Biomedical subjects

D de Vienne

Publications and source records attributed to D de Vienne.

At least 19 recordsLinked to original sources

PubMed2001

Optimisation of enzyme concentrations for unbranched reaction chains: the concept of combined response coefficient.

In the metabolic control theory, the control coefficient is a key parameter in quantifying the sensitivity of the flux towards an infinitesimal variation of enzyme activity. This concept does not apply just as it is for variations of enzyme concentrations whenever there is spatial, energy or resources limitations in the cell. Due to constraint on total enzyme concentration, the variation of concentration of any given enzyme may affect the concentrations of other enzymes. To take into account these correlations between enzyme concentrations, we propose the concept of "combined response coefficient". Its definition is similar to that of the control coefficient, but its mathematical expression is different. Its range of variation is from -infinity to +1, the null value corresponding to optimum enzyme concentration, i.e. to concentrations that maximise the flux, and the negative values to concentrations beyond the optimum value. A summation property could be derived using a simple weighting of the combined response coefficients, the sum of the weighed coefficient being 0.

Energy Metabolism↗

PubMed2001

Genetic and nongenetic bases for the L-shaped distribution of quantitative trait loci effects.

The L-shaped distribution of estimated QTL effects (R(2)) has long been reported. We recently showed that a metabolic mechanism could account for this phenomenon. But other nonexclusive genetic or nongenetic causes may contribute to generate such a distribution. Using analysis and simulations of an additive genetic model, we show that linkage disequilibrium between QTL, low heritability, and small population size may also be involved, regardless of the gene effect distribution. In addition, a comparison of the additive and metabolic genetic models revealed that estimates of the QTL effects for traits proportional to metabolic flux are far less robust than for additive traits. However, in both models the highest R(2)'s repeatedly correspond to the same set of QTL.

Linkage Disequilibrium↗

PubMed2000

Proteomics: a link between genomics, genetics and physiology.

Thanks to spectacular advances in the techniques for identifying proteins separated by two-dimensional electrophoresis and in methods for large-scale analysis of proteome variations, proteomics is becoming an essential methodology in various fields of plant biology. In the study of pleiotropic effects of mutants and in the analysis of responses to hormones and to environmental changes, the identification of involved metabolic pathways can be deduced from the function of affected proteins. In molecular quantitative genetics, proteomics can be used to map translated genes and loci controlling their expression, which can be used to identify proteins accounting for the variation of complex phenotypic traits. Linking gene expression to cell metabolism on the one hand and to genetic maps on the other, proteomics is a central tool for functional genomics.

Genomics↗

PubMed1999

Proteomics for genetic and physiological studies in plants.

Proteomics is becoming a necessity in plant biology, as it is in medicine, zoology and microbiology, for deciphering the function and role of the genes that are or will be sequenced. In this review we focus on the various, mainly genetic, applications of the proteomic tools that have been developed in recent years: characterization of individuals or lines, estimation of genetic variability within and between populations, establishment of genetic distances that can be used in phylogenetic studies, characterization of mutants and localization of the genes encoding the revealed proteins. Improvements in specifically devoted software have permitted precise quantification of the variation in amounts of proteins, leading to the concept of "protein quantity loci" which, combined with the "quantitative trait loci" approach, results in testable hypotheses regarding the role of "candidate proteins" in the metabolism or phenotype under study. This new development is exemplified by the reaction of plants to drought, a trait of major agronomic interest. The accumulation of data regarding genomic and cDNA sequencing will be connected to the protein databases currently developed in plants.

Chromosome Mapping↗

PubMed1999

Fluxes and metabolic pools as model traits for quantitative genetics. I. The L-shaped distribution of gene effects.

The fluxes through metabolic pathways can be considered as model quantitative traits, whose QTL are the polymorphic loci controlling the activity or quantity of the enzymes. Relying on metabolic control theory, we investigated the relationships between the variations of enzyme activity along metabolic pathways and the variations of the flux in a population with biallelic QTL. Two kinds of variations were taken into account, the variation of the average enzyme activity across the loci, and the variation of the activity of each enzyme of the pathway among the individuals of the population. We proposed analytical approximations for the flux mean and variance in the population as well as for the additive and dominance variances of the individual QTL. Monte Carlo simulations based on these approximations showed that an L-shaped distribution of the contributions of individual QTL to the flux variance (R(2)) is consistently expected in an F(2) progeny. This result could partly account for the classically observed L-shaped distribution of QTL effects for quantitative traits. The high correlation we found between R(2) value and flux control coefficients variance suggests that such a distribution is an intrinsic property of metabolic pathways due to the summation property of control coefficients.

Enzymes↗

PubMed1998

Characterization of storage proteins in Daucus carota L.: two novel proteins display zygotic embryo specificity.

Although maturation-related proteins are well known in the endosperm of albuminous seeds, an important question is whether the zygotic embryo possesses its own maturation proteins. We report on the isolation and partial characterization of storage proteins of carrot (Daucus carota L. var Nandor) dry achenes and isolated zygotic embryos, using one- and two-dimensional electrophoresis techniques, HPLC and amino acid sequencing. The presence of a series of abundant polypeptides showing charge heterogeneity, that are rapidly degraded upon germination, was revealed in the endosperm. These proteins consisted of glycoproteins, the most abundant of which displayed a molecular mass (M(r)) of 58,000, albumins of M(r) 42,000 comprising at least one beta-1,3-glucanase, and two globulins of M(r) 90,000 and 50,000-55,000 respectively, the second being an oligomer composed of three subunits of M(r) 13,000, 20,000 and 30,000. None of these storage proteins identified in the endosperm were detected in zygotic embryos. In contrast, two novel proteins were isolated from zygotic embryos, namely a globulin family of M(r) 50,000 and pI 6.3-6.8, which was named "daucin", and a late embryogenesis abundant (LEA) protein family of M(r) 25,000 and pI 6.3-6.6, named "RAB25". Since the latter proteins are apparently absent of the endosperm, these results suggest that the maturation of carrot zygotic embryos requires its own specific set of storage and LEA proteins.

Albumins↗

PubMed1998

Somatic and zygotic embryos of Daucus carota L. display different protein patterns until conversion to plants.

Total protein patterns of different developmental stages of carrot zygotic and somatic embryos revealed by one- and two-dimensional gel electrophoresis were compared using statistical dissimilarity index matrix, and some major polypeptides were partially sequenced. In spite of similar morphology, the protein patterns of somatic embryos at the torpedo stage were clearly different from those of zygotic embryos. In particular, none of the proteins specific of zygotic embryos required for maturation, previously identified, were accumulated in somatic embryos, namely the daucin (a globulin-type storage protein), the RAB25 protein (a late embryogenesis abundant protein) (Dodeman et al. 1998), as well as a novel globulin of M(r) 30,000, that we proposed to name apiacin. Somatic plantlets and seedlings also showed different patterns. This discrepancy likely reflects culture conditions, since somatic embryos recover a protein pattern close to that of seedlings after conversion to plant and growth on a carbon-free medium.

Daucus carota↗

PubMed1996

Amino acid analysis of proteins separated by two-dimensional electrophoresis in maize: isoform detection and function identification.

The possibility of using experimentally determined amino acid composition to assess relatedness between 75 proteins separated by two-dimensional electrophoresis (2-DE) and to identify them was tested on maize. Two independent parameters, the relative Euclidean distance and the correlation coefficient between the amino acid compositions, were evaluated and used. Previous sequence information for 31 out of the 75 proteins made it possible to evaluate the method for the detection of isoforms and for identification. However, the extension of the interrogation beyond maize to all plant sequences raised the problem of false positives that could nevertheless be limited by replications and by using additional information. The efficiency of the method to assess relatedness between proteins should make amino acid composition analysis a valuable tool in large protein characterization programs based on 2-DE, by facilitating the transfer of information from one well-documented organ/tissue or genotype to another.

Amino Acids↗

PubMed1995

Characterizing allelic proteins for genome mapping in maize.

Mapping cDNA probes in order to construct genetic linkage maps is becoming a widespread strategy for genome analysis and gene isolation, particularly in cultivated plant species. Nevertheless, almost all cDNAs reveal two or more unlinked loci, making it difficult to identify the gene(s) actually expressed. In a highly polymorphic species, such as maize, two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) of proteins may circumvent this limitation. With the analysis of various segregating populations, we previously showed that the apparent position shifts of proteins on the 2-D gels are monogenic and codominant. In this paper we compared allelic proteins on the basis of their high performance liquid chromatography (HPLC) profile and partial amino acid sequences. In a sample of 20 position shifts, the allelic proteins appeared to be similar in all but one case, strongly suggesting that polymorphism of structural genes is involved. Thus 2-D PAGE could prove to be a useful tool for genome mapping: when a cDNA probe detects several loci, a position shift of the encoded protein will allow the identification of the gene translated in the organ considered.

Alleles↗

PubMed1994

Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression.

A methodology to dissect the genetic architecture of quantitative variation of numerous gene products simultaneously is proposed. For each individual of a segregating progeny, proteins extracted from a given organ are separated using two-dimensional electrophoresis, and their amounts are estimated with a computer-assisted system for spot quantification. Provided a complete genetic map is available, statistical procedures allow determination of the number, effects and chromosomal locations of factors controlling the amounts of individual proteins. This approach was applied to anonymous proteins of etiolated coleoptiles of maize, in an F2 progeny between two distant lines. The genetic map included both restriction fragment length polymorphism and protein markers. Minimum estimates of one to five unlinked regulatory factors were found for 42 of the 72 proteins analyzed, with a large diversity of effects. Dominance and epistasis interactions were involved in the control of 38% and 14% of the 72 proteins, respectively. Such a methodology might help understanding the architecture of regulatory networks and the possible adaptive or phenotypic significance of the polymorphism of the genes involved.

Chromosome Mapping↗

PubMed1994

Mapping factors controlling genetic expression.

A methodology relying on two-dimensional (2D) electrophoresis and genetic mapping is proposed to dissect the genetic architecture of the quantitative control of gene products. Seventy-two anonymous polypeptide spots resolved using silver-stained high-resolution 2D gels of maize coleoptile extracts were automatically quantified for every individual of an F2 progeny between distant lines. A complete genetic linkage map, including 70 RFLP and 39 protein markers, allowed us to map Mendelian factors underlying quantitative variation for 42 polypeptides. One to 5 unlinked chromosomal regions were found to affect single polypeptides, 27% of which resulted in more than a doubling of the polypeptide spot intensity. Dominance was observed for half of the factors, with high amount dominant over low amount in most cases, which is consistent with the observation that the relative abundance of proteins in F1 hybrids is in average deviated to the high parental values. Epistatic interactions were shown to be involved in the control of 14% of the proteins. These features contrast sharply with the observations from 20 agromorphological traits measured in the same progeny, where limited substitution and dominance effects, and no epistatic interaction, were found.

Alleles↗

PubMed1993

Analysis of scaling methods to minimize experimental variations in two-dimensional electrophoresis quantitative data: application to the comparison of maize inbred lines.

The analysis of two-dimensional (2-D) electrophoresis quantitative data from a design involving 21 maize genotypes revealed a significant experimental variation. In order to minimize this variation, we investigated the possible causes and found that it was essentially due to global effects, affecting all the spots in a gel in a similar way, and occurring during the 2-D run/staining procedure. Three scaling methods to discard these experimental variations were analyzed: the linear scaling method, a method based on principal component analysis, and a combined method that unites the advantages of both of the former. Comparing these three methods, we found that they led to consistent results with regard to the factor under study, i.e. the genetic factor in our case. However, the combined scaling method was the most efficient in reducing experimental variations.

Data Interpretation, Statistical↗

PubMed1992

Characterization of a Novel Protein Induced by Progressive or Rapid Drought and Salinity in Brassica napus Leaves.

Under progressive drought stress, Brassica napus displays differential leaf modifications. The oldest leaves, developed before the onset of water deficit, wilt gradually, whereas the youngest leaves harden. Hardening was distinguished by leaf turgor and bluish wax bloom when the shoot water potential was below -3 MPa and the leaf water saturation deficit was about 60%. This adaptive change was accompanied by modifications in two-dimensional protein profiles. Ten percent of the polypeptides had altered abundance or were unique to drought-stressed plants. Two-dimensional analysis of in vitro translation products did not reveal a general decrease in mRNA population. A 22-kD double polypeptide was increased by progressive or rapid water stress and salinity and disappeared upon rehydration. These polypeptides have a common N-terminal sequence, which does not reveal homology with any known water-stress protein but which contains the signature motif of soybean Künitz trypsin inhibitors. Immunoprecipitation allowed these polypeptides to be identified on two-dimensional gels of in vitro translation products. They appeared to be synthesized as a 24-kD precursor, and their transcript was present in the control well-watered leaves, where the polypeptides were never detected, indicating a possible translational regulation. A putative function of this protein, named BnD22, in the retardation of drought-induced leaf senescence is discussed.

Journal Article↗

PubMed1992

A Brassica napus transcript encoding a protein related to the Künitz protease inhibitor family accumulates upon water stress in leaves, not in seeds.

A cDNA clone encoding a Brassica napus drought-induced 22 kDa (BnD22) protein has been isolated and characterized. The BnD22 transcript accumulated in response to drought reversibly, and to other conditions of leaf water deficit such as rapid water stress or salt acclimation, but not to cold acclimation or heat shock. Exogenously applied abscisic acid induced both changes in leaf morphology similar to the drought-adaptive response and a pronounced accumulation of the BnD22 mRNA. In control and drought-adapted plants, the BnD22 transcript was expressed in an organ-specific manner: the mRNA level was highest in leaves, low in hypocotyls and undetectable in roots. Sequence analysis indicates that the BnD22 protein is related to the Künitz family of protease inhibitors. In contrast to most members of this family, and also to most polypeptides expressed in vegetative tissues upon drought, the BnD22 mRNA was absent in seeds, before or during the seed desiccation phase. The BnD22 gene represents a new class of genes which are strictly induced in vegetative tissues upon environmental stress, and its pattern of expression shows that the responses to water deficit differ, at least partially, in seeds and in leaves.

Amino Acid Sequence↗

PubMed1988

Genetic aspects of variation of protein amounts in maize and pea.

Using high-resolution two-dimensional polyacrylamide gel electrophoresis we studied the polymorphism of protein amounts in some genotypes of maize and pea. This type of variability seems to be rather common and insensitive to environmental conditions, as attested by the comparison of the patterns of two maize lines harvested in two different years. A large-scale experiment involving 5 lines, 7 of their hybrids, and 6 organs (or physiological stages) of maize allowed us to examine numerous polypeptides regarding their genetic variability, their amount differences between organs and the inheritance of their abundance. Genetic and organ variations are not independent: polypeptides whose amount varies from one organ to another are, for the most part, genetically variable (59%), while the stable polypeptides are not often genetically variable (18%). We found a striking organ specificity for (i) the extent of quantitative variability (from 2.3-15.4% of the polypeptides), (ii) the occurrence and the type of variation for a given polypeptide (an intensity difference seen in an organ can disappear or even be reversed in another one), (iii) the kind of inheritance (additive/non-additive): combining the 6 organs and the 7 hybrids we found 101 cases of non-additivity (4% of the total) which concern as many as 72 different spots, that is to say that in most cases a polypeptide displaying nonadditivity in an organ seems to display additivity in the other ones. Moreover, for most of the polypeptides with nonadditive inheritance the hybrid spot presents an intensity similar to that of the most intense parental spot.(ABSTRACT TRUNCATED AT 250 WORDS)

Electrophoresis, Gel, Two-Dimensional↗

PubMed1988

Differential Two-Dimensional Protein Patterns as Related to Tissue Specificity and Water Conditions in Brassica napus var oleifera Root System.

Differential two-dimensional protein patterns as related to tissue specificity and water conditions were investigated within Brassica napus var oleifera root system. The different parts of the root system (tap root, lateral roots, and drought-induced short roots) were analyzed under various moisture regimes (regular watering at field capacity, progressive drought stress, and rewatering). Tissue specificity was evident from 25 differences in protein patterns (qualitative and quantitative) between well-watered lateral and tap roots. Twice as many polypeptides (52) were drought-affected and the response to the water stress was shown to be similar in both root types. In addition, more than half of the polypeptides detected as organ-specific were affected by drought. Based upon the trend of variation observed under drought and rehydration, three categories of polypeptides could be defined that might be differently involved in drought susceptibility or tolerance. A highly differentiated protein pattern characterized the drought-induced short roots. This pattern appeared as far from the watered as from the water-stressed normal roots. In particular, 13 unique polypeptides were detected which could be relevant to their adaptive morphogenesis and/or their specific drought tolerance induction. Upon rehydration, their polypeptide pattern and their specific morphology returned to a normal well-watered lateral root type.

Journal Article↗

PubMed1987

Drought-Induced Changes in Protein Patterns of Brassica napus var. oleifera Roots.

Drought-induced changes in two-dimensional silver stained protein patterns of Brassica napus L. var. oleifera M. root system were detected both at quantitative and qualitative levels. Particularly, 13 new polypeptides of low molecular weight were evidenced in the drought-stressed tap root, 12 of which were also present in the short tuberized roots, a specific drought-induced root type. The reversibility of these modifications, observed after 3 days rehydration, suggests that they might be involved in drought tolerance.

Journal Article↗

PubMed1986

Silver staining of proteins: standardized procedure for two-dimensional gels bound to polyester sheets.

A system for the simultaneous silver staining of numerous two-dimensional gels bound to polyester sheets is proposed. Under controlled conditions, a very good reproducibility of staining can be obtained, even between different experiments. Procedures to avoid artifacts due to polyester sheets (background, silver mirror, and vertical streaking) are described.

Electrophoresis, Polyacrylamide Gel↗