PIONEERING COMPUTATIONAL GENOMICS 

   Our genome projects

Foreword / Avertissement

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  doi: 10.1007/BF02099961   36

Ce travail était destiné à explorer une approche d'intelligence artificielle pour découvrir des caractères encore inconnus dans les séquences. Nous avons identifié ici dix-sept descripteurs, presque tous inconnus, caractérisant les peptides signaux bactériens. Ce travail antériorise un très grand nombre d'études réalisées bien plus tard

This  work was meant to explore the power of artificial intelligence to uncover signals that would have not yet been known. Here we identified seventeen descriptors, most of them unknown, that characterized signal peptides. This work predates much of later studies in the domain

Origin of the concept of in silico experiments (1989)

A Danchin
Complete genome sequencing: future and prospects
commission of the European Communities Directorate general Science, Research and Development; Biotechnology Action Programme 1988-1989 (1988) Chapter I: pp 1-24
In this report meant to justify bacterial genome sequencing, within the yeast genome programme, we show that the minimal genome gene set should amount to less than 400 genes, with about 250 essential genes.

A. Danchin, invited to the European Commission Biology Action Programme as an observer at the Meeting on Sequencing of the Yeast Chromosome III (october 31 - november 2, 1989, Tutzing, Germany) stresses the importance of using computers in genome studies and proposes the concept of "in silico" experiments: " From the information technologies perspective, we are faced with the need to create databases where we will recognize relevant features in response to learning processes. The creation of descriptors, the genesis of exploratory hypotheses will add to the traditional methods of biology, in vivo and in vitro experiments "in silico." Some examples of projects were presented, in the domain of protein secretion." see also, in French, the summary of a recommendation to the CNRS and the Institut Pasteur presented at the Seillac INSERM meeting in 1990

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 know how thus acquired was applied to Bacillus subtilis. Specific examples of the general procedure are given.]
Res Microbiol (1991) 142: 913-916   doi: 10.1016/0923-2508(91)90073-J   18

L'apparition des ordinateurs a complètement modifié notre accès à la biologie, en particulier au moment de la création des programmes de génomique. J'ai 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 utilisée 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.

The expression "in silico" has been used in White Papers written to support the creation of bacterial genome programs. 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. [...]"

2007-present, 1985 - 1997

The Bacillus subtilis genome programme

Le domaine des bactéries est divisé en deux grandes branches où les Firmicutes, dont le modèle est Bacillus subtilis, occupent un espace considérable. Le séquençage du génome a impliqué plus de trente laboratoires, avec des expertises diverses, avec l'intention de les combiner pour associer l'information expérimentale à la séquence. Cela a eu la conséquence inévitable que l'expertise en séquençage était très différente selon les groupes, en particulier à un moment où ce travail était particulièrement long et difficile. L'apparition de nouvelles techniques, très rapides et efficaces, nous a incités à reprendre le travail et à le compléter par une annotation approfondie, en collaboration avec l'Institut Suisse de Bioinformatique. Nous avons orienté l'annotation en fonction de la division entre le paléome (gènes qui assurent la vie et la perpétue) et le cénome (gènes qui permettent l'occupation d'une niche écologique spécifique. Nous observons ainsi que B. subtilis est un épiphyte, et la nouvelle annotation devrait permettre d'explorer des expériences de validation pour comprendre la croissance et la survie, ainsi que permettre l'établissement de phylogénies robustes.

The bacterial domain is split into large branches among which the Firmicutes occupy a considerable space. Bacillus subtilis has been the model of Firmicutes for decades. Sequencing the genome involved more than thirty laboratories, with different expertises, in a attempt to make most of the experimental information associated to the sequence. This had the expected drawback that the sequencing expertise varied among the groups involved, especially at a time when sequencing genomes was extremely hard work. The development of efficient, fast and accurate sequencing techniques, in parallel with the development of high level annotation platforms motivated the resequencing work. The updated sequence has been reannotated in agreement with the UniProt protein knowledge base, keeping in perspective the split between the paleome (genes necessary for sustaining and perpetuating life) and the cenome (genes required for occupation of a niche, suggesting here that B. subtilis is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies.

	R Borriss, A Danchin, CR Harwood, C Médigue, EPC Rocha, A Sekowska, D Vallenet Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement Microb Biotechnol. (2018) 11: 3-17 doi: 10.1111/1751-7915.12461 54
	E Belda E, A Sekowska, F Le Fèvre, A Morgat, D Mornico, C Ouzounis, D Vallenet, C Médigue, A Danchin An updated metabolic view of the Bacillus subtilis 168 genome Microbiology (2013) 159: 757-770 57

V Barbe, S Cruveiller, F Kunst, P Lenoble, G Meurice, A Sekowska, D Vallenet, T Wang, I Moszer, C Médigue, A Danchin
From a consortium sequence to a unified sequence: The Bacillus subtilis 168 reference genome a decade later
Microbiology (2009) 155: 1758-1775  doi: 10.1099/mic.0.027839-0
  260

Identification of variations between the original 1997 sequence and the 2009 reannoated sequence. Comparative genomics is the cornerstone of identification of gene functions. The immense number of living organisms precludes experimental identification of functions except in a handful of model organisms. The bacterial domain is split into large branches among which the Firmicutes occupy a considerable space. Bacillus subtilis has been the model of Firmicutes for decades and its genome has been a reference for more than ten years. Sequencing the genome involved more than thirty laboratories, with different expertises, in a attempt to make most of the experimental information that could be associated to the sequence. This had the expected drawback that the sequencing expertise was quite varied among the groups involved, especially at a time when sequencing genomes was extremely hard work. The recent development of very efficient, fast and accurate sequencing techniques, in parallel with the development of high level annotation platforms motivated the present resequencing work. The updated sequence has been reannotated in agreement with the UniProt protein knowledge base, keeping in perspective the split between the paleome (genes necessary for sustaining and perpetuating life) and the cenome (genes required for occupation of a niche, suggesting here that B. subtilis is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies.

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 

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 107

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 325^o to 333^o
Mol Microbiol (1993) 10: 371-384  doi: 10.1111/j.1365-2958.1993.tb01963.x
187

Présenté à Elounda, en Crète, ce travail marquait la première grande découverte de la génomique: dans le chromosome III de la levure, et dans près de 100 kb du génome de Bacillus subtilis on remarquait une bonne moitié de gènes totalement inconnus. Piotr Slonimski les nomme alors les "EEC genes" (comme l'acronyme de l'Union Européenne de ce temps) pour "elusive, esoteric, conspicuous genes". La construction de bases de données relationnelles introduit le concept de voisinage dans l'analyse des génomes

Presented at Elounda in Crete, this work summarized the first major discovery of genomics: in yeast chromosome III as well as in a contiguous segment of almost 100 kb of Bacillus subtilis one found some half of the genes of totally unknown structure and function. Piotr Slonimski coins the name"EEC genes" (as the acronym of European Union at that early time) for "elusive, esoteric, conspicuous" genes. The construction of relational microbial genome databases introduces the concept of neighborhood in genome analysis

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  doi: 10.1128/jb.176.22.6802-6811.1994 98

F Kunst, A Vassarotti, A Danchin
Organization of the European Bacillus subtilis genome sequencing project
Microbiology (1995) 141 ( Pt 2): 249-255  31

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   16

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: 261-268  170

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: 2987-2991  16

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  3035

Ce travail, fruit d'une collaboration fructueuse entre l'Europe et le Japon, donne à la communauté internationale la référence obligée de la séquence des génomes des bactéries à coloration de Gram positive. Il est resté le seul de son genre pendant près de cinq ans, en raison des difficultés particulières du séquençage, expliquées par l'absence de protéine S1 dans le ribosome : il s'en suit que les signaux de démarrage de la traduction sont particulièrement forts dans la bactérie hôte, ce qui rend l'ADN de B. subtilis très souvent toxique. En effet les gènes sont alors exprimés à très haut niveau. La base de données SubtiList, a servi de référence à l'annotation des génomes bactériens dans le monde entier. C'est pour nous l'occasion de nous souvenir de son coordinateur, Frank Kunst, disparu prématurément.

This work is the resulta of a fruitful collaboration between Europe and Japan. It provides the international community with the reference genome for Gram positive bacteria, with which other genomes are compared and annotate. It remained the only genome of this category to be sequenced for almost five years, because of intrinsic difficulties in sequencing. This is accounted for by the absence of ribosomal protein S1: as a consequence the translation initiation signals are particularly strong, making the B. subtilis DNA often toxic in the host bacteria. Indeed, its genes are often expressed at a very high level, killing the host. The SubtiList database was the reference for annotation of bacterial genomes world-wide. We remember the untimely death of its coordinator, Frank Kunst.

In memoriam Frank Kunst, let us remember that, when the article reporting the first complete sequencing of the genome appeared in 1997, Chet Raymo, for the Boston Globe wrote (january 5th, 1998): Beauty bare on the spiral staircase […] « Euclid alone has looked on Beauty bare, » wrote the poet Edna St. Vincent Millay. Here, in this exquisite geometrical molecule [DNA], we look on Beauty bare. I felt the same response recently when I looked at a schematic map of the complete genome (genetic material) of the bacterium Bacillus subtilis in the journal Nature. […] I was looking at the gene map for Bacillus subtilis in the college library, with the 8-page foldout spread across a table. Several students stopped to look over my shoulder, curious as to what the colorful chart might be. « This is the blueprint for making a living organism, » I said. I started to provide a more complete explanation, but fell silent. The map spoke for itself. Elegant. Simple. Unfathomably profound. Beauty bare.

Meeting on Sequencing of Bacterial Genomes
Dormy House Hotel, Broadway, Worcestershire
23 – 26 april 1995 (summary by Richard Moxon and Hamilton Smith)

Genome studies in silico (Antoine Danchin)

The presentation gives reports of the completion of two microbial genomes, and much other sequence data in progress. This rapid pace of production of data indicates that the limiting factor in genome sequence studies will be analysis of data until appropriate informatics tools are developed and widely used. In the future it will be possible to undertake useful experiments using only computer analysis. The types of tools used in the Bacillus subtilis genome sequencing (see Kunst presentation, session 3) provide a good example.

One problem in the system presently used by all organisms is that data reported to data banks, either DNA or protein data, are not peer reviewed and many errors accumulate in the data banks. This creates a need for specialised data bases. One person, or a group (a « curator ») needs to take formal responsability for validating and updating the sequences for each particular organism. Some such curators, working formally or informally, exist, but their mode of operations differ in different organisms. The work of these groups needs to be supported, and the bioinformatics field should be given more recognition.

The data in data banks is in flat file format. After the data for a specific organism are assembled, the curator of the data base must set up a system which allows appropriate analysis. This report describes briefly the database system used for Bacillus : « SubtiList ». The data from the Bacillus genome are made available to all persons via an FTP site on the Internet.

A new platform integrating knowledge on the sequence data with knowledge on the methods used to analyse the data was described. The newest aspect of this approach is a formal representation of any complex chaining of analysis methods, which can then be manipulated by the user at will. This permits one to obtain a first automatic analysis of the raw data with validation, using a graphical interface. The system allows the sequences to be  addressed by diverse analysis methods, including sequence searching, sequence comparison, analysis of features, (eg ribosome binding sites) and open reading frames. It allows « rules » about sequence features to be defined (and refined) and then used in further sequence analysis. For example, the results of a BLAST searching, analysis of potential ribosome binding sites, and of codon usage patterns, can be combined in an attempt to define the « real » genes. It then creates a recursive loop, integrating learning techniques which can be used to analyse in more depth the data already analysed by the first raw analysis.

Discussion

Based on experience with organisms such as E. coli and Bacillus, the best data base systems to use depend in part on availability of systems. The SQL system should be used if possible. If many persons will be using the system, it must be fairly simple and user-friendly. The Subtilist database uses Fourth Dimension, but it will be also transferred on the World Wide Web and use SyBase. The present system is relational and can use images, and this is important, for example for educational purposes. One major problem in deciding what system to use is that no-one knows how much data will be produced. In fact, it is not yet known whether present systems will be able to carry the increasing load and variety of data, which means that we still need research in informatics with the aim of improving data handling and analysis.

Escherichia sp 1990-1997, 2007-present

Escherichia coli O104:H4

The sequencing of the genome of the strain of the dangerous outbreak affecting Germany and several European countries has been obtained remarkably fast, and deposited at the MaGe platform at the Genoscope. AMAbiotics SAS (renamed Stellate Therapeutics) was associated to this effort.

H Rohde, J Qin, Y Cui, D Li, NJ Loman, M Hentschke, W Chen, Fei Pu, Y Peng, J Li, F Xi, S Li, Y Li, Z Zhang, X Yang, M Zhao, Peng Wang, Y Guan, Z Cen, X Zhao, M Christner, R Kobbe, S Loos, J Oh, L Yang, A Danchin, GF Gao, Y Song, Y Li, H Yang, J Wang, J Xu, the E. coli O104:H4 Genome Analysis Crowd-sourcing consortium, MJ Pallen, J Wang, M Aepfelbacher, R Yang Open-source genomics of an isolate from a german family outbreak of Shiga-toxin-producing Escherichia coli O104:H4 New England Journal of Medicine (2011) On line july 27th  313

Escherichia fergusonii and various Escherichia coli strains

The ColiScope project

M Touchon, C Hoede, O Tenaillon, V Barbe, S Baeriswyl, P Bidet, E Bingen, S Bonacorsi, C Bouchier, O Bouvet, A Calteau, H Chiapello, O Clermont, S Cruveiller, A Danchin, M Diard, C Dossat, M El Karoui, E Frapy, L Garry, JM Ghigo, AM Gilles, J Johnson, C Le Bouguénec, M Lescat, S Mangenot, V Martinez-Jéhanne, I Matic, X Nassif, S Oztas, MA Petit, C Pichon, Z Rouy, C Saint Ruf, D Schneider, J Tourret, B Vacherie, D Vallenet, C Médigue, EPC Rocha, E Denamur Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths PLoS Genetics (2009) 5: e1000344 795

Data organisation for the genome sequence and annotation of Escherichia coli

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  70

C Médigue, A Hénaut, A Danchin
Escherichia coli molecular genetic map (1000 kbp): update I
Mol Microbiol (1990) 4: 1443-1454  21

C Médigue, A Viari, A Hénaut, A Danchin
Escherichia coli molecular genetic map (1500 kbp): update II
Mol Microbiol (1991) 5: 2629-2640  41

C Médigue, A Viari, A Hénaut, A Danchin
Colibri: a functional data base for the Escherichia coli genome
Microbiol Rev (1993) 57: 623-654   71

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  299

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 horizontal (aussi nommé "latéral" par ceux qui évitent de remonter aux sources) 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.

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 horizontal gene transfer (also named "lateral" by those who try to hide the original sources of the demonstration of the importance of the process) 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.

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  87

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   45

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

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 Res (1997) 4: 257-265 

	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  8

Environmental pathogens 1998 - 2009

Photorhabdus luminescens TT01

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 Nat Biotechnol (2003) 21: 1307-1313  466

Psychrophiles 2003-present

M Riley, JT Staley, A Danchin, TZ Wang, TS Brettin, LJ Hauser, ML Land, LS Thompson Genomics of an extreme psychrophile, Psychromonas ingrahamii BMC Genomics (2008) 9: 210   82

This article is the final scientific contribution of Monica Riley, who played a pioneering role in the study of the model for all bacteria, Escherichia coli

Pseudoalteromonas haloplanktis TAC125   L P S N

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  296

R Papa, S Glagla, A Danchin, T Schweder, G Marino, A Duilio
Proteomic identification of a two-component regulatory system in Pseudoalteromonas haloplanktis TAC125
Extremophiles (2006) 10: 483-490  13

E Parrilli, M Giuliani, C Pezzella, A Danchin, G Marino, ML Tutino
PhPssA is required for alpha-amylase secretion in Antarctic Pseudoalteromonas haloplanktis
Microbiology (2010) 156: 211-219  7

F Piette, S D’Amico, C Struvay, G Mazzucchelli, J Renaut, ML Tutino, A Danchin, P Leprince, G Feller Proteomics of life at low temperatures: trigger factor is the primary chaperone in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 Molecular Microbiology (2010) 76: 120-132 70

Environmental microbiology and metagenomics 2006 - present

Herminiimonas arsenicoxydans
(previously known as Cenibacter arsenoxidans, Caenibacter arsenoxydans, Cenibacterium arsenoxidans)

D Muller, C Medigue, S Koechler,V Barbe, M Barakat, E Talla, V Bonnefoy, E Krin, F Arsene-Ploetze, C Carapito, M Chandler, B Cournoyer, S Cruveiller, C Dossat, S Duval, M Heymann, E Leize, A Lieutaud, D Lievremont, Y Makita, S Mangenot, W Nitschke, P Ortet, N Perdrial, B Schoepp, P Siguier, DD Simeonova, Z Rouy, B Segurens, E Turlin, D Vallenet, A Van Dorsselaer, S Weiss, J Weissenbach, MC Lett, A Danchin, PN Bertin A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genetics (2007) 3: e53  129

C Carapito, D Muller, E Turlin, S Koechler, A Danchin, A Van Dorsselaer, E Leize-Wagner, PN Bertin, MC Lett
Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome
Biochimie (2006) 8: 595-606   35

Pseudomonas putida KT2440

	E Belda, RG van Heck, MJ Lopez-Sanchez, S Cruveiller, V Barbe, C Fraser, HP Klenk, J Petersen, A Morgat, PI Nikel, D Vallenet, Z Rouy, A Sekowska, VA Martins Dos Santos, V de Lorenzo, A Danchin, C Médigue The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis Environ Microbiol (2016) 18: 3403-3424. doi: 10.1111/1462-2920.13230 187
	PI Nikel, M Chavarría, A Danchin, V de Lorenzo From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions Curr Opin Chem Biol (2016) 34: 20-29 doi: 10.1016/j.cbpa.2016.05.011 138

Symbiotic Mycoplasmas from deep-sea organisms

Y Wang, JK Yang, OO Lee, TG Li, A Al-Suwailem, A Danchin, PY Qian Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments. PLoS One (2011) 6: e29149  7

Y Wang, J Yang, OO Lee, S Dash, SC Lau, A Al-Suwailem, TY Wong, A Danchin, PY Qian
Hydrothermally generated aromatic compounds are consumed by bacteria colonizing in Atlantis II Deep of the Red Sea.
ISME J (2011) 5: 1652-1659  27

Y Wang, JM Huang, SL Wang, ZM Gao, AQ Zhang, A Danchin, LS He Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod Bathynomus sp. Environ Microbiol (2016) 18: 2646-2659 doi: 10.1111/1462-2920.13411 30

2000-2003 Genome sequencing in collaboration with China, while creating genomics at the HKU-Pasteur Research Centre in Hong Kong

Leptospira interrogans Lai                L P S N

SX Ren, G Fu, XG Jiang, R Zeng, YG Miao, H Xu, YX Zhang, H Xiong, G Lu, LF Lu, HQ Jiang, J Jia, YF Tu, JX Jiang, WY Gu, YQ Zhang, Z Cai, HH Sheng, HF Yin, Y Zhang, GF Zhu, M Wan, HL Huang, Z Qian, SY Wang, W Ma, ZJ Yao, Y Shen, BQ Qiang, QC Xia, XK Guo, A Danchin, I Saint Girons, RL Somerville, YM Wen, MH Shi, Z Chen, JG Xu, GP Zhao
Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing
Nature (2003) 422: 888-893  431

Staphylococcus epidermidis ATCC 12228

YQ Zhang, SX Ren, HL Li, YX Wang, G Fu, J Yang, ZQ Qin, YG Miao, WY Wang, RS Chen,Y Shen, Z Chen, ZH Yuan, GP Zhao, D Qu, A Danchin, YM Wen
Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228)
Mol Microbiol (2003) 49: 1577-1593  303

1998-present: metabolism and meta-metabolism in perspective

Indigo and the concept of neighborhood: a database for placing genomes in context

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  46

Genome studies allowed us to review sulfur metabolism in Escherichia coli and Bacillus subtilis. In a specific series of studies we deciphered the methionine salvage pathway in a series of works that serve as a reference to understand this interesting pathway.

CM Chan, A Danchin, P Marlière, A Sekowska
Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis
Environ Microbiol (2014) 16: 101 doi: 10.1111/1462-2920.12210.  23

 Microme: a project for standardizing metabolic knowledge

A Danchin, A Sekowska The logic of metabolism and its fuzzy consequences Environ Microbiol (2014) 16: 19-28 20

V de Lorenzo, A Sekowska, A Danchin, Chemical reactivity drives spatiotemporal organisation of bacterial metabolism FEMS Microbiology Reviews (2015) 39: 96-119 57 Abstract We examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects