Marie-France Giraud

The rhamnose pathway

L-Rhamnose is a deoxy sugar found widely in bacteria and plants. Evidence continues to emerge about its essential role in many pathogenic bacteria. The crystal structures of two of the four enzymes involved in its biosynthetic pathway have been reported and the other two have been submitted for publication. This pathway does not exist in humans, making enzymes of this pathway very attractive targets for therapeutic intervention.

Is there a relationship between the supramolecular organization of the mitochondrial ATP synthase and the formation of cristae

Blue native polyacrylamide gel electrophoresis (BN-PAGE) analyses of detergent mitochondrial extracts have provided evidence that the yeast ATP synthase could form dimers. Cross-linking experiments performed on a modified version of the i-subunit of this enzyme indicate the existence of such ATP synthase dimers in the yeast inner mitochondrial membrane. We also show that the first transmembrane segment of the eukaryotic b-subunit (bTM1), like the two supernumerary subunits e and g, is required for dimerization/oligomerization of ATP synthases. Unlike mitochondria of wild-type cells that display a well-developed cristae network, mitochondria of yeast cells devoid of subunits e, g, or bTM1 present morphological alterations with an abnormal proliferation of the inner mitochondrial membrane. From these observations, we postulate that an anomalous organization of the inner mitochondrial membrane occurs due to the absence of ATP synthase dimers/oligomers. We provide a model in which the mitochondrial ATP synthase is a key element in cristae morphogenesis.

RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase

Deoxythymidine diphosphate (dTDP)-l-rhamnose is the precursor of l-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. dTDP-l-rhamnose is synthesized from glucose-1-phosphate and deoxythymidine triphosphate (dTTP) via a pathway involving four distinct enzymes. This pathway does not exist in humans and the enzymes involved in dTDP-l-rhamnose synthesis are potential targets for the design of new therapeutic agents. Here, the crystal structure of dTDP-6-deoxy-d-xylo-4-hexulose 3,5 epimerase (RmlC, EC5.1.3.13) from Salmonella enterica serovar Typhimurium was determined. The third enzyme of the rhamnose biosynthetic pathway, RmlC epimerizes at two carbon centers, the 3 and 5 positions of the sugar ring. The structure was determined by multiwavelength anomalous diffraction to a resolution of 2.17 Å. RmlC is a dimer and each monomer is formed mainly from two β-sheets arranged in a β-sandwich. The structure of a dTDP-phenol–RmlC complex shows the substrate-binding site to be located between the two β-sheets; this site is formed from residues of both monomers. Sequence alignments of other RmlC enzymes confirm that this region is very highly conserved. The enzyme is distinct structurally from other epimerases known and thus, is the first example of a new class of carbohydrate epimerase.

Epimerases: structure, function and mechanism

Abstract. Carbohydrates are ideally suited for molecular recognition. By varying the stereochemistry of the hydroxyl substituents, the simple six-carbon, six-oxygen pyranose ring can exist as 10 different molecules. With the further addition of simple chemical changes, the potential for generating distinct molecular recognition surfaces far exceeds that of amino acids. This ability to control and change the stereochemistry of the hydroxyl substituents is very important in biology. Epimerases can be found in animals, plants and microorganisms where they participate in important metabolic pathways such as the Leloir pathway, which involves the conversion of galactose to glucose-1-phosphate. Bacterial epimerases are involved in the production of complex carbohydrate polymers that are used in their cell walls and envelopes and are recognised as potential therapeutic targets for the treatment of bacterial infection. Several distinct strategies have evolved to invert or epimerise the hydroxyl substituents on carbohydrates. In this review we group epimerisation by mechanism and discuss in detail the molecular basis for each group. These groups include enzymes which epimerise by a transient keto intermediate, those that rely on a permanent keto group, those that eliminate then add a nucleotide, those that break then reform carbon-carbon bonds and those that linearize and cyclize the pyranose ring. This approach highlights the quite different biochemical processes that underlie what is seemingly a simple reaction. What this review shows is that each position on the carbohydrate can be epimerised and that epimerisation is found in all organisms.

Crystal Structure of the Mg·ADP-inhibited State of the Yeast F1c10-ATP Synthase

The F1c10 subcomplex of the yeast F1F0-ATP synthase includes the membrane rotor part c10-ring linked to a catalytic head, (αβ)3, by a central stalk, γδϵ. The Saccharomyces cerevisiae yF1c10·ADP subcomplex was crystallized in the presence of Mg·ADP, dicyclohexylcarbodiimide (DCCD), and azide. The structure was solved by molecular replacement using a high resolution model of the yeast F1 and a bacterial c-ring model with 10 copies of the c-subunit. The structure refined to 3.43-Å resolution displays new features compared with the original yF1c10 and with the yF1 inhibited by adenylyl imidodiphosphate (AMP-PNP) (yF1(I–III)). An ADP molecule was bound in both βDP and βTP catalytic sites. The αDP-βDP pair is slightly open and resembles the novel conformation identified in yF1, whereas the αTP-βTP pair is very closed and resembles more a DP pair. yF1c10·ADP provides a model of a new Mg·ADP-inhibited state of the yeast F1. As for the original yF1 and yF1c10 structures, the foot of the central stalk is rotated by ∼40 ° with respect to bovine structures. The assembly of the F1 central stalk with the F0 c-ring rotor is mainly provided by electrostatic interactions. On the rotor ring, the essential cGlu59 carboxylate group is surrounded by hydrophobic residues and is not involved in hydrogen bonding.

Supramolecular organization of the yeast F1Fo‐ATP synthase

Background information. The yeast mitochondrial F1Fo‐ATP synthase is a large complex of 600 kDa that uses the proton electrochemical gradient generated by the respiratory chain to catalyse ATP synthesis from ADP and Pi. For a large range of organisms, it has been shown that mitochondrial ATP synthase adopts oligomeric structures. Moreover, several studies have suggested that a link exists between ATP synthase and mitochondrial morphology.

Structure of ubiquitin-conjugating enzyme 9 displays significant differences with other ubiquitin-conjugating enzymes which may reflect its specificity for sumo rather than ubiquitin.

The three-dimensional structure of ubiquitin-conjugating enzyme 9 (Ubc9) has been obtained to a resolution of 2.8 A by molecular replacement followed by a combination of automated refinement and graphical intervention. Diffraction data were recorded on a single crystal in space group P43 with cell dimensions a = b = 73.9, c = 42. 9 A. The final model has an R factor of 21.3% for all data to 2.8 A. Only the N-terminal methionine, a two-residue N-terminal extension and a four-residue loop are not located by the final electron-density map. Ubc9 is now known to be the first sumo, a new ubiquitin-like protein, conjugating enzyme and does not conjugate ubiquitin. The structure of Ubc9 shows important differences compared with the structures of known ubiquitin-conjugating enzymes. At the N-terminal helix, the structural and sequence alignments are out of register by one amino acid giving Ubc9 a different recognition surface compared to ubiquitin-conjugating enzymes. This is coupled to a profound change in the electrostatic surface of the molecular face remote from the catalytic site. These differences may be important in recognition of other proteins in the Sumo conjugation pathway. The catalytic cysteine in Ubc9 has a positively charged lip and a negatively charged ridge nearby. Both these features seem confined to sumo-conjugating enzymes, and a sequence alignment of sumo and ubiquitin suggests how these might play a role in sumo/ubiquitin discrimination.

A γ2(R43Q) Mutation, Linked to Epilepsy in Humans, Alters GABAA Receptor Assembly and Modifies Subunit Composition on the Cell Surface

Genetic defects leading to epilepsy have been identified in γ2 GABAA receptor subunit. A γ2(R43Q) substitution is linked to childhood absence epilepsy and febrile seizure, and a γ2(K289M) mutation is associated with generalized epilepsy with febrile seizures plus. To understand the effect of these mutations, surface targeting of GABAA receptors was analyzed by subunit-specific immunofluorescent labeling of living cells. We first transfected hippocampal neurons in culture with recombinant γ2 constructs and showed that the γ 2(R43Q) mutation prevented surface expression of the subunit, unlike γ2(K289M) substitution. Several γ2-subunit constructs, bearing point mutations within the Arg-43 domain, were expressed in COS-7 cells with α3- and β3-subunits. R43Q and R43A substitutions dramatically reduced surface expression of the γ2-subunit, whereas R43K, P44A, and D39A substitutions had a lesser, but still significant, impact and K289M substitution had no effect. Whereas the mutant γ2(R43Q) was retained within intracellular compartments, αβ complexes were still targeted at the cell membrane. Coimmunoprecipitation experiments showed that γ2(R43Q) was able to associate with α3- or β3-subunits, although the stoichiometry of the complex with α3 was altered. Our data show that γ2(R43Q) is not a dominant negative and that the mutation leads to a modification of GABAA receptor subunit composition on the cell surface that impairs the synaptic targeting in neurons. This study reveals an involvement of the γ2-Arg-43 domain in the control of receptor assembly that may be relevant to the effect of the heterozygous γ2(R43Q) mutation leading to childhood absence epilepsy and febrile seizure.

Overexpression, purification, crystallization and preliminary structural study of dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD), the fourth enzyme of the dTDP-L-rhamnose synthesis pathway, from Salmonella enterica serovar Typhimurium

L-Rhamnose is an essential component of the cell wall of many pathogenic bacteria. Its precursor, dTDP-L-rhamnose, is synthesized from alpha-D-glucose-1-phosphate and dTTP via a pathway requiring four distinct enzymes: RmlA, RmlB, RmlC and RmlD. RmlD catalyses the terminal step of this pathway by converting dTDP-6-deoxy-L-lyxo-4-hexulose to dTDP-L-rhamnose. RmlD from -Salmonella enterica serovar Typhimurium has been overexpressed in Escherichia coli. The recombinant protein was purified by a two--step protocol involving anion-exchange and hydrophobic chromatography. Dynamic light-scattering experiments indicated that the recombinant protein is monodisperse. Crystals of native and selenomethionine-enriched RmlD have been obtained using the sitting-drop vapour-diffusion method with polyethylene glycol as precipitant. Diffraction data have been collected from orthorhombic crystals of both native and selenomethionyl-derivatized protein, allowing tracing of the protein structure.

F1‐catalysed ATP hydrolysis is required for mitochondrial biogenesis in Saccharomyces cerevisiae growing under conditions where it cannot respire

Mutant strains of yeast Saccharomyces cerevisiae lacking a functional F1‐ATPase were found to grow very poorly under anaerobic conditions. A single amino acid replacement (K222 > E222) that locally disrupts the adenine nucleotide catalytic site in the β‐F1 subunit was sufficient to compromise anaerobic growth. This mutation also affected growth in aerated conditions when ethidium bromide (an intercalating agent impairing mtDNA propagation) or antimycin (an inhibitor of respiration) was included in the medium. F1‐deficient cells forced to grow in oxygen‐limited conditions were shown to lose their mtDNA completely and to accumulate Hsp60p mainly under its precursor form. Fluorescence microscopy analyses with a modified GFP containing a mitochondrial targeting presequence revealed that aerobically growing F1‐deficient cells stopped importing the GFP when antimycin was added to the medium. Finally, after total inactivation of the catalytic α3β3 subcomplex of F1, mitochondria could no longer be energized by externally added ATP because of either a block in assembly or local disruption of the adenine nucleotide processing site. Altogether these data strengthen the notion that in the absence of respiration, and whether the proton translocating domain (F0) of complex V is present or not, F1‐catalysed hydrolysis of ATP is essential for the occurrence of vital cellular processes depending on the maintenance of an electrochemical potential across the mitochondrial inner membrane.