protein from milk, was studied in aqueous ethanol solutions at room temperature. The phase state diagrams as a function of pH and ethanol concentration showed that a gel structure appeared after a period ranging from 1 min to 1 week, depending on the physico-chemical conditions. The in-situ kinetics of aggregation were followed by several methods in order to obtain a better understanding of the building of aggregates by the addition of ethanol. It was shown that the aggregation kinetics highly depended upon the pH, the process being fastest at pH 7. Viscoelasticity and infrared measurements indicated that alcohol-induced gelation would proceed via a two-step mechanism: small aggregates loosely connected between them were first built up; a real network took place in a second step. The coarse and irregular structures formed in aqueous ethanol gels revealed by confocal laser scanning microscopy could be analysed in terms of a phase separation. This observation was supported by a syneresis phenomenon visible in the final gel state. BLG in water-ethanol solution would undergo either an inhibition of the demixing by gelation or a binary phase separation accompanied by an irreversible gelation transition.

A causal link between respiration and senescence in Podospora anserina

Senescence, a progressive degenerative process leading to age-related increase in mortality, is found in most eukaryotes. However, the molecular events underlying aging remain largely unknown. Understanding how longevity is regulated is a fundamental problem. Here we demonstrate that the respiratory function is a key factor that contributes to shortening lifespan of the filamentous fungus Podospora anserina. In this organism, senescence is systematically associated with mitochondrial DNA instabilities. We show that inactivation of the nuclear COX5 gene encoding subunit V of the cytochrome c oxidase complex leads to the exclusive use of the alternative respiratory pathway and to a decrease in production of reactive oxygen species. This inactivation results in a striking increase of longevity associated with stabilization of the mitochondrial chromosome. Moreover, accumulation of several senescence-specific mitochondrial DNA molecules is prevented in this nuclear mutant. These findings provide direct evidence of a causal link between mitochondrial metabolism and longevity in Podospora anserina.

Oil/Alkanethiol Layers for the Study of Emulsified Protein Conformation by Surface Plasmon Resonance Using Monoclonal Antibodies

A method combining surface plasmon resonance and epitope mapping was developed to study the protein conformation at the oil/water interface of an emulsion. The conformation of beta-lactoglobulin stabilizing dodecane/water and miglyol/water interfaces was investigated using five anti-beta-lactoglobulin monoclonal antibodies. The developed method allows us to specifically recognize the emulsified beta-lactoglobulin at the surface of a sensor chip with good repeatability; i.e., standard deviations range between 0.7 and 3.6%. Considering that the monoclonal antibodies, recognizing conformational epitopes, still bind to beta-lactoglobulin at oil/water interfaces, it is concluded that the protein retains a globular conformation. It is shown that the inhibition-binding values of two pairs of Mabs are different for beta-lactoglobulin stabilizing dodecane/water and miglyol/water interfaces. This indicates that the conformations of emulsified beta-lactoglobulin are slightly different according to the nature of the oil phase. Copyright 2000 Academic Press.

Structural investigation of beta-lactoglobulin gelation in ethanol/water solutions

The aggregation and gelation properties of beta-lactoglobulin (BLG), a globular protein from milk, was studied in hydro-ethanolic solutions (50/50% (v/v)) at room temperature. The phase state diagrams as a function of pH and ethanol concentration showed that a gel structure appeared after a period ranging from 1 min to 1 week depending on the physico-chemical conditions. The aggregation kinetics, studied by infrared spectroscopy and dynamical rheological measurements, highly depended upon the pH; the process being the fastest at pH 7. Alcohol-induced aggregation of BLG was characterized by the formation of intermolecular hydrogen bonded beta-sheet structures. Small angle neutron scattering indicated that the aggregates structures in the final gels were similar at pH 7, 8 and 9. Through the data obtained at the molecular and macroscopic levels, it can be concluded that the kinetics of gelation were pH dependent while the spatial arrangements of the aggregates were similar in the final structures. The heterogeneous structures formed in hydro-ethanolic gels could be analysed in terms of a phase separation, the syneresis being the final visible state.

Mitochondrial group II introns, cytochrome c oxidase, and senescence in Podospora anserina

Podospora anserina is a filamentous fungus with a limited life span. It expresses a degenerative syndrome called senescence, which is always associated with the accumulation of circular molecules (senDNAs) containing specific regions of the mitochondrial chromosome. A mobile group II intron (alpha) has been thought to play a prominent role in this syndrome. Intron alpha is the first intron of the cytochrome c oxidase subunit I gene (COX1). Mitochondrial mutants that escape the senescence process are missing this intron, as well as the first exon of the COX1 gene. We describe here the first mutant of P. anserina that has the alpha sequence precisely deleted and whose cytochrome c oxidase activity is identical to that of wild-type cells. The integration site of the intron is slightly modified, and this change prevents efficient homing of intron alpha. We show here that this mutant displays a senescence syndrome similar to that of the wild type and that its life span is increased about twofold. The introduction of a related group II intron into the mitochondrial genome of the mutant does not restore the wild-type life span. These data clearly demonstrate that intron alpha is not the specific senescence factor but rather an accelerator or amplifier of the senescence process. They emphasize the role that intron alpha plays in the instability of the mitochondrial chromosome and the link between this instability and longevity. Our results strongly support the idea that in Podospora, "immortality" can be acquired not by the absence of intron alpha but rather by the lack of active cytochrome c oxidase.

Tyrosine 319 in the interdomain B of ZAP-70 is a binding site for the Src homology 2 domain of Lck

T-cell antigen receptor-induced signaling requires both ZAP-70 and Lck protein-tyrosine kinases. One essential function of Lck in this process is to phosphorylate ZAP-70 and up-regulate its catalytic activity. We have previously shown that after T-cell antigen receptor stimulation, Lck binds to ZAP-70 via its Src homology 2 (SH2) domain (LckSH2) and, more recently, that Tyr319 of ZAP-70 is phosphorylated in vivo and plays a positive regulatory role. Here, we investigated the possibility that Tyr319 mediates the SH2-dependent interaction between Lck and ZAP-70. We show that a phosphopeptide encompassing the motif harboring Tyr319, YSDP, interacted with LckSH2, although with a lower affinity compared with a phosphopeptide containing the optimal binding motif, YEEI. Moreover, mutation of Tyr319 to phenylalanine prevented the interaction of ZAP-70 with LckSH2. Based on these results, a gain-of-function mutant of ZAP-70 was generated by changing the sequence Y319SDP into Y319EEI. As a result of its increased ability to bind LckSH2, this mutant induced a dramatic increase in NFAT activity in Jurkat T-cells, was hyperphosphorylated, and displayed a higher catalytic activity compared with wild-type ZAP-70. Collectively, our findings indicate that Tyr319-mediated binding of the SH2 domain of Lck is crucial for ZAP-70 activation and consequently for the propagation of the signaling cascade leading to T-cell activation.

Tyrosine 319, a newly identified phosphorylation site of ZAP-70, plays a critical role in T cell antigen receptor signaling

Following T cell antigen receptor (TCR) engagement, the protein tyrosine kinase (PTK) ZAP-70 is rapidly phosphorylated on several tyrosine residues, presumably by two mechanisms: an autophosphorylation and a trans-phosphorylation by the Src-family PTK Lck. These events have been implicated in both positive and negative regulation of ZAP-70 activity and in coupling this PTK to downstream signaling pathways in T cells. We show here that Tyr315 and Tyr319 in the interdomain B of ZAP-70 are autophosphorylated in vitro and become phosphorylated in vivo upon TCR triggering. Moreover, by mutational analysis, we demonstrate that phosphorylation of Tyr319 is required for the positive regulation of ZAP-70 function. Indeed, overexpression in Jurkat cells and in a murine T cell hybridoma of a ZAP-70 mutant in which Tyr319 was replaced by phenylalanine (ZAP-70-Y319F) dramatically impaired anti-TCR-induced activation of the nuclear factor of activated T cells and interleukin-2 production, respectively. Surprisingly, an analogous mutation of Tyr315 had little or no effect. The inhibitory effect of ZAP-70-Y319F correlated with a substantial loss of its activation-induced tyrosine phosphorylation and up-regulation of catalytic activity, as well as with a decreased in vivo capacity to phosphorylate known ZAP-70 substrates, such as SLP-76 and LAT. Collectively, our data reveal the pivotal role of Tyr319 phosphorylation in the positive regulation of ZAP-70 and in TCR-mediated signaling.

Cross-linking localization of a HIV-1 reverse transcriptase peptide involved in the binding of primer tRNALys3

Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) initiates the synthesis of DNA from the 3' end of its specific primer, tRNALys3. The regions of tRNALys3 in close contact with RT are well known, while a precise knowledge of the RT regions interacting with tRNALys3 is not yet available. To address this question we cross-linked the heterodimeric p66/p51 RT to tRNALys3 using cis-aquahydroxydiammino-platinum. Ribonucleoprotein complexes of molecular masses higher than the p66 subunit were obtained. After RNase A digestion of the RT-tRNA complex, a labeled oligoribonucleotide (ORN) was mainly found associated to the p66 subunit. This labeled p66-ORN complex was then proteolyzed with Staphylococcus aureus V8 protease. A highly purified radioactive peptide was obtained after two chromatographic purification steps. Its N-terminal sequence corresponded with amino acid residues 241VQPI244. Using the crystallographic structure of HIV-1 RT, this peptide was localized at the beta14-sheet end, near to the hairpin formed by beta12 and beta13-sheets ("primer grip") and the alphaH-helix. The so called "VQPI peptide" is in the border of the thumb and the palm subdomains of the p66 subunit. This study palliates the absence of a three- dimensional structure of the RT-tRNA complex and led to a peptide in interaction with tRNALys3 present in all HIV-1 RT isolates.

Conformation of beta-Lactoglobulin at an Oil/Water Interface as Determined from Proteolysis and Spectroscopic Methods

The rates of appearance of tryptic peptides following the hydrolysis of beta-lactoglobulin in solution or adsorbed at the oil/water interface of an emulsion were investigated as a function of time. It was also shown using hydrophobic labeling that the region 15-40 of beta-lactoglobulin was in the oil phase. The fluorescence results suggested that the conformation of beta-lactoglobulin was modified upon adsorption at the oil/water interface and that at least one tryptophan in adsorbed beta-lactoglobulin was in a more hydrophobic environment. The data obtained by circular dichroism in the peptidic region indicated that the adsorbed beta-lactoglobulin was characterized by a higher content in alpha-helix than the protein in solution. Copyright 1998 Academic Press.

Synthesis of amidrazones using an engineered papain nitrile hydratase

To demonstrate the usefulness of an engineered papain nitrile hydratase as a biocatalyst, a peptide amidrazone was prepared by incubation of the nitrile MeOCO-Phe-Alanitrile with the Gln19Glu papain mutant in the presence of salicylic hydrazide as a nucleophile. The amidrazone results from nucleophilic attack by salicylic hydrazide at the imino carbon of the thioimidate adduct formed between the enzyme and the peptide nitrile substrate. Compared to wild-type enzyme, the engineered nitrile hydratase causes a better than 4000-fold increase in the rate of amidrazone formation and yields a product of much higher purity. The advantages over other nitrile-hydrolyzing enzymes and current limitations of the papain nitrile hydratase are discussed.

Autocatalytic processing of recombinant human procathepsin L. Contribution of both intermolecular and unimolecular events in the processing of procathepsin L in vitro

The autocatalytic processing of procathepsin L was investigated in vitro using purified recombinant proenzyme expressed in Pichia pastoris. Pure intermolecular processing was studied by incubating the mutant procathepsin L (C25S), which cannot autoactivate with a small amount of mature active cathepsin L. The results clearly establish that, contrary to recent reports, intermolecular processing of procathepsin L is possible. The main cleavage sites are located at or near the N terminus of the mature enzyme, in an accessible portion of the proregion, which contains sequences corresponding to the known substrate specificity of cathepsin L. Contrary to procathepsins B, K, and S, autocatalytic processing of procathepsin L can generate the natural mature form of the enzyme. A continuous assay using the substrate benzyloxycarbonyl-Phe-Arg 4-methylcoumarinyl-7-amide hydrochloride has also been used to obtain information on the nature of the steps involved in the autocatalytic processing of wild-type procathepsin L. Processing is initiated by decreasing the pH from 8.0 to 5.3. The influence of proenzyme concentration on the rate of processing indicates the existence of both unimolecular and bimolecular steps in the mechanism of processing. The nature of the unimolecular event that triggers processing remains elusive. Circular dichroism and fluorescence measurements indicate the absence of large scale conformational change in the structure of procathepsin L on reduction of pH. However, the bimolecular reaction can be attributed to intermolecular processing of the zymogen.

p66/p51 and p51/p51 recombinant forms of reverse transcriptase from human immunodeficiency virus type 1--interactions with primer tRNA(Lys3), initiation of cDNA synthesis, and effect of inhibitors

Human immunodeficiency virus type-1 (HIV-1) reverse transcriptase (RT) initiates reverse transcription from tRNA(Lys3). HIV-1 RT is a heterodimer consisting of two polypeptides, p66 and p51. In this work, the possible role of each subunit of RT in the interaction with its natural primer tRNA(Lys3) was studied. Two recombinant forms of HIV-1 RT, heterodimer p66/p51 and homodimer p51/p51, were used. Previously we have expressed and purified recombinant RT p51/p51 which possesses DNA polymerase activity [El Dirani-Diab, R., Andreola, M. L., Nevinsky, G., Tharaud, D., Barr, P. J., Litvak, S. & Tarrago-Litvak, L. (1992) FEBS Lett. 301, 23-28]. Here we show that HIV-1 RT p51/p51 displays certain properties very similar to the p66/p51 recombinant enzyme. The homodimer was able to anneal tRNA(Lys3) to the primer-binding site of the HIV-1 RNA template leading to a functional complex capable of synthesizing cDNA. Further, the p51/p51 enzyme behaved like RT p66/p51 concerning the strong inhibition produced by a non-nucleoside RT inhibitor. These data show that for RT p51/p51, one of the subunits of the homodimer adopts a conformation similar to the catalytic subunit (p66) present in the heterodimeric form. Part of this work was devoted to the study of the complex between the recombinant forms of HIV-1 RT and its primer tRNA. Each enzymatic form was cross-linked to tRNA(Lys3) in the presence of a platinum derivative, giving different ribonucleoprotein complexes of molecular masses higher than 100 kDa, suggesting that primer tRNA may interact with both subunits in the heterodimeric enzyme. After RNase A treatment of the complex RT p66/p51 x tRNA, the label was mainly found to migrate with the p66 subunit, although some cross-linking was also found associated to the p51 subunit. These results show that the p66 and p51 subunits of RT interact with tRNA(Lys3). Moreover, cross-linking of tRNA(Lys3) with HIV-1 RT p66/p51 in the presence of a DNA template containing the primer-binding-site sequence yielded an enzymatically active complex.