2006

M Bailly-Bechet, A Danchin, M Iqbal, M Marsili, M Vergassola
Codon usage domains over bacterial chromosomes
PLoS Computational Biology (2006) 2: e37 

Addendum (October 18, 2006)

( 20 K)

An issue left unexplained in this paper is the striking quantitative difference between E. coli and B. subtilis. This is clearly visible in Fig. 6, where it is shown the probability that two genes at distance l belong to the same cluster of codon usage. Clusters are characterized by a similar codon bias and were identified using a novel information-based clustering method. While both curves decay on distances sizably longer than what could be accounted by operons, B. subtilis curve manifestly features much longer correlations. It is hard to develop a biologically well-founded explanation for such a striking difference between the two organisms. More (64 K)....

(28 K)

The codon usage bias in genomes has long been associated to specific biological processes, and in particular to the horizontal transfer of genes. A finer analysis of the neighborhoods of genes with similar codon biases has uncovered an important functional correlation between neighboring genes. However, until the present work, the exact influence of translation had not been demonstrated. We show that the diffusion of rare or moderately expressed transfer RNAs is reflected in genomes by the formation of islands of common codon usage bias significantly longer than operons (30 kilobases in E. coli and 150 kilobases in B. subtilis) and that the distribution of these islands is correlated with the functions they code for.

Le biais d'usage des codons dans les génomes a depuis longtemps été associé à des processus biologiques spécifiques, et en particulier au transfert horizontal des gènes. Une analyse plus fine des voisinages d'usage des mêmes codons a montré une importante corrélation fonctionnelle. Mais, jusqu'au travail ici présenté, l'influence exacte de la traduction n'avait pas été mise en évidence. Nous montrons que la diffusion des ARN de transfert rares ou modérément représentés se reflète dans les génomes par la formation d'îlots nettement plus longs que les opérons (30 kilobases chez E. coli et 150 kilobases chez B. subtilis) et que la répartition de ces îlots est corrélée aux fonctions qu'ils codent.

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

A Danchin Genomics in the fight against mycobacterial diseases In: Development of New Antituberculosis Drugs (Editor WW Yew), Nova Science Publishers, Hauppauge NY, USA, (2006) pp 17-28

S Even, P Burguière, S Auger, O Soutourina, A Danchin, I Martin-Verstraete
Global control of cysteine metabolism by CymR in Bacillus subtilis
J Bacteriol (2006) 188: 2184-2197

U Mechold, V Ogryzko, S Ngo, A Danchin
Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells
Nucleic Acids Res (2006) 34: 2364-2373

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

G Pascal, C Médigue, A Danchin
Persistent biases in the amino-acid composition of prokaryotic proteins
Bioessays (2006) 28: 726-738  

Z Qin, J Zhang, B Xu, L Chen, Y Wu, X Yang, X Shen, S Molin, A Danchin, H Jiang, D Qu
Structure-based discovery of inhibitors of the YycG histidine kinase: New chemical leads to combat Staphylococcus epidermidis infections
BMC Microbiology (2006) 6: 96

E Turlin, G Pascal, JC Rousselle, P Lenormand, S Ngo, A Danchin, S Derzelle
Proteome analysis of the phenotypic variation process in Photorhabdus luminescens
Proteomics (2006) 6: 2705-2725

W Wei, ZW Cao, YL Zhu, XJ Wang, GH Ding, H Xu, PL Jia, D Qu, A Danchin, YX Li
Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228
BMC Genomics (2006) 7: 112  

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2007

S Chalabaev, E Turlin, JF Charles, A Namane, S Pagès, A Givaudan, E Brito-Fravallo, A Danchin, Biville F
The HcaR regulatory protein of Photorhabdus luminescens affects the production of proteins involved in oxidative stress and toxemia
Proteomics (2007) 7: 4499-4510

A Danchin
Archives or palimpsests? Bacterial genomes unveil a scenario for the origin of life
Biological Theory (2007) 2: 52-61

A Danchin An interplay between metabolic and physicochemical constraints: Lessons from the psychrophilic prokaryote genomes In: Physiology and biochemistry of extremophiles (C Gerday & N Glansdorff, Editors), ASM Press, Washington (2007) pp 208-220

A Danchin, G Fang, S Noria
The extant core bacterial proteome is an archive of the origin of life
Proteomics (2007) 7: 875-889

MF Hullo, S Auger, O Soutourina, O, Barzu, M Yvon, A Danchin, I Martin-Verstraete
The conversion of methionine to cysteine in Bacillus subtilis and its regulation
J Bacteriol (2007) 189: 187-197

Y Makita, MJL de Hoon, A Danchin
Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes
BMC Bioinformatics (2007) 8: 47

U Mechold, G Fang, S Ngo, V Ogryzko, A Danchin
YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity
Nucleic Acids Res (2007) 35: 4552-4561

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

This article describes the genome of an arsenophilic bacterium. Some of its resistance comes from management of oxido-reduction of arsenite and arsenate, but this cannot be the whole solution. In depth-analysis of the genome (unpublished in this article) suggests that formation of monothioarsenate is used to detoxify arsenic. This observation should have prevented publication of the arsenic nightmare, based on gullibility of mass media and common hype.

Cet article décrit le génome d'une bactérie arsénophile. Une partie de sa résistance au poison vient de la façon dont elle gère l'oxydo-réduction de l'équilibre arsenite / arsenate. Une analyse en profondeur du génome (non publiée dans cet article) suggère que la formation de monothioarsenate est utilisée pour détoxifier l'arsenic. Cette observation aurait dû prévenir la publication d'un article de cauchemar, fondé sur la crédulité des media de masse, et l'attitude désormais commune de développer les croyances de la foule.

TW Ng, G Turinici, WK Ching, SK Chung, A Danchin
A parasite vector-host epidemic model for TSE propagation
Medical Science Monitor (2007) 13: 59-66

G Turinici, A Danchin SARS: an alarm clock In: Encyclopedia of infectious diseases. Modern methodologies (M Tibayrenc, Editor), Wiley, NY (2007) pp 151-162 This chapter discusses epidemics superimposed on previous, immunologically related (not necessarily phylogenetically related) viral diseases (double epidemic), with SARS coronavirus as an example of our many tiny foes. The 2009 pattern of H1N1 influenza epidemic is highly consistent with a double epidemic pattern, explaining the considerable difference in virulence in different regions.

	RM Watt, J Wang, M Leong, HF Kung, KS Cheah, D Liu, A Danchin, JD Huang
	Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes
	Nucleic Acids Res (2007) 35: e37

Y Wu, K Yu, B Xu, L Chen, X Chen, J Mao, A Danchin, X Shen, D Qu, H Jiang
Potent and selective inhibitors of Staphylococcus epidermidis tryptophanyl-tRNA synthetase
J Antimicrobial Chemotherapy (2007) 60: 502-509

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2008

G André, S Even, H Putzer, P Burguière, C Croux, A Danchin, I Martin-Verstraete, O Soutourina
S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum
Nucleic Acids Res (2008) 36: 5955-5969

H Ashida, Y Saito, T Nakano, N Tandeau de Marsac, A Sekowska, A Danchin, A Yokota
RuBisCO-like proteins as the enolase enzyme in the methionine salvage pathway: functional and evolutionary relationships between RuBisCO-like proteins and photosynthetic RuBisCO
J Exp Bot (2008) 59: 1543-1554

S Chalabaev, E Turlin, S Bay, C Ganneau, E Brito-Fravallo, J-F Charles, A Danchin, F Biville
Cinnamic acid, an autoinducer of its own biosynthesis, is processed via Hca enzymes in Photorhabdus luminescens
Appl Environ Microbiol (2008) 74:1717-1725

V de Lorenzo, A Danchin
Synthetic biology: discovering new worlds and new words
EMBO Rep (2008) 9: 822-827

G Fang, EP Rocha, A Danchin
Persistence drives gene clustering in bacterial genomes
BMC Genomics (2008) 9: 4

E Krin, S Derzelle, K Bedard, M Adib-Conquy, E Turlin, P Lenormand, M-F Hullo, I Bonne, N Chakroun, C Lacroix, A Danchin
Regulatory role of UvrY in adaptation of Photorhabdus luminescens growth inside the insect
Environmental Microbiology (2008) 10: 1118–1134

A Ménard, A Danchin, S Dupouy, F Mégraud, P Lehours
A variable gene in a conserved region of the Helicobacter pylori genome: Isotopic gene replacement or rapid evolution?
DNA Res (2008) 5: 163-168

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   

C Tanous, O Soutourina, B Raynal, MF Hullo, PMervelet, AM Gilles, P Noirot, A Danchin, P England, I Martin-Verstraete
The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in Bacillus subtilis
J Biol Chem (2008) 283: 35551-35560

C You , A Sekowska, O Francetic, I Martin-Verstraete, Y Wang, A Danchin
Spx mediates oxidative stress regulation of the methionine sulfoxide reductases operon in Bacillus subtilis
BMC Microbiol (2008) 8: 128  

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2009 Creation of, metabolic bioremediation

V Barbe, S Cruveiller, F Kunst, P Lenoble, G Meurice, A Sekowska, D Vallenet, TZ 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  

This article describes the re-sequencing of the Bacillus subtilis genome. It is dedicated to the memory of Frank Kunst, who was instrumental in the whole B. subtilis genome project, victim of an unjust law which forces active scientists to retire, without any consideration for their contribution to creation and diffusion of knowledge.

Cet article rapporte le reséquençage du génome de Bacillus subtilis. Il est dédié à la mémoire de Frank Kunst, sans qui le projet n'aurait jamais pu être mené à son terme en 1997. Frank Kunst a été victime d'une loi inique qui force les chercheurs encore actifs à cesser leur activité sans aucune considération de l'apport qu'ils peuvent avoir à la création et la diffusion du savoir.

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.

A Danchin
Natural selection and immortality
Biogerontology (2009) 10: 503-516  

A Danchin
Bacteria as computers making computers
FEMS Microbiol Rev (2009) 33: 3-26

A Danchin
A phylogenetic view of bacterial ribonucleases
Prog Nucleic Acid Res Mol Biol (2009) 85: 1-41

A Danchin
Nature, artifice and emerging diseases
EMBO Reports (2009) 10: 418-419

A Danchin
Cells need safety valves
Bioessays (2009) 31: 769-773

In Escherichia coli, the role of lacA, the third gene of the lactose operon, has remained an enigma. I suggest that its role is the consequence of the need for cells to have safety valves that protect them from the osmotic effect created by their permeases. Safety valves allow them to cope with the buildup of osmotic pressure under accidental transient conditions. Multidrug resistance (MDR) efflux, thus named because of our anthropocentrism, is ubiquitous. Yet, the formation of simple leaks would result in futile influx/efflux cycles. Versatile modification enzymes with low sensitivity solve the problem if the modified metabolite is the one exported by MDR permeases. This may account for the pervasive presence of acetyltransferases, such as LacA, associated to acetyl-metabolite exporters. This scenario of constraints imposed by efficient influx of metabolites provides us with a model that should be followed when constructing synthetic cells

A Danchin
Sélection naturelle et immortalité
in: Les mondes darwiniens (T Heams, P Huneman, G Lecointre, M Silberstein, eds), Syllepse (2009) pp 445-470

Tous les organismes – bactéries incluses – vieillissent et meurent. En raison de l’incroyable diversité de ce processus (les plantes vieillissent lentement, par exemple), c’est un lieu commun des études sur le vieillissement que de considérer qu’il s’agit d’un paradoxe, qui requiert par conséquent une explication en profondeur. Cette observation a suscité une profusion d’études fascinantes (et de discussions enflammées) destinées à mettre au jour la variété des causes et des mécanismes impliqués dans le vieillissement. Dans ce contexte, l’« immortalité » est considérée comme la norme. Pourquoi et comment vieillissons-nous ? Ce n’est pas cette question que je traiterai ici, je vais prendre le chemin exactement opposé. Considérant que le vieillissement est une conséquence directe de la physique – et c’est en effet l’une des conclusions majeures à laquelle parviennent ceux qui analysent le vieillissement en profondeur quand il repensent les théories de l’« avalanche d’erreurs» d’Orgel ou le « cliquet de Muller –, j’observe au contraire que c’est l’immortalité (que nous observons dans le cancer) qui soulève un paradoxe...

唐善﹒安東
向合成细胞迈进：细胞与计算机的复制过程中的遗传问题
微生物与感染 Journal of Microbes and Infection (2009) 4: 12

A. Danchin
Information of the chassis and information of the program in synthetic cells
Syst Synth Biol (2009) 3(1-4):125-134

A Danchin
Myopic selection of novel information drives evolution
Curr Opin Biotechnol (2009) 20: 504-508

A Danchin
Crystal ball – 2009: Living organisms are information traps: making Synthetic Biology innocuous
Environmental Microbiology Reports (2009) 1: 4-5

A Danchin
A challenge to vaccinology: Living organisms trap information
Vaccine (2009) 27S6: G13-G16

A Danchin, A Sekowska
Physico-chemical prerequisites for the construction of a synthetic cell
in: Synthetic Chemistry, May 26th - 30th, 2008, in Bozen, Italy
Beilstein Institut for the Advancement of Chemical Sciences (2009) 1-13

M Fang, WM Zeisberg, C Condon, V Ogryzko, A Danchin, U Mechold
Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis
Nucleic Acids Res (2009) 37: 5114-5125

Y Jin, RM Watt, A Danchin, JD Huang
Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli
BMC Genomics (2009) 10: 165

Y Jin, RM Watt, A Danchin, JD Huang
Use of a riboswitch-controlled conditional hypomorphic mutation to uncover a role for the essential csrA gene in bacterial autoaggregation
J Biol Chem (2009) 284: 28738-28745

C Médigue, A Danchin Annotating bacterial genomes (Chapter 4.2) In: Modern Genome Annotation. The BioSapiens Network (D Frishman, A Valencia, Editors), SpringerWienNewYork, NY (2009) pp 165-190

	Y Saito, H Ashida, T Sakiyama, N Tandeau de Marsac, A Danchin, A Sekowska, A Yokota
	Structural and functional similarities between a RuBisCO-like protein from Bacillus subtilis and photosynthetic RuBisCO
	J Biol Chem (2009) 284:13256-13264

A Sekowska, JB Masson, A Celani, A Danchin, M Vergassola
Repulsion and metabolic switches in the collective behavior of bacterial colonies
Biophys J (2009) 97: 688-698

O Soutourina, O Poupel, JY Coppée, A Danchin, T Msadek, I Martin-Verstraete
CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulfur source utilization and plays a role in biofilm formation
Mol Microbiol (2009) 73: 194-211

J Thornton and the BioSapiens Network
Annotations for all by all - the BioSapiens network
Genome Biology (2009) 10: 2  

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

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2010 First year of, metabolic bioremediation

A Danchin
Perfect time or perfect crime?
EMBO Reports (2010) 11: 74
Opening: Imagine the situation: “[O]ne day, you notice an old country woman crossing a downtown street, just about to put one foot down on the rails of the streetcar line. […] Suppose, now, that at the very moment she puts her foot on the rail a streetcar comes rushing down the tracks toward her. If the old woman does not notice the car and continues across the tracks nothing will happen. But if someone should happen to shout ‘Look out, old woman!’ what would be her natural reaction? […] she would suddenly become flustered and would pause to decide whether to go on or step back […] the mere words ‘Look out, old woman!’ would be as dangerous a weapon as any knife or firearm. […] the man who sounds the warning actually becomes a murderer!" (Ranpo, 1956). In this sense, the Asilomar conference on genetic engineering in 1974 was the perfect crime in using cautionary exclamations asa weapon that had far-reaching consequences for the emerging field of molecular biology: a moratorium stopped research in some places while others proceeded and took the lead. The same fate may lie in store for synthetic biology (SB). The usual crooners have understood the importance of resorting to appeals to ethics and playing on people’s fears to make themselves known and have begun a discussion of the purported dangers of creating organisms a la carte. Such clamouring for attention may yet end up being a shot to our own feet. Moreover, does minimization of a bacterial genome really pose ethical questions? Should we worry, and if so why? After all, what is the purpose of SB? We need to explore the knowledge that we are required to master to (re)construct life in order to gain a better idea of the economic and ethical questions that we have to ask before we start asking them.

A Danchin
Motivated research
EMBO Reports (2010) 11: 488
Opening: Three years ago, a senior politician attended his country’s Annual Congress for the Advancement of Science to give the introductory lecture. He asked the attending scientists to make science and research more attractive to young students and the general public, and asked his countrymen to support scientists to address the urgent challenges of global climate change, energy needs and dwindling water resources. It was neither a European nor a US politician, but the Indian Prime Minister Manmohan Singh who made this speech about the relationship between research and its practical applications. This is such an important topic that one might think it deserves appropriate attention in Europe, yet we fail to address it properly. Instead, we just discuss how science should serve society or contribute to the ‘knowledge-based economy’, or how ‘basic’ or ‘fundamental’ research is opposed to ‘applied’ or ‘industrial’ research and how funding for ‘big science’ comes at the expense of ‘little academic’ research.

A Danchin
A path from predation to mutualism
Molecular Microbiology (2010) 77: 1346-1350  

A Danchin
Science and arsenic fool's gold: a toxic broth
Journal of Cosmology (2010) 13 : 3617-3620  
Abstract: Making stable informational polymers in water at 300K limits chemical variations within extremely narrow borders. This is why the basic atoms of life — those that are found in meteoritic molecules — are hydrogen, carbon, nitrogen and oxygen. In these same conditions, management of energy to support life used the unique property of phosphorus to make energy-rich metastable phosphoester or polyphosphate bonds. Analysis of the genome of arsenic-loving bacteria suggests that arsenic can nevertheless be accumulated in bacteria via formation of innocuous derivatives that may decorate inert (mostly non informational) biopolymers. However, arsenic cannot replace phosphorus in this core function of life. This has been previously firmly established by numerous biochemical experiments. Likewise, recent claims by Wolfe-Simon et al. (2010) that this replacement could happen, have not been experimentally verified, and are based on experiments lacking proper controls; the purpose of which was to substantiate these beliefs. However, the authors are not sole to be blamed, but the journals that try to maintain their high impact factors at all cost, publishing articles that should never have reached the public

A Danchin, G Fang
Babies are born very young. The synthesis of change
Journal of Cosmology (2010) 7: May 2010 Artificial Life

A Danchin, A Sekowska The role of information in evolutionary genomics of bacteria In: Evolutionary genomics and systems biology (G Caetano-Anollés, Editor), Wiley & sons, Hoboken, NJ (2010) pp 81-94

E Krin, A Danchin, O Soutourina
RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli
Res Microbiol (2010) 161: 363-371

E Krin, A Danchin, O Soutourina
Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli
BMC Microbiology (2010) 10: 273

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

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

G Postic, A Danchin, U Mechold
Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae
Symplectic Biology (2010) 1: c390t9c12uxx.1   

M Vayssier-Taussat, D Le Rhun, HK Deng, F Biville, S Cescau, A Danchin, G Marignac, E Lenaour, HJ Boulouis, M Mavris, L Arnaud, H Yang, J Wang, M Quebatte, P Engel, H Saenz, C Dehio
The Trw type IV secretion system of Bartonella mediates host-specific adhesion to erythrocytes.
PLoS Pathogens (2010) 6: e1000946

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Dernière mise à jour 31 décembre 2010

Last update december 31st, 2010