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 |
Yeast adenylate cyclase catalytic domain is carboxy
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
A
Danchin
Hérédité génétique,
hérédité
épigénétique
Confrontations psychiâtriques (1986) 27: 43-61
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
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
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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au début |
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1988 Double hybrid cloning of class II adenylate 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
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 
| 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, and develops the idea of acquisitive evolution |
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 et développe l'idée de l'évolution
thésaurisante |
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
| This
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 |
Cette
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
| Revenir
au début |
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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
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 see further
developments about the origin of life in 
| 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
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
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
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
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 .
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. |
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
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
"Experimentation in silico |
|
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
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 again an updated view of HGT in year 2000 under the name of "lateral gene transfer"... Nominalism is still extant |
|
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
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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
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
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
| Revenir
au début |
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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 part
1 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 |
|
A Danchin
Informatics
and genome sequencing programs
Biochimie (1993) 75: 319
A
Danchin 唐善
"Lun Ke Xue Mou Shi"
In: Shi hua xia Editions 93 de l'Université Sun Yat Sen (Zhong
Shan Da Xue) 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
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 |
|
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
| Revenir
au début |
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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
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
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
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
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
| In
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. |
Dans
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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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
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
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
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
A Danchin
In silico comparison of bacterial genomes
Microbial Comparative Genomics (1996) 1: 201
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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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
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 
| Deoxyribonucleotides
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 |
|
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
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 
| 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). Ce travail doit infiniment à Frank Kunst, prématurément
disparu le 2 avril 2009, victime d'une loi inique qui ne permet pas à
ceux dont l'intelligence est intacte de poursuivre leur activité. Il
doit aussi beaucoup à Hiroshi
Yoshikawa qui insista pour permettre au
Japon d'avoir une contribution considérable dans ce projet. |
|
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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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 
| A
Danchin La Barque de Delphes, ce que révèle le texte des génomes Odile Jacob, (1998) |
 |
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
|
|
EPC Rocha, A Viari, A Danchin
Oligonucleotide bias in Bacillus subtilis: general
trends and taxonomic comparisons
Nucleic Acids Res (1998) 26: 2971-2980
A Sekowska, P Bertin, A Danchin
Characterization of polyamine synthesis pathway in Bacillus
subtilis 168
Mol Microbiol (1998) 29: 851-858
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 
| 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 |
|
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au début |
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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
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
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
| 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 |
|
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
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
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
EPC Rocha, A Danchin, A Viari
Functional and evolutionary roles of long repeats in
prokaryotes
Res Microbiol (1999) 150: 725-733
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
EPC Rocha, A Danchin, A Viari
Universal replication biases in bacteria
Mol Microbiol (1999) 32: 11-16
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
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
