Biomedical subjects

P Gouet

Publications and source records attributed to P Gouet.

At least 19 recordsLinked to original sources

PubMed1999

Conformational changes induced by phosphorylation of the FixJ receiver domain.

BACKGROUND: A variety of bacterial adaptative cellular responses to environmental stimuli are mediated by two-component signal transduction pathways. In these phosphorelay cascades, histidine kinases transphosphorylate a conserved aspartate in the receiver domain, a conserved module in the response regulator superfamily. The main effect of this phosphorylation is to alter the conformation of the response regulator in order to modulate its biological function. The response regulator FixJ displays a typical modular arrangement, with a phosphorylatable N-terminal receiver domain and a C-terminal DNA-binding domain. In the symbiotic bacterium Sinorhizobium meliloti, phosphorylation of this response regulator activates transcription of nitrogen-fixation genes. RESULTS: The crystal structures of the phosphorylated and of the unphosphorylated N-terminal receiver domain of FixJ (FixJN) were solved at 2.3 A and 2.4 A resolution, respectively. They reveal the environment of the phosphoaspartate in the active site and the specific conformational changes leading to activation of the response regulator. Phosphorylation of the conserved aspartate induces major structural changes in the beta 4-alpha 4 loop, and in the signaling surface alpha 4-beta 5 that mediates dimerization of the phosphorylated full-length response regulator. A site-directed mutant at this protein-protein interface decreases the affinity of the phosphorylated response regulator for the fixK promoter tenfold. CONCLUSIONS: The cascade of phosphorylation-induced conformational changes in FixJN illustrates the role of conserved residues in stabilizing the phosphoryl group in the active site, triggering the structural transition and achieving the post-phosphorylation signaling events. We propose that these phosphorylation-induced conformational changes underly the activation of response regulators in general.

Amino Acid Sequence↗

PubMed1999

Structural transitions in the FixJ receiver domain.

BACKGROUND: Two-component signal transduction pathways are sophisticated phosphorelay cascades widespread in prokaryotes and also found in fungi, molds and plants. FixL/FixJ is a prototypical system responsible for the regulation of nitrogen fixation in the symbiotic bacterium Sinorhizobium meliloti. In microaerobic conditions the membrane-bound kinase FixL uses ATP to transphosphorylate a histidine residue, and the response regulator FixJ transfers the phosphoryl group from the phosphohistidine to one of its own aspartate residues in a Mg(2+)-dependent mechanism. RESULTS: Seven X-ray structures of the unphosphorylated N-terminal receiver domain of FixJ (FixJN) have been solved from two crystal forms soaked in different conditions. Three conformations of the protein were found. In the first case, the protein fold impairs metal binding in the active site and the structure reveals a receiver domain that is self-inhibited for catalysis. In the second conformation, the canonical geometry of the active site is attained, and subsequent metal binding to the protein induces minimal conformational changes. The third conformation illustrates a non-catalytic form of the protein where unwinding of the N terminus of helix alpha 1 has occurred. Interconversion of the canonical and self-inhibited conformations requires a large conformational change of the beta 3-alpha 3 loop region. CONCLUSIONS: These unphosphorylated structures of FixJN stress the importance of flexible peptide segments that delineate the active site. Their movements may act as molecular switches that define the functional status of the protein. Such observations are in line with structural and biochemical results obtained on other response regulator proteins and may illustrate general features that account for the specificity of protein-protein interactions.

Amino Acid Sequence↗

PubMed1999

The highly ordered double-stranded RNA genome of bluetongue virus revealed by crystallography.

The concentration of double-stranded RNA within the bluetongue virus core renders the genome segments liquid crystalline. Powder diffraction rings confirm this local ordering with a 30 A separation between strands. Determination of the structure of the bluetongue virus core serotype 10 and comparison with that of serotype 1 reveals most of the genomic double-stranded RNA, packaged as well-ordered layers surrounding putative transcription complexes at the apices of the particle. The outer layer of RNA is sufficiently well ordered by interaction with the capsid that a model can be built and extended to the less-ordered inner layers, providing a structural framework for understanding the mechanism of this complex transcriptional machine. We show that the genome segments maintain local order during transcription.

Animals↗

PubMed1999

ESPript: analysis of multiple sequence alignments in PostScript.

MOTIVATION: The program ESPript (Easy Sequencing in PostScript) allows the rapid visualization, via PostScript output, of sequences aligned with popular programs such as CLUSTAL-W or GCG PILEUP. It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information. RESULTS: ESPript can be run via a command file or a friendly html-based user interface. The program calculates an homology score by columns of residues and can sort this calculation by groups of sequences. It offers a palette of markers to highlight important regions in the alignment. ESPript can also paste information on residue conservation into coordinate files, for subsequent visualization with a graphics program. AVAILABILITY: ESPript can be accessed on its Web site at http://www.ipbs.fr/ESPript. Sources and helpfiles can be downloaded via anonymous ftp from ftp.ipbs.fr. A tar file is held in the directory pub/ESPript.

Amino Acid Sequence↗

PubMed1999

A chromodomain protein encoded by the arabidopsis CAO gene is a plant-specific component of the chloroplast signal recognition particle pathway that is involved in LHCP targeting.

A recessive mutation in Arabidopsis, named chaos (for chlorophyll a/b binding protein harvesting-organelle specific; designated gene symbol CAO), was isolated by using transposon tagging. Characterization of the phenotype of the chaos mutant revealed a specific reduction of pigment binding antenna proteins in the thylakoid membrane. These nuclear-encoded proteins utilize a chloroplast signal recognition particle (cpSRP) system to reach the thylakoid membrane. Both prokaryotes and eukaryotes possess a cytoplasmic SRP containing a 54-kD protein (SRP54) and an RNA. In chloroplasts, the homolog of SRP54 was found to bind a 43-kD protein (cpSRP43) rather than to an RNA. We cloned the CAO gene, which encodes a protein identified as Arabidopsis cpSRP43. The product of the CAO gene does not resemble any protein in the databases, although it contains motifs that are known to mediate protein-protein interactions. These motifs include ankyrin repeats and chromodomains. Therefore, CAO encodes an SRP component that is unique to plants. Surprisingly, the phenotype of the cpSRP43 mutant (i.e., chaos) differs from that of the Arabidopsis cpSRP54 mutant, suggesting that the functions of the two proteins do not strictly overlap. This difference also suggests that the function of cpSRP43 is most likely restricted to protein targeting into the thylakoid membrane, whereas cpSRP54 may be involved in an additional process(es), such as chloroplast biogenesis, perhaps through chloroplast-ribosomal association with chloroplast ribosomes.

Amino Acid Sequence↗

PubMed1998

The atomic structure of the bluetongue virus core.

The structure of the core particle of bluetongue virus has been determined by X-ray crystallography at a resolution approaching 3.5 A. This transcriptionally active compartment, 700 A in diameter, represents the largest molecular structure determined in such detail. The atomic structure indicates how approximately 1,000 protein components self-assemble, using both the classical mechanism of quasi-equivalent contacts, which are achieved through triangulation, and a different method, which we term geometrical quasi-equivalence.

Amino Acid Sequence↗

PubMed1998

Structural studies of orbivirus particles.

We are using crystallographic methods to investigate the structure of AHSV and BTV. Our initial approach was to investigate the structure of the major protein component of the viral core, VP7(T13). This trimeric protein has been studied in several crystal forms from both orbiviruses and reveals a structure made up of conserved domains, capable of conformational changes and possessing a cleavage site. Further crystallographic analyses of native particles have provided a picture of the VP7(T13) and VP3(T2) layers of the BTV core. The VP7(T13) layer consists of 260 trimers arranged rather symmetrically and possessing very similar structures, thereby following the rules of quasi equivalence. The VP3(T2) layer is thin and contains 120 copies of 100 kDa protein arranged as 60 approximate dimers. This type of icosahedral construction has not been observed before and appears to contain a genome which is highly ordered. We anticipate that all of these features will be common to AHSV.

African Horse Sickness Virus↗

PubMed1997

Structures of orbivirus VP7: implications for the role of this protein in the viral life cycle.

BACKGROUND: Bluetongue virus (BTV) is the prototypical virus of the genus orbivirus in the family Reoviridae and causes an economically important disease in domesticated animals, such as sheep. BTV is larger and more complex than any virus for which comprehensive atomic level structural information is available. Its capsid is made primarily from four structural proteins two of which, VP3 and VP7, form a core which remains intact as the virus penetrates the host cell. Each core particle contains 780 copies of VP7. The architecture of the trimeric VP7 molecule has been revealed by crystallographic analysis and is unlike other viral coat proteins reported to date. RESULTS: Two new crystal structures of VP7 have been solved, one (a cleavage product) at close to atomic resolution and the other at lower resolution. The VP7 subunit consists of two domains. The smaller, 'upper', domain is exposed on the core surface and has the beta jelly-roll motif common to many capsid proteins. The second, 'lower', domain is composed of a bundle of alpha helices. The cleavage product comprises the upper domain, which forms a rigid invariant trimeric fragment. The lower resolution structure of the intact molecule indicates that the alpha-helical domain can rotate about the linker to the upper domain to adopt radically different orientations with respect to the threefold axis in the intact protein. CONCLUSIONS: The crystal structures of VP7 reveal a remarkable mix of rigidity and flexibility that may provide insights towards understanding how VP7 interacts with the other capsid proteins of different stoichiometries. These results suggest that substantial conformational changes in VP7 occur at some stage in the viral life cycle. Such changes may be related to the central role that VP7 is likely to play in cell attachment and membrane penetration.

Bluetongue virus↗

PubMed1997

Competition between ruminal cellulolytic bacteria for adhesion to cellulose.

Competition for adhesion to cellulose among the three main ruminal cellulolytic bacterial species was studied using differential radiolabeling (14C/3H) of cells. When added simultaneously to cellulose, Ruminococcus flavefaciens FD1 and Fibrobacter succinogenes S85 showed some competition; however, both species were surpassed competitively by Ruminococcus albus 20. When R. flavefaciens FD1 and F. succinogenes S85 were already adherent, R. albus 20 adhesion occurred without inhibition but involved R. flavefaciens FD1 detachment.

Animals↗

PubMed1997

Structural analysis of compound I in hemoproteins: study on Proteus mirabilis catalase.

Ferryl catalysis has attracted considerable interest, because a diverse variety of enzymes use ferryl intermediates to perform difficult chemistry. The structure of the reactional intermediate compound I of Proteus mirabilis catalase (PMC) has been solved using time-resolved X-ray diffraction techniques and single crystal microspectrophotometry. Formation of compound I is characterized by significant changes in the absorbance spectrum, and the creation of an oxoferryl group on the distal side of the heme. This group is clearly visible in the X-ray electron density maps. An unidentified electron density, likely to be an anion because of the nature of its environment, appears during the reaction, in a site distant from the heme. The structure of compound I in PMC is compared with that of compound I in cytochrome c peroxidase (CCP).

Catalase↗

PubMed1996

Quantitative determination of H2-utilizing acetogenic and sulfate-reducing bacteria and methanogenic archaea from digestive tract of different mammals.

Total number of bacteria, cellulolytic bacteria, and H2-utilizing microbial populations (methanogenic archaea, acetogenic and sulfate-reducing bacteria) were enumerated in fresh rumen samples from sheep, cattle, buffaloes, deer, llamas, and caecal samples from horses. Methanogens and sulfate reducers were found in all samples, whereas acetogenes were not detected in some samples of each animal. Archaea methanogens were the largest H2-utilizing populations in all animals, and a correlation was observed between the numbers of methanogens and those of cellulolytic microorganisms. Higher counts of acetogens were found in horses and llamas (1 x 10(4) and 4 x 10(4) cells ml-1 respectively).

Acetates↗

PubMed1996

Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy.

Various enzymes use semi-stable ferryl intermediates and free radicals during their catalytic cycle, amongst them haem catalases. Structures for two transient intermediates (compounds I and II) of the NADPH-dependent catalase from Proteus mirabilis (PMC) have been determined by time-resolved X-ray crystallography and single crystal microspectrophotometry. The results show the formation and transformation of the ferryl group in the haem, and the unexpected binding of an anion during this reaction at a site distant from the haem.

Binding Sites↗

PubMed1996

Crystal structure of the top domain of African horse sickness virus VP7: comparisons with bluetongue virus VP7.

The baculovirus-expressed core protein VP7 of African horse sickness virus serotype 4 (AHSV-4) has been purified to homogeneity and crystallized in the presence of 2.8 M urea. The X-ray structure has been solved to a 2.3-Angstroms (1 Angstrom = 0.1 nm) resolution with an Rfactor of 19.8%. The structure of AHSV VP7 reveals that during crystallization, the two-domain protein is cleaved and only the top domain remains. A similar problem was encountered previously with bluetongue virus (BTV) VP7 (whose structure has been reported), showing that the connections between the top and the bottom domains are rather weak for these two distinct orbiviruses. The top domains of both BTV and AHSV VP7 are trimeric and structurally very similar. The electron density maps show that they both possess an extra electron density feature along their molecular threefold axes, which is most likely due to an unidentified ion. The characteristics of the molecular surface of BTV and AHSV VP7 suggest why AHSV VP7 is much less soluble than BTV VP7 and indicate the possibility of attachment to the cell via attachment of an Arg-Gly-Asp (RGD) motif in the top domain of VP7 to a cellular integrin for both of these orbiviruses.

African Horse Sickness Virus↗

PubMed1996

Effects of a strain of Saccharomyces cerevisiae (Levucell SC1), a microbial additive for ruminants, on lactate metabolism in vitro.

The effect of Levucell SC, a strain of Saccharomyces cerevisiae marked as a feed additive for ruminants, was investigated in vitro on lactate metabolism by the ruminal bacteria Streptococcus bovis and Megasphaera elsdenii. The coculture between 10(7) live cells x mL(-1) of SC and a Streptococcus bovis strain in the presence of glucose reduced lactate production by the bacterial strain. Live yeast cells were able to compete with Streptococcus bovis for glucose utilization in strictly anaerobic conditions, so less glucose was available for the bacterium. SC also stimulated L-lactate utilization by a strain of M. elsdenii. The effect depended on the concentration of yeast cells added. Bacterial growth and fermentation end-product concentrations were also increased in the presence of SC. Some amino acids and vitamins, but not dicarboxylic acids, stimulated the bacterial specific activity of L-lactate uptake. SC was able to provide amino acids to M. elsdenii. In a coculture of Streptococcus bovis and M. elsdenii on glucose, the reduction of lactate concentration was improved by SC, the same trend being observed when maltose or soluble starch were used as carbon and energy source. These results indicate that SC can be a very useful tool to reduce lactate accumulation in vitro during fermentation of soluble sugars.

Acetates↗

PubMed1995

Simulations of electron transfer in the NADPH-bound catalase from Proteus mirabilis PR.

Catalase-bound NADPH both prevents and reverses the accumulation of compound II, an inactive form of catalase that is generated from the normal active intermediate form (compound I) when catalase is exposed to a steady flow of hydrogen peroxide. The mechanism for the regeneration reaction is unknown although NADPH could act either as a one-electron or a two-electron donor. Recently, a reaction scheme has been proposed in which the formation of compound II from compound I generates a neighboring radical species within the protein. NADPH would then donate two electrons, one to compound II for reduction of the iron and the other to the protein free radical. In this paper, we report calculations to find the dominant electron tunneling pathways between NADPH and the heme iron in the catalase from the peroxide-resistant mutant of Proteus mirabilis. Two major tunneling pathways are found which fuse together on Ser-196. It is suggested that the sequence Gly-Ser of the loop that divides the beta 5-strand is the key element for shielding a radical amino acid.

Algorithms↗

PubMed1995

Most probable number enumeration of H2-utilizing acetogenic bacteria from the digestive tract of animals and man.

A method is proposed that allows the enrichment and most probable number estimation of H2/CO2(-)utilizing acetogenic bacteria. It is based on the difference in acetate production for serial dilutions incubated under either a test H2/CO2 (4:1), or a control N2/CO2 (4:1) headspace atmosphere. A nutritionally non-selective medium was used, containing bromoethane-sulfonic acid as inhibitor of methanogenic archaea and 10% pre-incubated clarified rumen fluid. Acetogenic bacteria were enumerated in rumen and hindgut contents of animals and in human feces. They ranged from below 10(2) to above 10(8) per gram wet weight gut content and their population levels were the highest in the absence of methanogenesis. The method described therein should prove useful to better understand the diversity and ecological importance of dominant gut acetogens.

Acetates↗

PubMed1995

Viral envelope glycoproteins swing into action.

Analysis of tick-borne encephalitis virus E protein reveals considerable structural diversity in the glycoproteins that clothe enveloped viruses and hints at the conformational gyrations in this molecule that lead to viral fusion.

Animals↗

PubMed1995

Crystal structure of Proteus mirabilis PR catalase with and without bound NADPH.

A catalase from a peroxide resistant mutant of Proteus mirabilis binds NADPH tightly. Interestingly, this enzyme can be stripped of NADPH without loss of the catalatic activity. It is the only known non-mammalian catalase able to bind NADPH. The structure without cofactor was solved by molecular replacement using the structure of beef liver catalase as a model. The structure was refined to an R-factor of 19.3% in the range 8 to 2.2 A resolution. According to the sequence, a methionine sulphone was positioned in the haem active site. This oxidized form of methionine is particular to Proteus mirabilis catalase and likely to produce some steric hindrance in the active site. Two important water molecules are positioned in the haem distal site. These two water molecules are not located in the structure of beef liver catalase, but are supposed to account for the catalytic mechanism. The liganded form was obtained by soaking crystals of the unliganded form into an NADPH solution. The structure was refined to an R-factor of 15.9% in the range of 8 to 3.1 A resolution using the unliganded structure as a model. The NADPH was clearly located in the electron density map with the same conformation as in beef liver catalase. The NADPH binding induces slight structural changes. However, the imidazole ring of a histidine residue (His284) rotates about 50 degrees to accommodate the cofactor. The electron transfer from NADPH to the haem molecule was examined and several pathways are proposed.

Amino Acid Sequence↗