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Génétique des Génomes Bactériens |
Genetics of
Bacterial Genomes
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Curriculum vitae (excerpts)
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A Danchin |
Not every truth is good. The dangers of publishing knowledge about potential bioweapons | |
-EMBO Rep (2002) 3: 102-104 |
An overview of this first work on adenylyl cyclases is summarised in:
A Danchin
Phylogeny of adenylate cyclases
Adv Second Messenger Phosphoprotein Res (1993) 27:
109-162
This article creates the international reference for the classification of adenylyl cyclases. Initially, three classes from different phylogenetic descent (convergent evolution) were identified: Class I, cyclases from enterobacteria and related bacteria; Class II, secreted toxic cyclases; Class III, "universal" class present in Bacteria and in Eukarya (including higher vertebrates). A fourth class, also from a completely different phylogenetic origin was discovered several years later in the Unit:
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
The "universal" cyclases class (class III) clusters together adenylyl and guanylyl cyclases, and an original selection procedure allows one to go from one type of specificity to the other one (this was one of the very first experiments showing that it is possible to change the specificity of an enzyme for its substrate):
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
Genome studies implied the creation of a global in silico analysis of the genome texts. A first analysis of 800 genes from E. coli allowed their clustering into three major classes: core metabolism, genes expressed at a high level under rapid growth, and genes coming from outside…
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 very early work of genomics in silico demonstrated for the first time that a large fraction (at least one sixth) of the genes of E. coli are derived from horizontal gene transfer. It also shows that antimutator genes are likely to be propagated by horizontal gene transfer, suggesting that bacteria in the environment are often in a highly mutable state, which is fixed in a much more rigid (invariable) form when they meet a stable biotope. Another observation from this study is the clustering of HGT genes in relation with particular cell processes, suggesting that genomes are organised entities:
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
The fact that this observation is general would be demonstrated later on, in the case of Bacillus subtilis. The importance of HGT is so well accepted nowadays that it has become common knowledge in biology:
I
Moszer, EPC Rocha, A Danchin
Codon usage and lateral gene transfer in Bacillus
subtilis
Curr Opin Microbiol (1999) 2: 524-528
The setting up of the sequencing of the genome of Bacillus subtilis, first project of this type launched for conceptual and not technological reasons, was publicly proposed by AD at the beginning of 1987. This resulted, in parallel with the same result obtained by the consortium sequencing the genome of Saccharomyces cerevisiae, in the first significant discovery of genomics, that found that many genes were completely unknown, not only in their sequence but also in their function and in the structure of their product:
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 [it is
amusing to note that this article is listed at PubMed with a
truncated authors' list: biologists were not, at the time,
familiar with the long lists of authors that are frequent in
physics]
This article shows, for the first time, that in a long DNA fragment sequenced in full, half of the genes did not look like anything known until then. This utterly unexpected result (the opponents to genome sequencing projects had "demonstrated" that we knew at least 95% of all possible gene classes and published this demonstration in the most fashionable journals), presented with a similar conclusion from the sequencing of the yeast's chromosome III, at the first genomics symposium organised by the commission of European Communities in Elounda in Crete in 1991, revealed the first major discovery obtained by genome projects.
Performed by a consortium associating Europe and Japan, the sequencing of the B. subtilis genome was completed in 1997, at the same time as that of E. coli. As early as 1995 the total length of continuous fragments from the organism was significantly larger than that of the genomes then sequenced by Craig Venter and his colleagues. This was not much noticed however: Science has now become an activity in the domain of show business. However this genome remained for five years the only example of its domain (the genomes of the Firmicutes are particularly difficult to sequence, because their DNA is usually toxic in the universal host used to construct DNA libraries, E. coli, for biochemical reasons well understood by the authors of this project) :
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
As an anecdote, it is amusing to remark that the length of this genome, 4 megabases, represented more than the total length of what The Institute for Genome Research, TIGR, with its well chosen name, had already sequenced. It was also, with the genome of E. coli which has a comparable length, the longest sequence of a known DNA fragment until that date.
The distribution of the corresponding sequence and annotations to the international community was coordinated by AD, in the form of a specialised database with no exact counterpart until now:
C
Médigue, A Viari, A Hénaut, A Danchin
Colibri: a functional data base for the Escherichia
coli genome
Microbiol Rev (1993) 57: 623-654
I
Moszer, P Glaser, A Danchin
SubtiList: a relational database for the Bacillus
subtilis genome
Microbiology (1995) 141 ( Pt 2): 261-268
I Moszer, LM Jones, S
Moreira, C Fabry, A Danchin
SubtiList: the reference database for the Bacillus
subtilis genome
Nucleic Acids Res (2002) 30: 62-65
Later on, AD participated to or organised several genome projects: Leptospira interrogans and Staphylococcus epidermidis, in collaboration with the Shanghai Genome Center, Photorhabdus luminescens, at the Institut Pasteur, and more recently, to try and understand the impact of the temperature constraints on genomes, the genome of the Antarctica bacteria Pseudoalteromonas haloplanktis TAC125, in collaboration with the Genoscope and several universities in the world. Within a few years, technological progresses both in vitro and in silico have been so extraordinary that this last project asked, in terms of workforce, one hundred times less person/years that that of B. subtilis:
E Duchaud, C Rusniok,
L Frangeul, C Buchrieser, A Givaudan, S Taourit, S Bocs, C
Boursaux-Eude, M Chandler, JF Charles, E Dassa, R Derose, S
Derzelle, G Freyssinet, S Gaudriault, C Médigue, A Lanois, K
Powell, P Siguier, R Vincent, V Wingate, M Zouine, P Glaser, N
Boemare, A Danchin, F Kunst
The genome sequence of the entomopathogenic
bacterium Photorhabdus luminescens
Nature Biotechnol (2003) 21: 1307-1313
C Médigue, E Krin, G
Pascal, V Barbe, A Bernsel, PN Bertin, F Cheung, S Cruveiller, S
D'Amico, A Duilio, G Fang, G Feller, C Ho, S Mangenot, G Marino,
J Nilsson, E Parrilli, EPC Rocha, Z Rouy, A Sekowska, ML Tutino,
D Vallenet, G von Heijne, A Danchin
Coping with cold: the genome of the versatile marine Antarctica
bacterium Pseudoalteromonas haloplanktis TAC125
Genome Res (2005) 15: 1325-1335
The corresponding data (sequence and annotations) is organised, together with the counterpart from genomes of bacteria interesting for medicine or environment, at the University of Hong Kong:
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G Fang, C Ho, YW Qiu, V Cubas, Z Yu, C Cabau, F Cheung, I Moszer, A Danchin |
Specialized microbial databases for inductive exploration of microbial genome sequences | |
BMC Genomics (2005) 6: 14 |
This is the very core of the work developed by AD for some twenty years: can one uncover rules in the organisation of genomes? Several laws have been discovered: first, there is a universal bias in the composition of the genes present in the leading and the lagging strand of DNA; second, and this is quite remarkable, the essential genes (experimentally identified after the sequecing project of B. subtilis) are specifically coded in the leading DNA strand:
EPC Rocha, A Danchin,
A Viari
Universal replication biases in bacteria
Mol Microbiol (1999) 32: 11-16
A Danchin, P
Guerdoux-Jamet, I Moszer, P Nitschké
Mapping the bacterial cell architecture into the
chromosome
Philos Trans R Soc Lond B Biol Sci (2000) 355:
179-190
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EPC Rocha, A Danchin |
Ongoing evolution of strand composition in bacterial genomes | |
Mol Biol Evol (2001) 18: 1789-1799 |
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EPC Rocha, A Danchin |
Essentiality, not expressiveness, drives gene-strand bias in bacteria | |
Nature Genetics (2003) 34: 377-378 |
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EPC Rocha, A Danchin |
Gene essentiality determines chromosome organisation in bacteria | |
Nucleic Acids Res (2003) 31: 6570-6577 |
Considering genomes as wholes, one knew for more than a decade that there exists a 10-11.5 period in the nucleotide distribution, and this is true from prokaryotes to eukaryotes. This bias is present throughout a given genome, both in coding and non-coding sequences. Using a technique for analysis of auto-correlations based on linear projection the sequences responsible for the bias were identified. These ubiquitous patterns were termed "class A flexible patterns". Each pattern is composed of up to ten conserved nucleotides or dinucleotides distributed into a discontinuous motif. Each occurrence spans a region up to 50 bp in length. There is some limited fluctuation in the distances between the nucleotides composing each occurrence of a given pattern, suggesting that they are constrained by DNA supercoiling and/or bending. When taken together, these patterns cover up to half of the genome in the majority of prokaryotes. They generate the previously recognized 11 bp periodic bias. Judging from the structure of the patterns, it was suggested that they may define a dense network of protein interaction sites in chromosomes:
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E Larsabal, A Danchin |
Genomes are covered with ubiquitous 11bp periodic patterns, the "class A flexible patterns" | |
BMC Bioinformatics (2005) 6: 206 |
The corresponding constraints are visible in the amino acid sequence of the proteins, suggesting that the sequence is more constrained by the genome organisation than by the protein function. These novel observations have considerable implications in terms of phylogenetic profiles when one analyses protein sequences:
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EPC Rocha, A Danchin |
Base composition bias might result from competition for metabolic resources | |
Trends Genet (2002) 18: 291-294 |
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G Pascal, C Médigue, A Danchin |
Universal biases in protein composition of model prokaryotes | |
Proteins (2005) 60: 27-35 |
This latter work characterises “orphan” proteins which form approximately 10% of any genome of a new species. These proteins are characterized by their enrichment in aromatic amino acids. This work proposes that many among the represent the "self" of the species, by behaving as “gluons” which bring about an extra contribution is the stability of multiprotein complexes in the cell. This would bring an essential contribution to the functional stabilisation of complex intracellular structures. More generally the approach thus defined allowed the investigators to define the essentiality of a gene in a real context, by measuring its persistence in many species, not only in sequence but also in its place in the genome:
G Fang, EPC
Rocha, A Danchin
How essential are non-essential genes?
Mol Biol Evol (2005) 22:
2147-2156
In summary, it appears that bacterial genomes are highly organised entities, contrary to a widely spread idea of a random "fluidity" of genomes. What are the selective constraints that support this organisation?
A
general analysis of the conservation of syntenies in a large
number of complete bacterial genomes has shown that two classes of
genes tend to stay together. The way the class of persistent genes
keep remaining grouped is organized in a way that is reminiscent
of a scenario of the origin
of life. This is why the corresponding set has been named
the paleome. In the same way, genes that are rarely found
in genomes make clusters that are easily horizontally transferred.
The corresponding genes allow the bacteria to live in a specific
niche. They are named, for this reason, the cenome (to
indicate the fact that they are shared by a community living in a
particular environment, and prone to be transferred):
A
Danchin
Archives or palimpsests? Bacterial genomes unveil a scenario for
the origin of life
Biological
Theory (2007) 2: 52-61
A Danchin, G Fang, S
Noria
The extant core bacterial proteome is an archive of the origin of
life
Proteomics (2007) 7: 875-889
The functional organisation of the genes in genomes must result from the selection pressure of simple physico-chemical principles. Beside physical causes such as the structure of water (the study of the genome of P. haloplanktis is meant to have access to some of those), AD made the simple hypothesis that gasses and radicals, because they are highly diffusible, may play a major role in cellular compartmentalisation, and might be the cause of some of the organisation of the genes in genomes. Sulfur metabolism is particularly sensitive to gasses and radicals, and it is therefore important to understand how it is organised. A first study demonstrated that sulfur-related genes are organised into islands:
EPC Rocha, A
Sekowska, A Danchin
Sulphur islands in the Escherichia coli
genome: markers of the cell's architecture?
FEBS Lett (2000) 476: 8-11
and a detailed analysis, mainly developed during the creation of the HKU-Pasteur Research Centre in Hong Kong permitted them to uncover the details of the “methionine salvage pathway”:
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A Sekowska, HF Kung, A Danchin |
Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction | |
J Mol Microbiol Biotechnol (2000) 2: 145-177 |
A Sekowska, JY Coppée,
JP Le Caer, I Martin-Verstraete, A Danchin
S-adenosylmethionine decarboxylase of Bacillus
subtilis is closely related to archaebacterial
counterparts
Mol Microbiol (2000) 36: 1135-1147
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A Sekowska, L Mulard, S Krogh, JK Tse, A Danchin |
MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis | |
BMC Microbiol (2001) 1: 15 |
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A Sekowska, A Danchin |
The methionine salvage pathway in Bacillus subtilis | |
BMC Microbiol (2002) 2: 8 |
The following work makes a synthesis of the catalytic activities involved in this ubiquitous cycle (it is also present in humans and plants), which has the interesting feature that it systematically recruited proteins of diverse structures to lead to the completion of the cycle. One of these proteins is likely to be related to the ancestor of ribulose-phosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme on the planet (this opens fascinating questions on the origin of catalytic activities):
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A Sekowska, V Dénervaud, H Ashida, K Michoud, D Haas, A Yokota, A Danchin |
Bacterial variations on the methionine salvage pathway | |
BMC Microbiol (2004) 4: 9 |
H Ashida, A
Danchin, A Yokota
Was photosynthetic RuBisCO recruited by acquisitive
evolution from RuBisCO-like proteins involved in sulfur
metabolism?
Res Microbiol (2005) 156: 611-618
This remarkable metabolic cycle has the surprising property as shown in this work, under particular conditions, to lead the cell to synthesize carbon monoxide. As this cycle exists in humans, this opens interesting perspective about possible controls mediated by CO, a gas different from nitric oxide, in the immune system and in the nervous systemx.
This work explored the role of selective stabilisation in learning and memory in the nervous system and in the immune system, opening concepts for later work in genomics.
JP Changeux, P Courrège, A Danchin
A theory of the epigenesis of neuronal networks by selective
stabilization of synapses
Proc Natl Acad Sci U S A (1973) 70:
2974-2978
A
Danchin, JP Changeux
Apprendre par stabilisation sélective de synapses en développement
In: "L'Unité de l'Homme" (Centre Royaumont pour une Science
de l'Homme) Le Seuil (1974): 320-350
JP Changeux, A Danchin
Selective stabilisation of developing synapses as a mechanism for
the specification of neuronal networks
Nature (1976) 264: 705-712
A Danchin
A selective theory for the epigenetic
specification of the monospecific antibody production in single
cell lines
Ann Immunol (Paris) (1976) 127: 787-804
A
Danchin
Stabilisation fonctionnelle et épigenèse: une approche biologique
de la genèse de l'identité individuelle
In: "L'Identité" (JM Benoist, ed) Grasset (1977): 185-221
A Danchin
The specification of the immune response: a general
selective model
Mol Immunol (1979) 16: 515-526
JP
Changeux, P Courrège, A Danchin, JM Lasry
Un mécanisme biochimique pour l'épigenèse de la
jonction neuro-musculaire
C R Séances Acad Sci III (1981) 292:
449-453
The question is now to try and understand how the future of daughter cells is organised at the time of cell divison, and what are the main selective stabilisation processes at work...
Ordre et Dynamique du Vivant. Chemins de la Biologie Moléculaire - Le Seuil, 1978.
L'Oeuf et la Poule. Histoires du code
génétique - Fayard, 1983.
In portuguese : O Ovo e a Galina. Historias do
Codigo genetico - Relogio d'agua, 1993.
Also in japanese
Une Aurore de Pierres. Aux origines de
la vie - Le Seuil, 1990.
In portuguese : Uma Aurora de Pedras. Nas origens
da vida - Almedina, 1992.
La Barque de Delphes. Ce que révèle le texte des génomes - Odile Jacob -1998
The Delphic Boat. What genomes tell us - Harvard University Press - 2003 [Comments in Nature, Nature Genetics, EMBO Reports]
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