Génétique des Génomes Bactériens
Genetics of Bacterial Genomes
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Régulation de l'Expression Génétique

Regulation of Gene Expression

1967-1971 1981 REG-1986 REG-1991 REG-1996 GGB-2001 GGB-2006
1972-1974 1982 REG-1987 REG-1992 REG-1997 GGB-2002
1975-1978 BRC-1983 REG-1988 REG-1993 REG-1998 GGB-2003
1979 BRC-1984 REG-1989 REG-1994 REG-1999 GGB-2004
2009
1980 BRC-1985 REG-1990 REG-1995 GGB-2000 GGB-2005  

Peer-reviewed publications are displayed in red


1986

O Gascuel, A Danchin
Protein export in prokaryotes and eukaryotes: indications of a difference in the mechanism of exportation
J Mol Evol (1986) 24: 130-142
In this paper we show that an approach based on artificial intelligence (learning by discrimination) allows one to identify seventeen descriptors of Escherichia coli signal peptides, while only three had been uncovered until then by specialists of protein export. This work was much used by legal advisors when analysing patent applications, to invalidate claims made by many creators of artificial systems for protein export   Dans cet article nous montrons qu'une approche d'intelligence artificielle (apprentissage par discrimination) permet d'identifier dix-sept descripteurs des peptides signaux du colibacille, alors que trois seulement avaient été identifiés jusque là par les spécialistes du domaine. Ce travail sera beaucoup utilisé par les cabinets d'analyse des demandes de brevets pour invalider les revendications de bien des constructeurs de systèmes artificiels de sécrétion des protéines

P Masson, G Lenzen, JM Jacquemin, A Danchin
Yeast adenylate cyclase catalytic domain is carboxy terminal
Curr Genet (1986) 10: 343-352

J Daniel, A Danchin
2-Ketoglutarate as a possible regulatory metabolite involved in cyclic AMP-dependent catabolite repression in Escherichia coli K12
Biochimie (1986) 68: 303-310

H De Reuse, E Touati, P Glaser, A Danchin
Low copy number plasmid vectors for gene cloning and for monitoring gene expression
FEMS Microbiology Letters (1986) 37: 193-197

fr A Danchin
Hérédité génétique, hérédité épigénétique
Confrontations psychiâtriques (1986) 27: 43-61

fr A Ullmann, A Danchin, F Gasser
Régulation de l'expression génétique: rôle de l'AMP cyclique. Microbiologie générale, protocoles expérimentaux
(1986) Hermann, Actualites Scientifiques et Industrielles, 151 pages
ISBN: 2705614168

fr A Danchin
Préface à la traduction de Schrödinger "What is life ?"
(1986) C Bourgois. pp 7-28

fr A Danchin
Les gelées de printemps ont un gène
La Recherche 174: 278-279

fr A Danchin
La musique des gènes
La Recherche 179: 976-977

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1987

I Saint Girons, AM Gilles, D Margarita, S Michelson, M Monnot, S Fermandjian, A Danchin, O Barzu
Structural and catalytic characteristics of Escherichia coli adenylate kinase
J Biol Chem (1987) 262: 622-629

B Boesten, G Lenzen, A Danchin, F O'Gara
Nucleotide sequence of a tRNAleu CAG gene from Rhizobium meliloti
Gene (1987) 55: 153-156

A Danchin
Membrane integration of carbohydrate transport in bacteria
Microbiol Sci (1987) 4: 267-269

A Danchin
The significance of split genes to developmental genetics
Adv Genet (1987) 24: 243-284

A Danchin
Escherichia coli and Saccharomyces cerevisiae adenylate cyclases: a case of phylogenetic convergence?
Isozymes Curr Top Biol Med Res (1987) 15: 141-151

G Lenzen, P Masson, JM Jacquemin, A Danchin
A TY1 element is inserted in the CYR1 control region of Saccharomyces cerevisiae strain AB320
FEBS Lett (1987) 219: 254-258

E Touati, A Danchin
Cloning and characterization of the pH 2.5 acid phosphatase gene, appA: cyclic AMP mediated negative regulation
Mol Gen Genet (1987) 208: 499-505

fr A Danchin
Naître et mourir
Corps Ecrit (1987) 21: 37-42

A Danchin
Order and Necessity
In "From enzyme adaptation to natural philosophy: heritage from J Monod" (E Quagliariello, G Bernardi, A Ullmann, Eds) Elsevier Sciences Publishers. (1987) pp 187-196 (Symposium "J Monod and molecular biology, Yesterday and Today". Trani. Italy: 13-15 dec 1986)

France Dans cette conférence à l'occasion du dixième anniversaire de sa mort, j'ai montré que l'épigraphe du livre célèbre de Jacques Monod, Le Hasard et la Nécessité, la citation qu'il attribue à Démocrite ne peut être correcte, mais que, bien au contraire, la pensée Grecque supposait le règne de l'ordre, et que les choses évoluent par l'exploration. Je montrais de plus que le concept d'entropie était associée de façon erronée au désordre, alors que, là encore, il aurait fallu l'associer à l'exploration. Quelques conséquences biologiques de ces observations étaient aussi discutées.   UKIn this lecture in memory of the tenth anniversary of his death, I showed that the epigraph of the famous book of Jacques Monod, Chance and Necessity, the quotation he attributes to Democritus cannot be correct, but that, in contrast, there was rule of order in Greek thought that allowed things to evolve through exploration. I further argued that the concept of entropy was wrongly associated to disorder, instead of, once again exploration. Some biological consequences of these views were also discussed.

fr A Danchin
L'étrange monotonie des récepteurs membranaires
La Recherche (1987) 185: 262-263

A Danchin
Biological foundations of language: a comment on Noam Chomsky's approach of syntactic structures
In: Noam Chomsky: Consensus and Controversy. (Ed. S & C Modgil) (1987) pp 29-39

A Danchin
Biological foundations of language: a reply to Dr. Marshall
In: Noam Chomsky: Consensus and Controversy. (Ed. S & C Modgil) (1987) pp 50-52

fr A Danchin
Signes Immuns
In: "Prospective et Santé": Immunologie, nouvelle frontière (1987) 42: 15-19

fr M Andler, A Danchin, P Thibaud, G Waysand
La Maîtrise du développement technologique. Extraits d'une discussion
Science et Culture
Esprit (1987) 128: 83-86

fr A Danchin
Les bases cérébrales du langage
Le Débat (1987) 47: 158-171

A Danchin, P Slonimski
Uno stratagemma dell'evoluzione: i geni discontinui
Scienza, Tecnica Annuario della EST (1987) Mondadori

E Touati, A Danchin
The structure of the promoter and amino terminal region of the pH 2.5 acid phosphatase structural gene (appA) of E. coli: a negative control of transcription mediated by cyclic AMP
Biochimie (1987) 69: 215-221

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1988 (Double hybrid cloning of class II adenylyl cyclases, the toxins from Bordetella pertussis and Bacillus anthracis)

H De Reuse, A Danchin
The ptsH, ptsI, and crr genes of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system: a complex operon with several modes of transcription
J Bacteriol (1988) 170: 3827-3837

A Danchin, G Lenzen
Structure and evolution of bacterial adenylate cyclase: comparison between Escherichia coli and Erwinia chrysanthemi
Second Messengers Phosphoproteins (1988) 12: 7-28

fr A Danchin
L'origine de la vie
La Recherche (1988) 201
: 878-886

fr A Danchin
Concept et langue, question de neurologie
Colloque Transcultura, (1988), Louvain-la-Neuve
In: "Connaissance et Réciprocité" (ed. Ciaco), pp 41-56

A Danchin
"High-dilution" experiments a delusion
Nature (1988) 334: 286

A Danchin
Origin of mutants disputed
Nature (1988) 336: 527

uk-flagCairns started a heated debate about the possibility of directed mutations ("adaptive mutations") in bacteria. This lettre challenges this interpretation by showing that the experimental setup is heavily biased. A series of experiments, performed with students of the Microbiology course at the Institut Pasteur later on demonstrated that bacteria could only be Lamarkian if they were very intelligent organisms! Modulation of mutagenesis under stressful conditions is enough to give rise to the behaviour observed.   fr-flagCairns a déclenché un débat houleux en croyant démontrer l'existence de mutations orientées chez les bactéries. Cette lettre met en doute cette interprétation en montrant que les conditions sont biaisées. Des expériences réalisées avec les étudiants du cours de Microbiologie de l'Institut Pasteur on démontré plus tard que si les bactéries étaient Lamarckistes, c'est qu'elles seraient très intelligentes. La modulation du taux de mutation dans des conditions difficiles suffit à rendre compte des observations.

O Gascuel, A Danchin
Data analysis using a learning program, a case study: an application of PLAGE to a biological sequence analysis
Proceedings of the European Conference on Artificial Intelligence, Munich, 1988 (ed. Pitman), pp 390-395

P Glaser, A Danchin, D Ladant, O Barzu, A Ullmann
Bordetella pertussis adenylate cyclase: the gene and the protein
Tokai J Exp Clin Med (1988) 13 Suppl: 239-252

P Glaser, D Ladant, O Sezer, F Pichot, A Ullmann, A Danchin
The calmodulin-sensitive adenylate cyclase of Bordetella pertussis: cloning and expression in Escherichia coli
Mol Microbiol (1988) 2: 19-30

P Glaser, H Sakamoto, J Bellalou, A Ullmann, A Danchin
Secretion of cyclolysin, the calmodulin-sensitive adenylate cyclase-haemolysin bifunctional protein of Bordetella pertussis
EMBO J (1988) 7: 3997-4004

S Lévy, A Danchin
Phylogeny of metabolic pathways: O-acetylserine sulphydrylase A is homologous to the tryptophan synthase beta subunit
Mol Microbiol (1988) 2: 777-783
pdf

This paper shows for the first time the common origin in tryptophan and cysteine biosynthesis (coded by the same box in the genetic code table). It substantiates the idea of homeotopic transformations at the origin of life   Cet article démontre pour la première fois la parenté entre la biosynthèse du tryptophane et celle de la cystéine (codés par la même case du tableau du code génétique). Il conforte l'idée de l'existence de transformations homéotopiques à l'origine de la vie

M Mock, E Labruyere, P Glaser, A Danchin, A Ullmann
Cloning and expression of the calmodulin-sensitive Bacillus anthracis adenylate cyclase in Escherichia coli
Gene (1988) 64: 277-284

UKThis toxin was part of an arsenal of dangerous toxins involved in biological warfare. Curiously, despite explicit discussions about the problem, in particular in Irak, it was almost obscene to allude to this subject at the time.   FranceCette toxine fait partie d'un arsenal utilisé dans la guerre biologique. Curieusement, malgré des mises en garde explicites à l'époque, en particulier à propos de l'Irak, il était en pratique obscène d'y faire la moindre allusion.

V Escuyer, E Duflot, O Sezer, A Danchin, M Mock
Structural homology between virulence-associated bacterial adenylate cyclases
Gene (1988) 71: 293-298

A Roy, P Glaser, A Danchin
Aspects of the regulation of adenylate cyclase synthesis in Escherichia coli K12
J Gen Microbiol (1988) 134 ( Pt 2): 359-367

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1989

P Glaser, A Elmaoglou-Lazaridou, E Krin, D Ladant, O Barzu, A Danchin
Identification of residues essential for catalysis and binding of calmodulin in Bordetella pertussis adenylate cyclase by site-directed mutagenesis
EMBO J (1989) 8: 967-972

A Danchin, O Sezer, P Glaser, P Chalon, D Caput
Cloning and expression of mouse-brain calmodulin as an activator of Bordetella pertussis adenylate cyclase in Escherichia coli
Gene (1989) 80: 145-149

fr A Danchin
Les bactéries sont-elles devenues lamarckiennes ?
La Recherche (1989) 209: 538-539

fr A Danchin
René Thom l'Aristotélicien. (Esquisse d'une sémiophysique, InterEditions 1988)
La Recherche (1989) 210: 508

fr A Danchin
Un retour des objections créationistes ? 20
La révolution des ARN, 216: 1518-1519

A Danchin
The tree and the ring. Hierarchical and acentered structures in biology [a paper in System's Biology that exposes the function of closure in creating global behaviour]
The Cancer Journal (1989) 2: 285-287

A Danchin
The PTS after 25 years
FEMS Microbiol Rev (1989)

H De Reuse, S Lévy, G Zeng, A Danchin
Genetics of the PTS components in Escherichia coli K-12
FEMS Microbiol Rev (1989) 5: 61-67

P Glaser, A Roy, A Danchin
Molecular characterization of two cya mutations, cya-854 and cyaR1
J Bacteriol (1989) 171: 5176-5178

S Goyard, C Orlando, JM Sabatier, E Labruyere, J d'Alayer, G Fontan, J van Rietschoten, M Mock, A Danchin, A Ullmann
Identification of a common domain in calmodulin-activated eukaryotic and bacterial adenylate cyclases
Biochemistry (1989) 28: 1964-1967

P Lejeune, P Bertin, C Walon, K Willemot, C Colson, A Danchin
A locus involved in kanamycin, chloramphenicol and L-serine resistance is located in the bglY-galU region of the Escherichia coli K12 chromosome
Mol Gen Genet (1989) 218: 361-363

A Danchin
Homeotopic transformation and the origin of translation
Progress in Biophysics and Molecular Biology (1989) 54: 81-86
pdf see  further developments about the origin of life in pdf

It is revealing to note that the title of this article has been misspelled at the Institute for Scientific Information, modifying "homeotopic" into "homeotropic", therefore substantially altering the concept   Il est amusant de constater qu'à l'Institute for Scientific Information, le titre de cet article a été changé et a confondu "homeotopic" avec "homeotropic", ce qui en modifie sensiblement la signification

S Lévy, H De Reuse, A Danchin
Antisense expression at the ptsH-ptsI locus of Escherichia coli
FEMS Microbiol Lett (1989) 48: 35-38

E Peters, A Wilderspin, O Sezer, A Danchin
Cloning and restriction mapping of the adenylate cyclase from B. liquifaciens
Biochemical Society Transactions (1989) 17: 778-779

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1990

P Lejeune, A Danchin
Mutations in the bglY gene increase the frequency of spontaneous deletions in Escherichia coli K-12
Proc Natl Acad Sci U S A (1990) 87: 360-363

In this work we identify bglY (now hns) as the first deletion-generating mutator gene. hns deficient E. coli mutants spontaneously make deletions and no more point mutations than the wild type. This suggests that bacteria have a specific mechanism to delete large sets of genes.   Dans cet article nous identifions le premier gène mutateur connu (bglY, connu aujourd'hui comme hns), dont l'action est de conduire systématiquement à des délétions de régions chromosomiques, plutôt qu'à des mutations ponctuelles. Cela suggère que les bactéries ont un mécanisme spécifique pour la délétion de gènes entiers.

P Bertin, P Lejeune, C Laurent-Winter, A Danchin
Mutations in bglY, the structural gene for the DNA-binding protein H1, affect expression of several Escherichia coli genes
Biochimie (1990) 72: 889-891

A Beuve, B Boesten, M Crasnier, A Danchin, F O'Gara
Rhizobium meliloti adenylate cyclase is related to eucaryotic adenylate and guanylate cyclases
J Bacteriol (1990) 172: 2614-2621

M Crasnier, A Danchin
Characterization of Escherichia coli adenylate cyclase mutants with modified regulation
J Gen Microbiol (1990) 136 ( Pt 9): 1825-1831

fr A Danchin
L'explication de la vie: perspectives et questions
Le Débat (1990) 60: 302-308

fr A Danchin
L'irruption de la morale
La Recherche (1990) 225: 1172-1173

fr A Danchin
La Permanence et le Changement
Repris avec modifications dans "La Querelle du Déterminisme" (K Pomian, ed.) Gallimard, Paris, 1990

fr A Danchin
Une Aurore de Pierres. Aux origines de la vie
Le Seuil (1990), 276 pp

A Danchin
Portuguese translation: "Uma aurora de pedras. Nas origens da vida", Almedina, Coimbra, 1992

V de Crécy-Lagard, P Glaser, P Lejeune, O Sismeiro, CE Barber, MJ Daniels, A Danchin
A Xanthomonas campestris pv. campestris protein similar to catabolite activation factor is involved in regulation of phytopathogenicity
J Bacteriol (1990) 172: 5877-5883

AM Gilles, H Munier, T Rose, P Glaser, E Krin, A Danchin, C Pellecuer, O Barzu
Intrinsic fluorescence of a truncated Bordetella pertussis adenylate cyclase expressed in Escherichia coli
Biochemistry (1990) 29: 8126-8130

P Glaser, A Danchin, O. Barzu, A Ullmann
Bordetella pertussis adenylate cyclase. IIIrd European Workshop on Bacterial
Protein Toxins, Urbino (Italie), 3-6 Juillet 1989.
In: "Bacterial Protein Toxins" (1990), Zbl. Bakt Suppl. 19, pp 375-382. Rappuoli R Alouf J, Free J,
Fehrenbach F, Wadstrom T and Witholt B (eds), Gustav Fisher, Stuttgart, New York

C Higgins, A Danchin
Editorial
Molecular Microbiology (1990) 4: 159

The exponential increase in sequence and mapping data for the Escherichia coli chromosome necessitates relatively sophisticated software for the analysis of new information and compile updates. In this issue (p. 169) Medigue et al. describe a programme for placing any DNA sequence on the known restriction map of the E. coli chromosome. Together with details of the software is the latest update of the E. coli chromosomal map Indicating the positions of restriction sites, known genes and sequenced regions. The map updates and corrects the original restriction map of Kohara et al. (1987). To provide a service to readers. Molecular Microbiology will publish a yearly update of this map. Antoine Danchin has kindly agreed to co-ordinate this effort, using sequences deposited in the EMBL/GenBank Data Libraries, as well as those sent directly to him. Furthermore, Antoine Danchin is prepared to analyse any unpublished sequences sent to him and locate them on the revised map. At regular intervals, as new data accumulate, a page of the Journal will be devoted to providing updated information on new genes or regions sequenced, their locations, and the workers from whom further information can be obtained. All sequence data should be sent directly to Antoine Danchin, at the address below, as an ASC II file through EARN/BITNET: REG@PASTEUR. If information Is required about other means of providing sequence data, Antoine Danchin should be contacted. We hope and intend that this initiative will provide a useful service for molecular geneticists working with E. coli.

S Lévy, GQ Zeng, A Danchin
Cyclic AMP synthesis in Escherichia coli strains bearing known deletions in the pts phosphotransferase operon
Gene (1990) 86: 27-33

C Médigue, JP Bouché, A Hénaut, A Danchin
Mapping of sequenced genes (700 kbp) in the restriction map of the Escherichia coli chromosome
Mol Microbiol (1990) 4: 169-187

C Médigue, A Hénaut, A Danchin
Escherichia coli molecular genetic map (1000 kbp): update I
Mol Microbiol (1990) 4: 1443-1454

RS Sarfati, VK Kansal, H Munier, P Glaser, AM Gilles, E Labruyere, M Mock, A Danchin, O Barzu
Binding of 3'-anthraniloyl-2'-deoxy-ATP to calmodulin-activated adenylate cyclase from Bordetella pertussis and Bacillus anthracis
J Biol Chem (1990) 265: 18902-18906

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1991

A Danchin, C Médigue, O Gascuel, H Soldano, A Hénaut
From data banks to data bases
[
Keywords: Data bank, Data base, Library; B. subtilis, E. coli, Nucleotide and protein sequences, Updating, Learning techniques, In silico.]
This paper summarizes a conference given at the beginning of the summer of 1990 on the biology of Bacillus subtilis and its genome program
[Abstract: The information collected in national and international libraries on nucleotide and protein sequences cannot be directly treated for proper handling by existing software. Therefore we evaluated the feasibility of constructing a data base for Escherichia coli using the data present in the banks. The knowhow thus acquired was applied to Bacillus subtilis. Specific examples of the general procedure are given.]
Res Microbiol (1991) 142: 913-916

The expression "in silico" has been coined by AD for White Papers written for the European Union to support the creation of bacterial genome programs in 1989-1990
The sentence where "in silico" appeared first publicly is the following:

"Experimentation in silico
Using the data available in libraries [...]
Two sets of experiments were performed on computers (experiments in silico) using the consistency of the data extracted. [...]"
See amusing or interesting comments.

 

L'apparition des ordinateurs a complètement modifié notre accès à la biologie, en particulier au moment de la création des programmes de génomique. AD a utilisé l'expression "in silico" pour exprimer ce fait que désormais, il faudrait compter, outre l'expérience in vivo et in vitro, l'expérience in silico, avec des ordinateurs. Cette expression a été reprise dans de nombreux exposés de présentation des programmes génomes, et elle est apparue probablement pour la première fois par écrit dans le compte rendu d'un exposé fait pour la réunion internationale du consortium de Bacillus subtilis au cours de laquelle le Japon a choisi de faire partie du programme.

V de Crécy-Lagard, OM Bouvet, P Lejeune, A Danchin
Fructose catabolism in Xanthomonas campestris pv. campestris. Sequence of the PTS operon, characterization of the fructose-specific enzymes
J Biol Chem (1991) 266: 18154-18161

V de Crécy-Lagard, P Lejeune, OM Bouvet, A Danchin
Identification of two fructose transport and phosphorylation pathways in Xanthomonas campestris pv. campestris
Mol Gen Genet (1991) 227: 465-472

H De Reuse, A Danchin
Positive regulation of the pts operon of Escherichia coli: genetic evidence for a signal transduction mechanism
J Bacteriol (1991) 173: 727-733

P Glaser, H Munier, AM Gilles, E Krin, T Porumb, O Barzu, R Sarfati, C Pellecuer, A Danchin
Functional consequences of single amino acid substitutions in calmodulin-activated adenylate cyclase of Bordetella pertussis
EMBO J (1991) 10: 1683-1688

P Glaser, F Kunst, M Debarbouille, A Vertes, A Danchin, R Dedonder
A gene encoding a tyrosine tRNA synthetase is located near sacS in Bacillus subtilis
DNA Seq (1991) 1: 251-261

C Médigue, T Rouxel, P Vigier, A Hénaut, A Danchin
Evidence for horizontal gene transfer in Escherichia coli speciation
J Mol Biol (1991) 222: 851-856

This article shows, for the first time, that in the genome of the best known bacteria, Escherichia coli, one sixth of the genes comes from outside. This result, that emphasizes the importance of lateral gene transfer (LGT, or HGT) in bacteria, also shows that replication accuracy is not a prime character of wild type species, but that genes coding for error proof-reading are propagated by horizontal transfer. The role of mutator strains in the environment is stressed, with HGT as a major mechanism allowing cells to adapt to a new biotope, including evolution from commensalism to pathogenicity.

Amusingly, the comment of the Assistant Editor of Nature to exclude publication was: "I have discussed your manuscript with my colleagues, and while we appreciate the interest of your observation suggesting the existence of an apparent 'third class of genes', the inference of horizontal gene transfer seems rather tentative, and for this reason we feel that the manuscript would be better suited to publication in a rather more specialized molecular evolution or microbiology journal." And this is probably why this same popular magazine had to publish an updated view of HGT in year 2000 under the name of "lateral gene transfer"...  Nominalism is still extant.

 

Cet article montre, pour la première fois, que dans le génome de la bactérie la mieux connue, Escherichia coli, un sixième des gènes provient d'ailleurs. Ce résultat, qui démontre l'importance considérable du transfert génétique latéral chez les bactéries, montre aussi que la fidélité de la réplication n'est pas le caractère premier des espèces, mais que les gènes de correction des erreurs se propagent par transfert horizontal. Ce travail met en évidence le rôle des souches mutatrices dans l'environnement, donnant au transfert génétique horizontal un rôle de premier plan pour l'adaptation à une nouvelle niche, en particulier au cours de l'évolution du commensalisme vers la pathogénicité.

C Médigue, A Viari, A Hénaut, A Danchin
Escherichia coli molecular genetic map (1500 kbp): update II
Mol Microbiol (1991) 5: 2629-2640

Well before the genome sequence was completed one third of the E. coli genome sequence was known. This permitted investigators to analyse the frequency of motifs, or words, in the genome. This article describes the distribution of the 16 palidromic tetranucleotides and shows that CTAG (and more generally CCTAGG) is particularly rare, while palidromic hexanucleotides are not distributed randomly in the E. coli genome.   Bien avant que sa séquence complète soit connue un tiers de la séquence du génome de E. coli se trouvait déjà dans les banques de données. Cela permettait d'analyser la fréquence des motifs, ou mots, dans le génome. Cet article décrit la répartition des 16 tétranucléotides palindromiques et montre que CTAG (et plus spécialement CCTAGG) est particulièrement rare, alors que les hexanucléotides palindromiques ne sont pas répartis au hasard dans le génome de E. coli

M Mock, M Crasnier, E Duflot, V Dumay, A Danchin
Structural and functional relationships between Pasteurella multocida and enterobacterial adenylate cyclases
J Bacteriol (1991) 173: 6265-6269

I Moszer, P Glaser, A Danchin
Multiple IS insertion sequences near the replication terminus in Escherichia coli K-12
Biochimie (1991) 73: 1361-1374

H Munier, AM Gilles, P Glaser, E Krin, A Danchin, R Sarfati, O Barzu
Isolation and characterization of catalytic and calmodulin-binding domains of Bordetella pertussis adenylate cyclase
Eur J Biochem (1991) 196: 469-474

EP Peters, AF Wilderspin, SP Wood, MJ Zvelebil, O Sezer, A Danchin
A pyruvate-stimulated adenylate cyclase has a sequence related to the fes/fps oncogenes and to eukaryotic cyclases
Mol Microbiol (1991) 5: 1175-1181

fr A. Danchin
Hérédité et intelligence: un débat faussé
La Recherche (1991) 230: 386-387

fr A. Danchin
Les frères Bogdanov, Jean Guitton et Dieu : Dieu est-t-il thermodynamicien ?
La Recherche (1991) 237: 1352-1353

fr A Danchin
Hasard et biologie moléculaire
In: "Le hasard aujourd'hui" (Entretien avec Emile Noel) Ed. Le Seuil (1991): pp 111-125

fr A Danchin
L'origine de la vie
In: "l'Etat des Sciences et des Techniques" La Découverte (1991): pp 197-201

fr A Danchin
Eugénisme et génétique
In: "l'Etat des Sciences et des Techniques" La Découverte (1991): pp 126-128

fr A Danchin
Ce que peut apporter le séquençage des grands génomes
In: "l'Etat des Sciences et des Techniques" La Découverte (1991): pp 227-229

fr A Danchin
La diversité génétique, atout à préserver
In: "l'Etat des Sciences et des Techniques" La Découverte (1991): pp 238-240

A Danchin
Permanenza e cambiamento
In: "Sul determinismo. La filosofia della scienza oggi." a cura di Krzysztof Pomian. Il Saggiatore (1991) pp 103-118

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1992

P Bertin, P Lejeune, C Colson, A Danchin
Mutations in bglY, the structural gene for the DNA-binding protein H1 of Escherichia coli, increase the expression of the kanamycin resistance gene carried by plasmid pGR71
Mol Gen Genet (1992) 233: 184-192

A Beuve, A Danchin
From adenylate cyclase to guanylate cyclase. Mutational analysis of a change in substrate specificity
J Mol Biol (1992) 225: 933-938

A Danchin
Are purine nucleoside triphosphate cyclases an example of convergent evolution?
In: "Adenine Nucleotides in Cellular Energy Transfer and Signal Transduction" (1992): pp 365-377

fr A Danchin
Les premières formes de vie (entretien avec Ruth Scheps)
In: "La mémoire de la terre" Le Seuil, (1992): pp. 151-167

fr A Danchin
Epistémologie, Différence Humaine, Ethique
In: "Patrimoine Génétique et Droits de l'Humanité" (F Gros, G Huber, ed) Odile Jacob (1992): pp. 512-514

fr A Danchin
Crick (Francis Harry Compton Crick)
Dictionnaire des Philosophes (A Jacob, ed.) (1992) Presses Universitaires de France, Paris

A Danchin
Science and Technology: A Western imbroglio
Projections (1992) 7/8: 39-48

A Danchin
Phylogeny of adenylyl and guanylyl cyclases
In: "Colloque International en hommage à Jean Pernès, Professeur à l'Université d'Orsay Paris XI" (1992): pp. 203-214, Editions Lavoisier

A Danchin
Conclusions and perspectives
In: From stars and minerals to life: is the paradigm changing? Frontiers of Life (J&K Trân Thanh Vân, JC Mounolou, J Schneider, C McKay, eds) Editions Frontières, Gif sur Yvette (1992): pp.399-414

fr A Danchin
Aux Frontières de la Vie
La Recherche 241: 368-369

H De Reuse, A Kolb, A Danchin
Positive regulation of the expression of the Escherichia coli pts operon. Identification of the regulatory regions
J Mol Biol (1992) 226: 623-635

H Munier, A Bouhss, E Krin, A Danchin, AM Gilles, P Glaser, O Barzu
The role of histidine 63 in the catalytic mechanism of Bordetella pertussis adenylate cyclase
J Biol Chem (1992) 267: 9816-9820

H Munier, E Krin, AM Gilles, P Glaser, A Bouhss, A Danchin and O. Barzu
Structural and functional organization of the catalytic domain of a bacterial toxin: Bordetella pertussis adenylate cyclase
In: "Adenine Nucleotides in Cellular Energy Transfer and Signal Transduction" (1992) pp 335-344

M Santana, F Kunst, MF Hullo, G Rapoport, A Danchin, P Glaser
Molecular cloning, sequencing, and physiological characterization of the qox operon from Bacillus subtilis encoding the aa3-600 quinol oxidase
J Biol Chem (1992) 267: 10225-10231

GQ Zeng, H De Reuse, A Danchin
Mutational analysis of the enzyme-IIIGlc of the phosphoenolpyruvate phosphotransferase system in Escherichia coli
Res Microbiol (1992) 143: 251-261

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1993

A Beuve, E Krin, A Danchin
Rhizobium meliloti adenylate cyclase: probing of a NTP-binding site common to cyclases and cation transporters
C R Acad Sci III (1993) 316: 553-559

A Bouhss, E Krin, H Munier, AM Gilles, A Danchin, P Glaser, O Barzu
Cooperative phenomena in binding and activation of Bordetella pertussis adenylate cyclase by calmodulin
J Biol Chem (1993) 268: 1690-1694

A Danchin, J Pidoux, E Krin, CJ Thompson, A Ullmann
The adenylate cyclase catalytic domain of Streptomyces coelicolor is carboxy-terminal
FEMS Microbiol Lett (1993) 114: 145-151

A Danchin
Phylogeny of adenylyl cyclases
Adv Second Messenger Phosphoprotein Res (1993) 27: 109-162
pdf part 1 pdf part 2

This article is the international reference for the classification of adenylyl (adenylate) cyclases, as made of three classes of phylogenetically independent origin (phylogenetic convergence). A fourth class, also of a different descent, has been later on discovered in the Unit.  An important feature of this work was the suggestion that the presence of multiple cyclases can be accounted for by the fact that it is not cyclic AMP per se which is the real regulator, but its spatial or, most probably, temporal distribution: specific variation in the concentration of cAMP are recognised by receptors-regulators which control in a highly discriminant way the action of each cyclase, in a way somewhat similar of the recognition of firing  pattern pulses in neurons  

Cet article constitue la référence internationale pour la classification des adénylcyclases, sous la forme de trois classes d'origine évolutive différente (convergence évolutive). Une quatrième classe, elle aussi d'origine différente a été découverte dans l'Unité quelques années plus tard. Un autre aspect de ce travail est de proposer que la présence de cyclase multiples s'explique par le fait que ce n'est pas la molécule d'AMPcyclique qui est l'effecteur réel, mais sa répartition dans l'espace, ou plus probablement sa répartition dans le temps : ce sont des variations particulières de la concentration de l'AMPc qui sont reconnues par des récepteurs-régulateurs, et qui contrôlent de façon spécifique l'action de telle ou telle cyclase

fr A Danchin
Pour l'unité de l'esprit scientifique
Le Débat (1993) 73: 71-76

fr A Danchin
Le séquençage des petits génomes. Vers la description complète d'un organisme vivant
La Recherche (1993) 251: 222-232
Version espagnole: La Secuenciacion de pequenos genomas. "Hacia la description completa de un organismo vivo"
Mundo Scientifico (1993) 134: 376-386

fr A Danchin
La science hors d'elle-même ? La science et les modèles du savoir
Esprit (1993) 191: 85-90

A Danchin
Informatics and genome sequencing programs
Biochimie (1993) 75: 319

A Danchin 唐善
"Lun Ke Shue Mou Shi"
In: Shi hua xia Editions 93 de l'Université Sun Yat Sen (Zhong Shan Da Shue) Canton (Guang Zhou) (1993) pp 231-246

A Danchin
O ovo e a galinha Historias do codigo genetico
Relogio d'agua, Lisboa (1993)

AM Gilles, O Sismeiro, H Munier, H Fabian, HH Mantsch, WK Surewicz, CC Craescu, O Barzu, A Danchin
Structural and physico-chemical characteristics of Bordetella pertussis adenylate kinase, a tryptophan-containing enzyme
Eur J Biochem (1993) 218: 921-927

fr A Danchin
La métaphore alphabétique de l'hérédité génétique
Revue Internationale de Psychopathologie (1993) 13: 859-883

C Médigue, A Viari, A Hénaut, A Danchin
Colibri: a functional data base for the Escherichia coli genome
Microbiol Rev (1993) 57: 623-654

H Munier, A Bouhss, AM Gilles, E Krin, P Glaser, A Danchin, O Barzu
Structural flexibility of the calmodulin-binding locus in Bordetella pertussis adenylate cyclase. Reconstitution of catalytically active species from fragments or inactive forms of the enzyme
Eur J Biochem (1993) 217: 581-586

P Glaser, F Kunst, M Arnaud, M-P Coudart, W Gonzales, M-F Hullo, M Ionescu, B Lubochinsky, L Marcelino, I Moszer, E Presecan, M Santana, E Schneider, J Schweizer, A Vertes, G Rapoport, A Danchin
Bacillus subtilis genome project: cloning and sequencing of the 97 Kb region from 325o to 333o
Mol Microbiol (1993) 10: 371-384
[this article is found in PubMed with a truncated list of authors]

Cet article montre, pour la première fois, que dans un long fragment génomique, la moitié des gènes ne ressemble à rien de connu jusqu'alors. Ce résultat, présenté à un symposium organisé par l'Union Européenne à Elounda en Crète, en 1991, marquait la première découverte majeure issue des programmes de séquençage des génomes  

This article shows, for the first time, that in a long genome fragment, half of the genes does not look like anything previously known. This observation, presented at a symposium organized by the European Union in Elounda in Crete, in 1991, was the landmark of the first major discovery stemming from genome sequencing programs

T Rouxel, A Danchin, A Hénaut
METALGEN.DB: metabolism linked to the genome of Escherichia coli, a graphics-oriented database
Comput Appl Biosci (1993) 9: 315-324

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1994

O Barzu, A Danchin
Adenylyl cyclases: a heterogeneous class of ATP-utilizing enzymes
Prog Nucleic Acid Res Mol Biol (1994) 49: 241-283

P Bertin, E Terao, EH Lee, P Lejeune, C Colson, A Danchin, E Collatz
The H-NS protein is involved in the biogenesis of flagella in Escherichia coli
J Bacteriol (1994) 176: 5537-5540

M Crasnier, V Dumay, A Danchin
The catalytic domain of Escherichia coli K-12 adenylate cyclase as revealed by deletion analysis of the cya gene
Mol Gen Genet (1994) 243: 409-416

fr A Danchin
Doute et création
In: "La Responsabilité, la condition de notre humanité"
Autrement (1994) 14:249-266

fr A Danchin
Les Evolutions, Phylogenèse de l'individuation. Presses Universitaires de France (1994) pp 219-245

fr A Danchin
Une Image inattendue de l'Identité, l'image alphabétique,
XXXIVes Rencontres Internationales de Genève 1993 - "Nos Identités" (1994) Editions de la Baconnière - Boudry-Neuchâtel (Suisse) pp 209-250

fr A Danchin
La mathématique e(s) t la vie ?
Contribution à l'ouvrage réalisé en hommage à René Thom à l'occasion de son soixante-dixième anniversaire
Passion des Formes, Collection Theoria, ENS Editions (1994) 2:569-583

JR Landgraf, M Levinthal, A Danchin
The role of H-NS in one carbon metabolism
Biochimie (1994) 76: 1063-1070

M Levinthal, P Lejeune, A Danchin
The H-NS protein modulates the activation of the ilvIH operon of Escherichia coli K12 by Lrp, the leucine regulatory protein
Mol Gen Genet (1994) 242: 736-743

M Santana, MS Ionescu, A Vertes, R Longin, F Kunst, A Danchin, P Glaser
Bacillus subtilis F0F1 ATPase: DNA sequence of the atp operon and characterization of atp mutants
J Bacteriol (1994) 176: 6802-6811

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1995

J Archdeacon, J Talty, B Boesten, A Danchin, F O'Gara
Cloning of the second adenylate cyclase gene (cya-2) from Rhizobium meliloti F34: sequence similarity to eukaryotic cyclases
FEMS Microbiol Lett (1995) 128: 177-184

F Betsou, O Sismeiro, A Danchin, N Guiso
Cloning and sequence of the Bordetella bronchiseptica adenylate cyclase-hemolysin-encoding gene: comparison with the Bordetella pertussis gene
Gene (1995) 162: 165-166

M Borodovsky, JD McIninch, EV Koonin, KE Rudd, C Médigue, A Danchin
Detection of new genes in a bacterial genome using Markov models for three gene classes
Nucleic Acids Res (1995) 23: 3554-3562

H Cruz Ramos, L Boursier, I Moszer, F Kunst, A Danchin, P Glaser
Anaerobic transcription activation in Bacillus subtilis: identification of distinct FNR-dependent and -independent regulatory mechanisms
EMBO J (1995) 14: 5984-5994

A Danchin
Why sequence genomes? The Escherichia coli imbroglio
Mol Microbiol (1995) 18: 371-376

A Danchin, E Krin
Filling the gap between hns and adhE in Escherichia coli K12
Microbiology (1995) 141 ( Pt 4): 959-960

fr A Danchin
Œdipe totalitaire ou l'énigme de la création
In: "Transmissible" "Intransmissible"
Césure (1995) 8: 49-71

fr F Jacob, A Danchin, O Postel-Vinay
François Jacob, trente ans après
La Recherche (1995) 280: 111-115

fr A Danchin
Chroniques 1995 dans La Recherche
Le cochon chinois, ça éternue ! 281: 76
Les animaux voient-ils avec la langue ? 282: 94
Eloge de l'absence
283: 95

V de Crécy-Lagard, M Binet, A Danchin
Fructose phosphotransferase system of Xanthomonas campestris pv. campestris: characterization of the fruB gene
Microbiology (1995) 141 ( Pt 9): 2253-2260

P Glaser, A Danchin, F Kunst, P Zuber, MM Nakano
Identification and isolation of a gene required for nitrate assimilation and anaerobic growth of Bacillus subtilis
J Bacteriol (1995) 177: 1112-1115

fr A Hénaut, A Danchin
Informatique et génomes ou l'expérimentation in silico
La Lettre du GREG (1995
)

F Kunst, A Vassarotti, A Danchin
Organization of the European Bacillus subtilis genome sequencing project
Microbiology (1995) 141 ( Pt 2): 249-255

C Laurent-Winter, P Lejeune, A Danchin
The Escherichia coli DNA-binding protein H-NS is one of the first proteins to be synthesized after a nutritional upshift
Res Microbiol (1995) 146: 5-16

C Médigue, I Moszer, A Viari, A Danchin
Analysis of a Bacillus subtilis genome fragment using a co-operative computer system prototype
Gene (1995) 165: GC37-51

C Médigue, T Vermat, G Bisson, A Viari, A Danchin
Cooperative computer system for genome sequence analysis
Proc Int Conf Intell Syst Mol Biol (1995) 3: 249-258

I Moszer, P Glaser, A Danchin
SubtiList: a relational database for the Bacillus subtilis genome
Microbiology (1995) 141 ( Pt 2): 261-268
  pdf

uk-flagIn this paper we present the reference database for the Bacillus subtilis genome. We show how this database can be used to extract high level information about the genome. As an example we illustrate the distribution of isoelectric points in all the proteins of B. subtilis. We discover that the distribution is uneven, and that there the region with pI approximately 7.6 lacks proteins. Remarkably, the proteins in the region are often annotated as related to functions involving protons or as secreted proteins. This is consistent with an internal level of protons availability that would correspond to this pI. Hence, the pI can be used as a specific neighborhood permitting inferences about the function of unknown proteins. This approach was proposed in many lectures as allowing efficient functional inference. It has been generalized later on by a variety of works.   fr-flagDans cet article nous présentons la base de données de référence pour le génome de Bacillus subtilis. Nous montrons comment elle peut être utilisée pour extraire une information de haut niveau à propos du génome. Nous donnons l'exemple de la répartition des points isoélectriques du protéome de B. subtilis, et découvrons qu'elle est bi-modale, avec un manque considérable de protéines ayant un pI de l'ordre de 7,6. C'est d'autant plus intéressant que les annotations des protéines de cette région du diagramme sont annotées comme mettant en œuvre des protons ou comme des protéines sécrétées. C'est compatible avec un niveau de protons accessibles correspondant à ce point isoélectrique. Le pI peut donc être utilisé pour faire des inférences fonctionnelles à propos des protéines de fonction inconnue. Cet exemple a été utilisé au cours de nombreuses conférences pour proposer la méthode des "voisinages" dans l'inférence fonctionnelle.

L Serina, C Blondin, E Krin, O Sismeiro, A Danchin, H Sakamoto, AM Gilles, O Barzu
Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP
Biochemistry (1995) 34: 5066-5074

BH Song, V de la Fuente, P Glaser, A Danchin
Direct isolation of the gerB - narA stretch from Bacillus subtilis chromosome by I- Sce l site insertion
Mol Cells (1995) 5: 77-80

G Villani, M Tattoli, N Capitanio, P Glaser, S Papa, A Danchin
Functional analysis of subunits III and IV of Bacillus subtilis aa3-600 quinol oxidase by in vitro mutagenesis and gene replacement
Biochim Biophys Acta (1995) 1232: 67-74

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1996

F Biville, C Laurent-Winter, A Danchin
In vivo positive effects of exogenous pyrophosphate on Escherichia coli cell growth and stationary phase survival
Res Microbiol (1996) 147: 597-608

A Bouhss, M Vincent, H Munier, AM Gilles, M Takahashi, O Barzu, A Danchin, J Gallay
Conformational transitions within the calmodulin-binding site of Bordetella pertussis adenylate cyclase studied by time-resolved fluorescence of Trp242 and circular dichroism
Eur J Biochem (1996) 237: 619-628

N Bucurenci, H Sakamoto, P Briozzo, N Palibroda, L Serina, RS Sarfati, G Labesse, G Briand, A Danchin, O Barzu, AM Gilles
CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases
J Biol Chem (1996) 271: 2856-2862

A Danchin
mRNA turnover and DNA synthesis: a lesson from bacterial genome comparisons
Mol Microbiol (1996) 20: 895-897

A Danchin
By way of introduction: some constraints of the cell physics that are usually forgotten, but should be taken into account for in silico genome analysis
Biochimie (1996) 78: 299-301

fr A Danchin
Séquençage des grands génomes et médecine.
In: "Biomedecine 2000 - Faits et réflexions sur les systèmes de santé de l'an 2000" Hénri Joly ed., Lavoisier (1996) pp 125-131

fr A Danchin
Postface à: "Le droit saisi par la biologie. Des Juristes au laboratoire". "Regards d'un biologiste"
Editions LGDJ (1996) pp 395-408

fr A Danchin
Dialogue entre Chine et Occident: une question d'énergie potentielle
In: "La Licorne et le Dragon" - Les Malentendus dans la Recherche de l'Universel - (Ed  D Yue, A Le Pichon) Peking University Press (1996) pp 66-77 pdf

A Danchin [Article écrit pour la clôture du Centenaire de la mort de Louis Pasteur à Marnes la Coquette (28.09.1995)]
Dai minerali alla vita
fr Des minéraux à la vie: une alternative à la soupe prébiotique
From minerals to life : an alternative to the prebiotic soup
Prometeo (1996)14 (54): 16-21

fr A Danchin
L'inutile cri de Cassandre
Le Monde / Mardi 27 Août 1996, P 11
pdf

A Danchin
On genomes and cosmologies
In: "Integrative Approaches to Molecular Biology" (J Collado-Vides, B Magasanik and TF Smith eds), The MIT Press (1996) pp 91-111 pdf

A Danchin
In silico
comparison of bacterial genomes
Microbial Comparative Genomics (1996) 1: 201

A Danchin
Noama Chomsky'ego Proba Rewolucji Naukowej, Tom 2
IFiS Publishers (1996) pp 193-208

fr A Danchin
Chroniques 1996 dans La Recherche
Un bricolage linguistique bien enrichissant, 283: 82
Les oiseaux préfèrent les papillons femelles, 284: 96
Eloge de la galanterie, 286: 97
Demain, l'avis faber ?, 287: 96
C'est l'opportunisme qui fait la fonction, 288: 95
Sélection en trompe l'oeil, 290: 95
Le cri du haricot, 291: 96
Les causes sérieuses n'ont pas de prix, 292: 96
Camouflage au parfum, 293: 94

V Dumay, A Danchin, M Crasnier
Regulation of Escherichia coli adenylate cyclase activity during hexose phosphate transport
Microbiology (1996) 142: 575-583

A Hénaut, T Rouxel, A Gleizes, I Moszer, A Danchin
Uneven distribution of GATC motifs in the Escherichia coli chromosome, its plasmids and its phages
J Mol Biol (1996) 257: 574-585

A Hénaut, A Danchin
Analysis and Predictions from Escherichia coli sequences or E. coli in silico
In: Escherichia coli and Salmonella, Cellular and Molecular Biology (Editor in Chief: Frederick C Neidhardt) vol. 1, chap 114, pp 2047-2065

I Moszer, F Kunst, A Danchin
The European Bacillus subtilis genome sequencing project: current status and accessibility of the data from a new World Wide Web site
Microbiology (1996) 142 ( Pt 11): 2987-2991

MM Nakano, P Zuber, P Glaser, A Danchin, FM Hulett
Two-component regulatory proteins ResD-ResE are required for transcriptional activation of fnr upon oxygen limitation in Bacillus subtilis
J Bacteriol (1996) 178: 3796-3802

P Trotot, O Sismeiro, C Vivarès, P Glaser, A Bresson-Roy, A Danchin
Comparative analysis of the cya locus in enterobacteria and related gram-negative facultative anaerobes
Biochimie (1996) 78: 277-287

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1997

C Biderre, F Duffieux, E Peyretaillade, P Glaser, P Peyret, A Danchin, M Pages, G Metenier, CP Vivarès
Mapping of repetitive and non-repetitive DNA probes to chromosomes of the microsporidian Encephalitozoon cuniculi
Gene (1997) 191: 39-45

MP Coudart-Cavalli, O Sismeiro, A Danchin
Bifunctional structure of two adenylyl cyclases from the myxobacterium Stigmatella aurantiaca
Biochimie (1997) 79: 757-767

A Danchin, A Hénaut
The map of the cell is in the chromosome
Curr Opin Genet Dev (1997) 7: 852-854
pdf

A Danchin
Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP
DNA Res (1997) 4: 9-18

uk-flagDeoxyribonucleotides are synthesized in an odd way: they start from ribonucleoside diphosphates, not triphosphates. However, there is no direct de novo synthesis of CDP, so that DNA synthesis would not be possible if CMP, or CDP were not produced through recycling processes. In prokaryotes, this is performed by mRNA turnover, and in eukaryotes, rich in membranes, this is produced by membranes biosynthesis  

fr-flagLes désoxyribonucléotides sont synthétisés de façon étrange : ils viennent des ribonucléoside diphosphates, pas des triphosphates. Or il n'y a pas de synthèse de novo du CDP, et la synthèse de l'ADN devrait être impossible si le CMP ou le CDP n'étaient produits par recyclage. Chez les procaryotes, cela est réalisé par la dégradation de l'ARN, et chez les eucaryotes riches en membranes, c'est le résultat de la synthèse des phospholipides

P Bertin S Goyard
Characterization of BpH3, an H-NS-like protein in Bordetella pertussis
Mol Microbiol (1997) 24: 815-823
PubMed

fr A Danchin
L'enfance de la Biologie Moléculaire
Aux Frontières de la Science (1997) P 50
Supplément CNRS à La Recherche

A Danchin, C Médigue, F Rechenmann
Integrated Genome Informatics.
In: "Bacterial Genomes, Physical Structure, Analysis" (F. J. de Bruijn, J. R. Lupski,, G. M. Weinstock eds) (1997) pp 567-582

fr A Danchin
Apologie de la Création
Information Génétique et Expression
JIB/Ethique (1997) 8: 63-75.

fr A Danchin
Chroniques 1997 dans La Recherche
Le nom de l'ancêtre, 294: 96
Mais que font les parents ? 295: 91
Que vaut la leçon du Professeur Sokal? Electrochoc pour schizophrène, 297: 94
L'algorithme de la queue, 298: 91
Le sexe obsolète, 299: 94
Le rouge et le noir, 301: 110
Vers la génétique de l'évolution, 302: 116
Intelligence et hérédité: un débat en cache un autre, 303: 108
Aller de la fonction à la structure. Et non l'inverse, 304: 108

P Guerdoux-Jamet, A Hénaut, P Nitschké, JL Risler, A Danchin
Using codon usage to predict genes origin: is the Escherichia coli outer membrane a patchwork of products from different genomes?
DNA Research (1997) 4: 257-265

F Kunst, N Ogasawara, I Moszer, AM Albertini, G Alloni, V Azevedo, MG Bertero, P Bessières, A Bolotin, S Borchert, R Borriss, L Boursier, A Brans, M Braun, SC Brignell, S Bron, S Brouillet, CV Bruschi, B Caldwell, V Capuano, NM Carter, SK Choi, JJ Codani, IF Connerton, NJ Cummings, RA Daniel, F Denizot, KM Devine, A Düsterhöft, SD Ehrlich, PT Emmerson, KD Entian, J Errington, C Fabret, E Ferrari, D Foulger, C Fritz, M Fujita, Y Fujita, S Fuma, A Galizzi, N Galleron, SY Ghim, P Glaser, A Goffeau, EJ Golightly, G Grandi, G Guiseppi, BJ Guy, K Haga, J Haiech, CR Harwood, A Hénaut, H Hilbert, S Holsappel, S Hosono, MF Hullo, M Itaya, L Jones, B Joris, D Karamata, Y Kasahara, M Klaerr-Blanchard, C Klein, Y Kobayashi, P Koetter, G Koningstein, S Krogh, M Kumano, K Kurita, A Lapidus, S Lardinois, J Lauber, V Lazarevic, SM Lee, A Levine, H Liu, S Masuda, C Mauël, C Médigue, N Medina, RP Mellado, M Mizuno, D Moesti, S Nakai, M Noback, D Noone, M O'Reilly, K Ogawa, A Ogiwara, B Oudega, SH Park, V Parro, TM Pohl, D Portetelle, S Porwollik, AM Prescott, E Presecan, P Pujic, B purnelle, G Rapoport, M Rey, S Reynolds, M Rieger, C Rivolta, E Rocha, B Roche, M Rose, Y Sadaie, T Sato, E Scalan, S Schleich, R Schroeter, F Scoffone, J Sekiguchi, A Sekowska, SJ Seror, P Serror, BS Shin, B Soldo, A Sorokin, E Tacconi, T Takagi, H Takahashi, K Takemaru, M Takeuchi, A Tamakoshi, T Tanaka, P Terpstra, A Tognoni, V Tosato, S Uchiyama, M Vandenbol, F Vannier, A Vassarotti, A Viari, R Wambutt, E Wedler, T Weitzenegger, P Winters, A Wipat, H Yamamoto, K Yamane, K Yasumoto, K Yata, K Yoshida, HF Yoshikawa, E Zumstein, H Yoshikawa, A Danchin
The complete genome sequence of the gram-positive bacterium Bacillus subtilis
Nature (1997) 390: 249-256
pdf   science_watch

L'idée du séquençage du génome de Bacillus subtilis, proposée à la Société Française de Microbiologie au début de l'année 1987 s'achevait dix ans plus tard après des péripéties compliquées (résumées dans La Barque de Delphes). De très nombreuses observations sont issues de ce programme, en particulier l'existence d'un très grand nombre de gènes à la fonction inconnue, et d'une frange de gènes "orphelins" dont les propriétés spécifiques ont été découvertes six ans plus tard. Comme dans le cas de E. coli, on trouvait aussi dans ce génome que bien des gènes se propagent par transfert horizontal. Ce génome a été si difficile à séquencer (pour des raisons moléculaires comprises un peu plus tard), qu'il est resté durant cinq an le seul connu de ce type (un génome riche en A+T de Firmicute)  

The idea of sequencing the Bacillus subtilis genome, proposed by the scientific coordinator at a meeting of the French Society for Microbiology in 1987, was completed ten years later after a quite hectic series of events (summarized in The Delphic Boat). Many fascinating observations came out of this programme, in particular the noteworthy existence of very many genes of unknown function, and a fraction of "orphan" genes with specific features uncovered six years later. As in in E. coli, one also observed in this genome that many genes are propagated by horizontal transfer. This genome was so difficult to sequence (for molecular reasons later understood), that it remained the only one of its kind (the genome of an A+T-rich Firmicute) for five years

C Laurent-Winter, S Ngo, A Danchin, P Bertin
Role of Escherichia coli histone-like nucleoid-structuring protein in bacterial metabolism and stress response--identification of targets by two-dimensional electrophoresis
Eur J Biochem (1997) 244: 767-773

I Moszer, P Glaser, A Danchin, F Kunst
Organization of the European Bacillus subtilis genome sequencing project
In: "Bacterial Genomes, Physical Structure, Analysis" (F. J. de Bruijn, J. R. Lupski, G. M. Weinstock eds) (1997) pp 457-467

E Presecan, I Moszer, L Boursier, HC Cruz Ramos, V de la Fuente, MF Hullo, C Lelong, S Schleich, A Sekowska, BH Song, G Villani, F Kunst, A Danchin, P Glaser
The Bacillus subtilis genome from gerBC (311 degrees) to licR (334 degrees)
Microbiology (1997) 143 ( Pt 10): 3313-3328

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1998

N Bucurenci, L Serina, C Zaharia, S Landais, A Danchin, O Barzu
Mutational analysis of UMP kinase from Escherichia coli
J Bacteriol (1998) 180: 473-477

A Danchin
The Delphic boat or what the genomic texts tell us
Bioinformatics (1998) 14: 383
 

fr A Danchin
La Barque de Delphes, ce que révèle le texte des génomes
Odile Jacob, (1998)

fr A Danchin
Des minéraux à la vie: une alternative à la soupe prébiotique ?
In: Dictionnaire de l'ignorance, Aux frontières de la Science (PUF) (1998) pp 196-212

fr A Danchin
Nankin 1965 - 1996: Mémoires chinois .
In: Culture: Diversité et coexistence dans le dialogue Chine - Occident, Actes du colloque international de Nanjing (1998) pp 149-156

fr A Danchin, P Glaser, F Kunst, I Moszer, G Rapoport
Bacillus subtilis dévoile ses gènes
Biofutur (1998) 174: 14-17

fr A Danchin
La "mémoire de l'eau", épisode extravagant de l'ordinaire pratique scientifique
Silice, basophiles et comités de lecture
La Recherche (1998) 310: 85-87

frA Danchin
Chroniques1998 dans La Recherche
Le déterminé n'est pas le prévisible 306: 114
L'opportunisme absolu de l'évolution 307: 108
Au fond des ocelles, 308: 108
La mémoire des efforts passés, 310: 111
Pilote fantôme, 311: 128
Variez vos poisons !, 312: 106
Mon clone, cet inconnu, 313: 126
La dissymétrie, est-ce la vie ?, 314: 111
Alzheimer et la génétique, 315: 110

F Delbac, P Peyret, G Metenier, D David, A Danchin, CP Vivarès
On proteins of the microsporidian invasive apparatus: complete sequence of a polar tube protein of Encephalitozoon cuniculi
Mol Microbiol (1998) 29: 825-834

A Hénaut, F Lisacek, P Nitschké, I Moszer, A Danchin
Global analysis of genomic texts: the distribution of AGCT tetranucleotides in the Escherichia coli and Bacillus subtilis genomes predicts translational frameshifting and ribosomal hopping in several genes
Electrophoresis (1998) 19: 515-527

P Nitschké, P Guerdoux-Jamet, H Chiapello, G Faroux, C Hénaut, A Hénaut, A Danchin
Indigo: a World-Wide-Web review of genomes and gene functions
FEMS Microbiol Rev (1998) 22: 207-227
pdf

Cet article illustre comment le concept de voisinage permet de faire des inférences efficaces. Il décrit la base de données Indigo où le voisinage des gènes d'organismes modèles peut être exploré. Cette approche a été présentée systématiquement de 1994 à 1998 dans les conférences et ateliers de la naissance de la génomique. Le détail de l'aventure correspondante est présenté dans La Barque de Delphes

 

This article illustrates how the concept of neighborhood allows investigators to perform inductive reasoning. It describes the Indigo database where a variety of gene neighborhoods can be explored. This approach has been presented on many occasions at conferences and workshops that participated to the birth of genomics as a new domain. The cognate history is presented in details in The Delphic Boat

EPC Rocha, A Viari, A Danchin
Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons
Nucleic Acids Res (1998) 26: 2971-2980
pdf

A Sekowska, P Bertin, A Danchin
Characterization of polyamine synthesis pathway in Bacillus subtilis 168
Mol Microbiol (1998) 29: 851-858
pdf

O Sismeiro, P Trotot, F Biville, C Vivarès, A Danchin
Aeromonas hydrophila adenylyl cyclase 2: a new class of adenylyl cyclases with thermophilic properties and sequence similarities to proteins from hyperthermophilic archaebacteria
J Bacteriol (1998) 180: 3339-3344
J_Bact

Cet article identifie une nouvelle classe d'adénylcyclases, très différentes des trois classes précédemment décrite par les travaux de l'Unité. Son origine est encore en cours d'exploration  

This article identifies a new (fourth) class of adenylyl cyclases, that differ considerably from the three classes previously described from the work of the Unit. Its origin is still under investigation

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1999

NN Baranova, A Danchin, AA Neyfakh
Mta, a global MerR-type regulator of the Bacillus subtilis multidrug-efflux transporters
Mol Microbiol (1999) 31: 1549-1559

P Bertin, N Benhabiles, E Krin, C Laurent-Winter, C Tendeng, E Turlin, A Thomas, A Danchin, R Brasseur
The structural and functional organization of H-NS-like proteins is evolutionarily conserved in gram-negative bacteria
Mol Microbiol (1999) 31: 319-329

A Danchin
From protein sequence to function
Curr Opin Struct Biol (1999) 9: 363-367
pdf

A. Danchin
Il Linguaggio della vita.
Nuova Secondaria Editrice La Scuola, (1999) XVII: 20-24.

fr A Danchin
Chroniques1999 dans La Recherche
Des souris mutantes à la viande rose 316: 105
Sida: le mirage du vaccin? 318: 106
Avenir imprévisible de l'homme 319: 105
La logique de Saint Thomas, 320: 107
Pierres, répétitions, barreaux 321: 110
La nécessité de mourir 322: 110
Du bon usage des métaphores 323: 106
Le tablier du moineau 324: 111
Pièges de la domestication 325: 108
L’habit ne fait pas le moine, 326: 28

A Danchin
From function to sequence, an integrated view of the genome texts
Physica A (1999) 273: 92-98

L Frangeul, KE Nelson, C Buchrieser, A Danchin, P Glaser, F Kunst
Cloning and assembly strategies in microbial genome projects
Microbiology (1999) 145 ( Pt 10): 2625-2634
pdf

S Landais, P Gounon, C Laurent-Winter, JC Mazie, A Danchin, O Barzu, H Sakamoto
Immunochemical analysis of UMP kinase from Escherichia coli
J Bacteriol (1999) 181: 833-840
J_Bact

Cet article démontre que, bien qu'elle se comporte in vitro comme une protéine cytoplasmique ordinaire, l'uridylate kinase est compartimentée à la surface de l'enveloppe bactérienne  

This article shows that, although it behaves in vitro as a standard cytoplasmic protein, uridylate kinase is associated to the cell's envelope, demonstrating compartmentalization of its activity

C Médigue, M Rose, A Viari, A Danchin
Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence
Genome Res (1999) 9: 1116-1127

C Médigue, F Rechenmann, A Danchin, A Viari
Imagene: an integrated computer environment for sequence annotation and analysis
Bioinformatics (1999) 15: 2-15

I Moszer, EPC Rocha, A Danchin
Codon usage and lateral gene transfer in Bacillus subtilis
Curr Opin Microbiol (1999) 2: 524-528
pdf

M Perrotte-Piquemal, A Danchin, F Biville
Pyrophosphate increases the efficiency of enterobactin-dependent iron uptake in Escherichia coli
Biochimie (1999) 81: 245-253

E Presecan-Siedel, A Galinier, R Longin, J Deutscher, A Danchin, P Glaser, I Martin-Verstraete
Catabolite regulation of the pta gene as part of carbon flow pathways in Bacillus subtilis
J Bacteriol (1999) 181: 6889-6897
J_Bact

EPC Rocha, A Danchin, A Viari
Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes
Mol Biol Evol (1999) 16: 1219-1230
pdf

EPC Rocha, A Danchin, A Viari
Functional and evolutionary roles of long repeats in prokaryotes
Res Microbiol (1999) 150: 725-733
pdf

EPC Rocha, A Danchin, A Viari
Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis
Nucleic Acids Res (1999) 27: 3567-3576
pdf

EPC Rocha, A Danchin, A Viari
Universal replication biases in bacteria
Mol Microbiol (1999) 32: 11-16
pdf

EPC Rocha, A Danchin, A Viari
Bacterial DNA strand compositional asymmetry: response
Trends Microbiol (1999) 7: 308

A Sekowska, A Danchin
Identification of yrrU as the methylthioadenosine nucleosidase gene in Bacillus subtilis
DNA Res (1999) 6: 255-264

O Soutourina, A Kolb, E Krin, C Laurent-Winter, S Rimsky, A Danchin, P Bertin
Multiple control of flagellum biosynthesis in Escherichia coli: role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the flhDC master operon
J Bacteriol (1999) 181: 7500-7508
J_Bact

G Villani, N Capitanio, A Bizzoca, LL Palese, V Carlino, M Tattoli, P Glaser, A Danchin, S Papa
Effects of site-directed mutagenesis of protolytic residues in subunit I of Bacillus subtilis aa3-600 quinol oxidase. Role of lysine 304 in proton translocation
Biochemistry (1999) 38: 2287-2294




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