Latifa Elantak

Structure of eIF3b RNA Recognition Motif and Its Interaction with eIF3j STRUCTURAL INSIGHTS INTO THE RECRUITMENT OF eIF3b TO THE 40 S RIBOSOMAL SUBUNIT

Mammalian eIF3 is a 700-kDa multiprotein complex essential for initiation of protein synthesis in eukaryotic cells. It consists of 13 subunits (eIF3a to -m), among which eIF3b serves as a major scaffolding protein. Here we report the solution structure of the N-terminal RNA recognition motif of human eIF3b (eIF3b-RRM) determined by NMR spectroscopy. The structure reveals a noncanonical RRM with a negatively charged surface in the β-sheet area contradictory with potential RNA binding activity. Instead, eIF3j, which is required for stable 40 S ribosome binding of the eIF3 complex, specifically binds to the rear α-helices of the eIF3b-RRM, opposite to its β-sheet surface. Moreover, we identify that an N-terminal 69-amino acid peptide of eIF3j is sufficient for binding to eIF3b-RRM and that this interaction is essential for eIF3b-RRM recruitment to the 40 S ribosomal subunit. Our results provide the first structure of an important subdomain of a core eIF3 subunit and detailed insights into protein-protein interactions between two eIF3 subunits required for stable eIF3 recruitment to the 40 S subunit.

The Crystal Structure of the Hexadeca-Heme Cytochrome Hmc and a Structural Model of Its Complex with Cytochrome c3

Sulfate-reducing bacteria contain a variety of multi-heme c-type cytochromes. The cytochrome of highest molecular weight (Hmc) contains 16 heme groups and is part of a transmembrane complex involved in the sulfate respiration pathway. We present the 2.42 A resolution crystal structure of the Desulfovibrio vulgaris Hildenborough cytochrome Hmc and a structural model of the complex with its physiological electron transfer partner, cytochrome c(3), obtained by NMR restrained soft-docking calculations. The Hmc is composed of three domains, which exist independently in different sulfate-reducing species, namely cytochrome c(3), cytochrome c(7), and Hcc. The complex involves the last heme at the C-terminal region of the V-shaped Hmc and heme 4 of cytochrome c(3), and represents an example for specific cytochrome-cytochrome interaction.

Structural Basis for Galectin-1-dependent Pre-B Cell Receptor (Pre-BCR) Activation.

Background: Galectin-1 (GAL1) is a ligand for the pre-BCR which is involved in the proliferation and differentiation of normal pre-BII cells. Results: GAL1-dependent pre-BCR clustering is driven mainly by hydrophobic contacts. Conclusion: Constitutive and ligand-induced pre-BCR activation can occur in a complementary manner. Significance: This is the first molecular snapshot of a pre-BCR/ligand interaction that helps pre-BCR clustering and activation. During B cell differentiation in the bone marrow, the expression and activation of the pre-B cell receptor (pre-BCR) constitute crucial checkpoints for B cell development. Both constitutive and ligand-dependent pre-BCR activation modes have been described. The pre-BCR constitutes an immunoglobulin heavy chain (Igμ) and a surrogate light chain composed of the invariant λ5 and VpreB proteins. We previously showed that galectin-1 (GAL1), produced by bone marrow stromal cells, is a pre-BCR ligand that induces receptor clustering, leading to efficient pre-BII cell proliferation and differentiation. GAL1 interacts with the pre-BCR via the unique region of λ5 (λ5-UR). Here, we investigated the solution structure of a minimal λ5-UR motif that interacts with GAL1. This motif adopts a stable helical conformation that docks onto a GAL1 hydrophobic surface adjacent to its carbohydrate binding site. We identified key hydrophobic residues from the λ5-UR as crucial for the interaction with GAL1 and for pre-BCR clustering. These residues involved in GAL1-induced pre-BCR activation are different from those essential for autonomous receptor activation. Overall, our results indicate that constitutive and ligand-induced pre-BCR activation could occur in a complementary manner.

Pre-B cell receptor binding to galectin-1 modifies galectin-1/carbohydrate affinity to modulate specific galectin-1/glycan lattice interactions

Galectins are glycan-binding proteins involved in various biological processes including cell/cell interactions. During B-cell development, bone marrow stromal cells secreting galectin-1 (GAL1) constitute a specific niche for pre-BII cells. Besides binding glycans, GAL1 is also a pre-B cell receptor (pre-BCR) ligand that induces receptor clustering, the first checkpoint of B-cell differentiation. The GAL1/pre-BCR interaction is the first example of a GAL1/unglycosylated protein interaction in the extracellular compartment. Here we show that GAL1/pre-BCR interaction modifies GAL1/glycan affinity and particularly inhibits binding to LacNAc containing epitopes. GAL1/pre-BCR interaction induces local conformational changes in the GAL1 carbohydrate-binding site generating a reduction in GAL1/glycan affinity. This fine tuning of GAL1/glycan interactions may be a strategic mechanism for allowing pre-BCR clustering and pre-BII cells departure from their niche. Altogether, our data suggest a novel mechanism for a cell to modify the equilibrium of the GAL1/glycan lattice involving GAL1/unglycosylated protein interactions.

Structural and genetic analyses reveal a key role in prophage excision for the TorI response regulator inhibitor.

TorI (Tor inhibition protein) has been identified in Escherichia coli as a protein inhibitor acting through protein-protein interaction with the TorR response regulator. This interaction, which does not interfere with TorR DNA binding activity, probably prevents the recruitment of RNA polymerase to the torC promoter. In this study we have solved the solution structure of TorI, which adopts a prokaryotic winged-helix arrangement. Despite no primary sequence similarity, the three-dimensional structure of TorI is highly homologous to the λXis, Mu bacteriophage repressor (MuR-DBD), and transposase (MuA-DBD) structures. We propose that the TorI protein is the structural missing link between the λXis and MuR proteins. Moreover, in vivo assays demonstrated that TorI plays an essential role in prophage excision. Heteronuclear NMR experiments and site-directed mutagenesis studies have pinpointed out key residues involved in the DNA binding activity of TorI. Our findings suggest that TorI-related proteins identified in various pathogenic bacterial genomes define a new family of atypical excisionases.

Glycan Dependence of Galectin-3 Self-Association Properties

Human Galectin-3 is found in the nucleus, the cytoplasm and at the cell surface. This lectin is constituted of two domains: an unfolded N-terminal domain and a C-terminal Carbohydrate Recognition Domain (CRD). There are still uncertainties about the relationship between the quaternary structure of Galectin-3 and its carbohydrate binding properties. Two types of self-association have been described for this lectin: a C-type self-association and a N-type self-association. Herein, we have analyzed Galectin-3 oligomerization by Dynamic Light Scattering using both the recombinant CRD and the full length lectin. Our results proved that LNnT induces N-type self-association of full length Galectin-3. Moreover, from Nuclear Magnetic Resonance (NMR) and Surface Plasmon Resonance experiments, we observed no significant specificity or affinity variations for carbohydrates related to the presence of the N-terminal domain of Galectin-3. NMR mapping clearly established that the N-terminal domain interacts with the CRD. We propose that LNnT induces a release of the N-terminal domain resulting in the glycan-dependent self-association of Galectin-3 through N-terminal domain interactions.

DnaJ (Hsp40 Protein) Binding to Folded Substrate Impacts KplE1 Prophage Excision Efficiency

Background: DnaJ positively modulates KplE1 prophage excision and is involved in lysogeny escape. Results: The recombination directionality factor TorI, from KplE1 prophage, interacts with the DnaJ chaperone, and they protect each other from limited trypsin digestion. Conclusion: DnaJ stabilizes TorI recombination directionality factor conformation. Significance: DnaJ cochaperone can bind folded substrates and induces the conformational stabilization of the TorI protein. Temperate phages mediate gene transfer and can modify the properties of their host organisms through the acquisition of novel genes, a process called lysogeny. The KplE1 prophage is one of the 10 prophage regions in Escherichia coli K12 MG1655. KplE1 is defective for lysis but fully competent for site-specific recombination. The TorI recombination directionality factor is strictly required for prophage excision from the host genome. We have previously shown that DnaJ promotes KplE1 excision by increasing the affinity of TorI for its site-specific recombination DNA target. Here, we provide evidence of a direct association between TorI and DnaJ using in vitro cross-linking assays and limited proteolysis experiments that show that this interaction allows both proteins to be transiently protected from trypsin digestion. Interestingly, NMR titration experiments showed that binding of DnaJ involves specific regions of the TorI structure. These regions, mainly composed of α-helices, are located on a surface opposite the DNA-binding site. Taken together, we propose that DnaJ, without the aid of DnaK/GrpE, is capable of increasing the efficiency of KplE1 excision by causing a conformational stabilization that allows TorI to adopt a more favorable conformation for binding to its specific DNA target.

Letter to the Editor: Sequential NMR assignment of the ferri-cytochrome c3 from Desulfovibrio vulgaris Hildenborough

Cytochromes c3 are low redox potential cytochromes involved in anaerobic metabolism. These periplasmic proteins contain four bi-histidinyl coordinated hemes. Multiheme cytochromes have been found in sulfate reducing bacteria of the genus Desulfovibrio. Preliminary analysis of Desulfovibrio vulgaris Hildenborough genome pointed out the existence of several putative genes encoding tetraheme cytochromes (http://www.tigr.org). Analysis of their genomic context showed that some of them are isolated (i.e., the gene encoding the well known soluble cytochrome c3 (Mr 13,000)) while others are part of multienzymatic complexes (i.e., the tetraheme cytochrome subunit in formate dehydrogenase (Sebban et al., 1995)). The large diversity of the tetraheme cytochromes in this organism must be correlated with the great specificity of these molecules for their oxidoreduction partners. We have recently reported a new approach to study electron transfer complexes combining NMR spectroscopy and theoretical calculations. 1H-15N HSQC are performed on an 15N-labelled redox partner, and we use the chemical shift variations induced upon complex formation to map the interacting site and to filter the ab initio models obtained by Bigger (Morelli et al., 2000). 1H-15N HSQC assignment is thus the first step of the functional study of cytochromes c3. We have initiated our studies with the soluble cytochrome c3 (Mr 13,000). The gene of this protein was cloned and sequenced (Voordouw et al., 1985) and the structure of this tetraheme cytochrome was solved by x-ray (Matias et al., 1993).

Structural and Mechanistic Insights into Unusual Thiol Disulfide Oxidoreductase

Background: TDOR are ubiquitous and catalyze important cell redox reactions. Results: Dtrx presents atypical physicochemical properties and a positive surface around its active site, suggesting a specificity for it(s) substrate(s). Conclusion: Active site histidine plays an important role in the molecular mechanism of Dtrx catalysis. Significance: Structural and functional studies of such atypical systems will give new insights into the TDOR catalytic mechanism. Cytoplasmic desulfothioredoxin (Dtrx) from the anaerobe Desulfovibrio vulgaris Hildenborough has been identified as a new member of the thiol disulfide oxidoreductase family. The active site of Dtrx contains a particular consensus sequence, CPHC, never seen in the cytoplasmic thioredoxins and generally found in periplasmic oxidases. Unlike canonical thioredoxins (Trx), Dtrx does not present any disulfide reductase activity, but it presents instead an unusual disulfide isomerase activity. We have used NMR spectroscopy to gain insights into the structure and the catalytic mechanism of this unusual Dtrx. The redox potential of Dtrx (−181 mV) is significantly less reducing than that of canonical Trx. A pH dependence study allowed the determination of the pKa of all protonable residues, including the cysteine and histidine residues. Thus, the pKa values for the thiol group of Cys31 and Cys34 are 4.8 and 11.3, respectively. The His33 pKa value, experimentally determined for the first time, differs notably as a function of the redox states, 7.2 for the reduced state and 4.6 for the oxidized state. These data suggest an important role for His33 in the molecular mechanism of Dtrx catalysis that is confirmed by the properties of mutant DtrxH33G protein. The NMR structure of Dtrx shows a different charge repartition compared with canonical Trx. The results presented are likely indicative of the involvement of this protein in the catalysis of substrates specific of the anaerobe cytoplasm of DvH. The study of Dtrx is an important step toward revealing the molecular details of the thiol-disulfide oxidoreductase catalytic mechanism.

Examination of Galectin-Induced Lattice Formation on Early B-Cell Development

Galectin-1 (GAL1) is a pre-B cell receptor (pre-BCR) ligand that induces pre-BCR clustering and leads to efficient pre-B cell proliferation and differentiation in the bone marrow. To study pre-BCR-GAL1 interactions and its functional consequence on the early steps of the B cell development, we combine structural nuclear magnetic resonance (NMR) approaches and B cell biology techniques. NMR is applied to identify the residues involved in pre-BCR-GAL1 interactions by monitoring chemical shift perturbations when the complex is formed. This structural information is then used at the cellular level to target specifically the complex formation during GAL1-induced pre-BCR clustering and lattice formation, using immunofluorescence techniques. Moreover, an in vivo assay was set up to study the consequence of synapse formation on the early steps of B cell development.