Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor Exploits Competition between L-Arginine Ligands and Resident Arginine Residues

An elegantly simple and probably ancient molecular mechanism of allostery is described for the Escherichia coli arginine repressor ArgR, the master feedback regulator of transcription in L-arginine metabolism. Molecular dynamics simulations with ArgRC, the hexameric domain that binds L-arginine with negative cooperativity, reveal that conserved arginine and aspartate residues in each ligand-binding pocket promote rotational oscillation of apoArgRC trimers by engagement and release of hydrogen-bonded salt bridges. Binding of exogenous L-arginine displaces resident arginine residues and arrests oscillation, shifting the equilibrium quaternary ensemble and promoting motions that maintain the configurational entropy of the system. A single L-arg ligand is necessary and sufficient to arrest oscillation, and enables formation of a cooperative hydrogen-bond network at the subunit interface. The results are used to construct a free-energy reaction coordinate that accounts for the negative cooperativity and distinctive thermodynamic signature of L-arginine binding detected by calorimetry. The symmetry of the hexamer is maintained as each ligand binds, despite the conceptual asymmetry of partially-liganded states. The results thus offer the first opportunity to describe in structural and thermodynamic terms the symmetric relaxed state predicted by the concerted allostery model of Monod, Wyman, and Changeux, revealing that this state is achieved by exploiting the dynamics of the assembly and the distributed nature of its cohesive free energy. The ArgR example reveals that symmetry can be maintained even when binding sites fill sequentially due to negative cooperativity, which was not anticipated by the Monod, Wyman, and Changeux model. The molecular mechanism identified here neither specifies nor requires a pathway for transmission of the allosteric signal through the protein, and it suggests the possibility that binding of free amino acids was an early innovation in the evolution of allostery

Caractérisation moléculaire du rôle de facteurs accessoires ArgR et PepA au niveau de la recombinaison spécifique sur le site cer

Mon projet de recherche avait pour but de caractériser le rôle de deux protéines, ArgR et PepA, qui agissent en tant que facteurs accessoires de la recombinaison au niveau de deux sites cer du plasmide ColE1 présent dans la bactérie Escherichia coli. Ces deux protéines, couplées aux deux recombinases à tyrosine XerC et XerD, permettent la catalyse de la recombinaison site spécifique au niveau de la séquence cer, convertissant les multimères instables de ColE1 en monomères stables. Cette étude a principalement porté sur la région C-terminale de la protéine ArgR. Cette région de la protéine ArgR possède une séquence en acides-aminés et une structure similaire à celle de la protéine AhrC de Bacillus subtilis. De plus, AhrC, le répresseur de l’arginine de cette bactérie, est capable de complémenter des Escherichia coli mutantes déficientes en ArgR. Les régions C-terminales de ces protéines, montrent une forte similarité. De précédents travaux dans notre laboratoire ont démontré que des mutants d’ArgR comprenant des mutations dans cette région, en particulier les mutants ArgR149, une version tronquée d’ArgR de 149 acides-aminés, et ArgR5aa, une version comprenant une insertion de cinq acides-aminés dans la partie C-terminale, perdaient la capacité de permettre la recombinaison au niveau de deux sites cer présents dans le plasmide pCS210. Malgré cette incapacité à promouvoir la réaction de recombinaison en cer, ces deux mutants étaient toujours capables de se lier spécifiquement à l’ADN et de réprimer une fusion argA :: lacZ. Dans ce travail, les versions mutantes et sauvages d’ArgR furent surexprimées en tant que protéines de fusion 6-histidine. Des analyses crosslinking ont montré que la version sauvage et ArgR5aa pouvaient former des hexamères in-vitro de manière efficace, alors qu’ArgR149 formait des multimères de plus faible poids moléculaire. Des formes tronquées d’ArgR qui comportaient 150 acides-aminés ou plus, étaient encore capables de permettre la recombinaison en cer. Les mutants par substitution ArgRL149A et ArgRL151A ont tous montré que les substitutions d’un seul acide-aminé au sein de cette région avaient peu d’effets sur la recombinaison en cer. Les expériences de crosslinking protéine-à-protéine ont montré que le type sauvage et les formes mutantes d’ArgR étaient capables d’interagir avec la protéine accessoire PepA, également impliquée dans la recombinaison en cer. Les expériences de recombinaison in-vitro utilisant la forme sauvage et les formes mutantes d’ArgR combinées avec les protéines PepA, XerC et XerD purifiées, ont montré que le mutant ArgR149 ne soutenait pas la recombinaison, mais que le mutant ArgR5aa permettait la formation d’une jonction d’Holliday. Des expériences de topologie ont montré que PepA était capable de protéger l’ADN de la topoisomérase 1, et d’empêcher ArgRWt de se lier à l’ADN. Les deux mutants ArgR149 et ArgR5aa protègent aussi l’ADN avec plus de surenroulements. Quand on ajoute PepA, les profils de migration montrent un problème de liaison des deux mutants avec PepA. D’autres expériences impliquant le triplet LEL (leucine-acide glutamique-leucine) et les acides-aminés alentour devraient être réalisés dans le but de connaitre l’existence d’un site de liaison potentiel pour PepA.My research project involved the role of two proteins, ArgR and PepA, which act as accessory factors in the ColE1 cer recombination system from the gram negative bacteria Escherichia coli. These two proteins, in addition to the tyrosine recombinases XerC and XerD, catalyze a site-specific recombination event at the cer sequence which converts unstable multimeric forms of ColE1 into more stable monomers. Our study mainly focused on the C-terminal end of the ArgR. This region of the ArgR protein possesses a structural and amino acid sequence similarity with the AhrC protein from Bacillus subtilis. Moreover, AhrC, the Arginine repressor of this bacterium, is able to complement Escherichia coli mutants deficient in ArgR. The C-terminal regions of these proteins, display a very high region of similarity. Previous work from our laboratory has shown that ArgR mutants with mutations in this region, especially the mutants ArgR149, a truncated 149 amino acids form of ArgR, and ArgR5aa, a form containing a five amino acid insertion in the C-terminal part, lost the ability to perform a recombination reaction at two cer sites in the plasmid pCS210. Despite this defect in promoting cer recombination, the mutants were still able to bind specifically to DNA, and to repress an argA :: lacZ genetic fusion. In this work, both wild type and mutant ArgR proteins were overexpressed as 6-histidine fusion proteins. Crosslinking analysis showed that both wild type and ArgR5aa efficiently formed hexamers in vitro, while ArgR149 formed lower molecular weight multimers. Truncated forms of ArgR that were 150 amino acids or longer, were able to support cer recombination. The substitution mutants between positions 149 to 151 all showed that single amino acid substitutions at this region had little effect on cer recombination. Protein-protein crosslinking experiments showed that wild type and mutant forms of ArgR, were able to interact with and the other accessory protein involved in cer recombination, PepA. In vitro recombination experiments using wild type and mutant forms of ArgR, combined with purified PepA, XerC and XerD showed that the ArgR149 mutant did not support recombination, but the ArgR5aa mutant did promote Holliday junction formation, raising the possibility that these two mutants interact differently with the Xer recombination machinery. Topology experiments showed that after adding topoisomerase 1, PepA is able to protect DNA from topoisomerase 1, and prevent ArgRWt binding to DNA. The two mutants ArgR149 and ArgR5aa are protecting DNA with more supercoiling. When PepA is added, migration profiles with the two mutants showed a binding problem with PepA. Other experiments involving the LEL triplet (leucine-glutamic acid-leucine) and amino-acids around it should be done in order to know the existence of a possible binding site for PepA

Regulación del metabolismo en Streptomyces: Control por ArgR

255 p.El metabolismo de arginina está reprimido por producto final en distintas bacterias, tanto Gram positivas como Gram negativas. Este efecto está mediado por ArgR, una proteína hexamérica que reprime los genes de biosíntesis de arginina utilizando L-arginina como corepresor. Esto ocurre en organismos como Escherichia coli, Pseudomonas, Bacillus subtilis, Lactococcus, Corynebacterium, etc. También es así en las distintas especies de Streptomyces. Dicha regulación se lleva a cabo mediante la unión de ArgR a las cajas ARG, constituidas por una secuencia palindrómica de 20 pb. La comparación transcriptómica mediante micromatrices llevada a cabo entre Streptomyces coelicolor M145 y su mutante S. coelicolor ¿argR en medio MG dio como resultado una transcripción diferencial de 1544 genes cuando se utiliza un valor p<0,01. En muchos casos el efecto se debe a la unión directa de ArgR a cajas ARG, pero a veces es indirecto a través de la regulación de la expresión de reguladores, factores sigma y anti-sigma. Los resultados indican que ArgR regula el metabolismo de arginina y otros aminoácidos, de purinas y pirimidinas y afecta al metabolismo del nitrógeno, a la producción de antibióticos (undecilprodigiosina y actinorrodina). La ausencia de ArgR también disminuye los niveles de los transcritos de las agrupaciones génicas para el poliquétido de tipo I CPK y el antibiótico dependiente de calcio CDA. ArgR afecta a la expresión de genes que codifican distintas proteínas de secreción y proteínas de membrana, genes implicados en la formación de estructuras celulares, morfología y esporulación. Afecta a la expresión de múltiples sistemas de dos componentes y transportadores ABC, a la síntesis de coenzimas, y a muchos genes implicados en la producción y conversión de energía, el transporte y metabolismo de carbohidratos y lípidos, entre otras funciones

53rd National Meeting of the Italian Society of Biochemistryand Molecular Biology (SIB)andNational Meeting of Chemistry of Biological Systems – Italian Chemical Society (SCI - Section CSB)

The 53rd National Congress of the Italian Society of Biochemistry and Molecular Biology (SIB), which will be held in Riccione from 23 to 26 September, is characterised by the elevated scientific level and interdisciplinary interest of the numerous sessions in which it is organised. The Scientific Programme comprises three joint Symposia of the SIB and the Chemistry of Biological Systems section of the Italian Chemistry Society (SCI) on Molecular Systems Biology, Chemistry of Nucleic Acids, Protein and Drug Structure, and Environmental Biotechnology. These Symposia address groundbreaking arguments, making the joint interest of the two societies particularly fascinating; the joint organisation of these events in fact signals the shared intention to proceed along the path of scientific exchange. The topics of the other sessions have been chosen by the Scientific Committee on the basis of their scientific relevance and topicality, with particular attention paid to the selection of the speakers. The SIB sessions will range from Signal Transduction and Biomolecular Targets, Protein Misfolding and its Relationship with Disease, Emerging Techniques in Biochemistry, Gene Silencing, Redox Signalling and Oxidative Stress, Lipids in Cell Communication and Signal Transduction, Mitochondrial Function and Dysfunction

53rd National Meeting of the Italian Society of Biochemistry and Molecular Biology (SIB) and National Meeting of Chemistry of Biological Systems – Italian Chemical Society (SCI - Section CSB)

Il 53° Congresso Nazionale della Società Italiana di Biochimica e Biologia Molecolare che si tiene a Riccione dal 23 al 26 Settembre si distingue per l'alto livello scientifico e l'interesse interdisciplinare delle numerose sessioni nelle quali è strutturato. Il Programma scientifico vede tre Simposi congiunti della SIB con la Sezione della Chimica dei Sistemi Biologici della Società Italiana di Chimica (SCI) su Molecular Systems Biology, Chemistry of Nucleic Acids, Protein and Drug Structure, Environmental Biotechnology. Questi Simposi, riguardano argomenti di avanguardia per i quali fa piacere l'interesse condiviso delle due Società, che per la prima volta organizzano dei Simposi congiunti a significare l'intento di procedere insieme negli scambi scientifici. Gli argomenti delle altre sessioni sono stati scelti dal comitato scientifico in base alla loro rilevanza e attualità scientifica, con particolare cura nella individuazione dei relatori. Le sessioni SIB spazieranno da Signal Transduction and Biomolecular Targets, Protein Misfolding and its Relationship with Diseases, Emerging Techniques in Biochemistry, Gene Silencing, Redox Signalling and Oxidative Stress, Lipids in Cell Communication and Signal Transduction, Mitochondrial Function and Dysfunction

Dichotomic role of NAADP/two-pore channel 2/Ca2+ signaling in regulating neural differentiation of mouse embryonic stem cells

Poster Presentation - Stem Cells and Pluripotency: abstract no. 1866The mobilization of intracellular Ca2+stores is involved in diverse cellular functions, including cell proliferation and differentiation. At least three endogenous Ca2+mobilizing messengers have been identified, including inositol trisphosphate (IP3), cyclic adenosine diphosphoribose (cADPR), and nicotinic adenine acid dinucleotide phosphate (NAADP). Similar to IP3, NAADP can mobilize calcium release in a wide variety of cell types and species, from plants to animals. Moreover, it has been previously shown that NAADP but not IP3-mediated Ca2+increases can potently induce neuronal differentiation in PC12 cells. Recently, two pore channels (TPCs) have been identified as a novel family of NAADP-gated calcium release channels in endolysosome. Therefore, it is of great interest to examine the role of TPC2 in the neural differentiation of mouse ES cells. We found that the expression of TPC2 is markedly decreased during the initial ES cell entry into neural progenitors, and the levels of TPC2 gradually rebound during the late stages of neurogenesis. Correspondingly, perturbing the NAADP signaling by TPC2 knockdown accelerates mouse ES cell differentiation into neural progenitors but inhibits these neural progenitors from committing to the final neural lineage. Interestingly, TPC2 knockdown has no effect on the differentiation of astrocytes and oligodendrocytes of mouse ES cells. Overexpression of TPC2, on the other hand, inhibits mouse ES cell from entering the neural lineage. Taken together, our data indicate that the NAADP/TPC2-mediated Ca2+signaling pathway plays a temporal and dichotomic role in modulating the neural lineage entry of ES cells; in that NAADP signaling antagonizes ES cell entry to early neural progenitors, but promotes late neural differentiation.postprin