earthquake
What would be later called the biotechnology industry emerged during the 1970s. The naming is itself significant because many of the projects the industry began with were old ones, some, such as fermentation processes, quite hoary. Whether projects such as beer making or producing antibiotics and vitamins should be considered precursors of the new biotechnology or holdovers from a previous time reflects the limits of epochal labels.

Paul RABINOW


Table of Contents

Related Topics

EU consortia

Origin of genome projects

The Human Genome
Databases
Bacillus subtilis

   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 PubMed ISI 36

 

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 knowhow thus acquired was applied to Bacillus subtilis. Specific examples of the general procedure are given.]
Res Microbiol
(1991) 142: 913-916 PubMed ISI 11

 

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. [...]"

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2007-present, 1985 - 1997

The Bacillus subtilis genome programme

 


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

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: 757-770PubMed pdf ISI 34

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 PubMed pdf ISI 177

resequencing

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 PubMed

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 PubMed ISI 103

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 PubMed [this article is found in PubMed with a truncated list of authors]
ISI 184

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 PubMed ISI 88

F Kunst, A Vassarotti, A Danchin
Organization of the European Bacillus subtilis genome sequencing project
Microbiology (1995) 141 ( Pt 2): 249-255 PubMed ISI30

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 PubMed ISI 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 PubMed

I Moszer, P Glaser, A Danchin
SubtiList: a relational database for the Bacillus subtilis genome
Microbiology (1995) 141: 261-268 PubMed ISI 164

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 PubMed ISI15

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 PubMed pdf ISI 2728

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.

Ninth Genome Sequencing and Analysis Conference

The complete genome sequence of Bacillus subtilis, a gram-positive bacterium, has been determined by a consortium of Japanese and European laboratories. As summarized by Antoine Danchin (Institut Pasteur), the 4,214,807-bp genome, of which 87% is coding, can specify more than 4000 genes. The task of obtaining this complete genomic sequence was made difficult because the B. subtilis DNA is very toxic in Escherichia coli. About half the ORFs specify single-copy genes. Around 60% of the genes could be assigned a sure or probable role or biological function. Another 25% had possible [probability lower than e10(-10) or putative e10(-6)] assignments, leaving about 15% with no role or function present in the searched databases. About 100 operons are conserved between B. subtilis and E. coli. Transcription of the B. subtilis genome is mainly in the same direction as replication. A significant proportion of the biosynthetic capacity of B. subtilis is for utilization of carbohydrates, for interaction of the bacterium with plants, and for metabolizing branched chain acids.

By Darrell Doyle, The Institute for Genomic Research

Plenary sessions were devoted to Microbial Genomes, Microarraying Technology, Functional Analysis, Eukaryotic Genomes, Genome Biology, Advanced Technology and New Approaches, and Analysis of Human Genomes. There were three well-attended breakout sessions on Informatics, Technology, and Genomics as well as poster sessions from 1 to 4 p.m. on Sunday, Monday, and Tuesday.

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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 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  PubMed microme ISI 256

Escherichia fergusonii and various Escherichia coli strains


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 PubMed ISI 592

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 PubMed ISI 70

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

C Médigue, A Viari, A Hénaut, A Danchin
Escherichia coli molecular genetic map (1500 kbp): update II
Mol Microbiol (1991) 5: 2629-2640 PubMed ISI 40

C Médigue, A Viari, A Hénaut, A Danchin
Colibri: a functional data base for the Escherichia coli genome
Microbiol Rev (1993) 57: 623-654 PubMed ISI 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 PubMed pdf ISI 285

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.  

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 PubMed ISI 77

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 PubMed ISI 44

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 PubMed DNA_Res

HKU_Pasteur
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 pubmed BMC biosapiens ISI 7

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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 PubMed PhotoList pdf ISI 376

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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
9: 210 PubMed  BMC F1000
ISI 60
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 <PubMed PsychroList TAC125 ISI 223

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 PubMed ISI 11

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 PubMed ISI 5


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: 120-132PubMed ISI 53

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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 PubMed codon usage ISI 85

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 PubMed PDF ISI 31

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 ISI 37

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 ISI 34

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 PubMed ISI 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 PubMed ISI 19


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

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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 PubMed LeptoList pdf ISI 366

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 PubMed SepiList pdf ISI 242

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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 pubmed pdf
ISI 44

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 (2013) Jul 16. doi: 10.1111/1462-2920.12210. pubmed ISI 9

 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 pubmed ISI 10

V de Lorenzo, A Sekowska, A Danchin,
Chemical reactivity drives spatiotemporal organisation of bacterial metabolism
FEMS Microbiology Reviews (2015) 39: 96-119 ISI 20
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

A Danchin, A Sekowska

The logic of metabolism
Perspectives in Science (2015) 6: 15-26


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