Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli (2009)
Jin, Ye, Watt, Rory M, Danchin, Antoine, Huang, Jian-dong
Abstract Background The low pH environment of the human stomach is lethal for most microorganisms; but not Escherichia coli , which can tolerate extreme acid stress. Acid resistance in E. coli is...
Microbiology (1999), 145, 2625–2634 Printed in Great Britain REVIEW ARTICLE Overview (2009)
Lionel Frangeul, Karen E. Nelson, Carmen Buchrieser, Antoine Danchin, Frank Kunst
The knowledge of an entire genome sequence not only provides a wealth of data, but also specific information that can not be obtained by other approaches. Only after...
Toward a Higher Quality of the Bacillus subtilis Genome Sequence (2009)
Claudine Médigue, Matthias Rose, Alain Viari, Antoine Danchin, Email Alerting, Claudine Médigue, ...
service
Touchon, Marie, Hoede, Claire, Tenaillon, Olivier, Barbe, Valérie, Baeriswyl, Simon, Bidet, Philippe, ...
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We...
Touchon, Marie, Hoede, Claire, Tenaillon, Olivier, Barbe, Valérie, Baeriswyl, Simon, Bidet, Philippe, ...
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We...
Touchon, Marie, Hoede, Claire, Tenaillon, Olivier, Barbe, Valérie, Baeriswyl, Simon, Bidet, Philippe, ...
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We...
Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis (2009)
Fang, Ming, Zeisberg, Wencke-Maria, Condon, Ciaran, Ogryzko, Vasily, Danchin, Antoine, Mechold, Undine
Escherichia coli possesses only one essential oligoribonuclease (Orn), an enzyme that can degrade oligoribonucleotides of five residues and shorter in length (nanoRNA). Firmicutes including Bacillus...
You, CongHui, Sekowska, Agnieszka, Francetic, Olivera, Martin-Verstraete, Isabelle, Wang, YiPing, Danchin, Antoine
Abstract Background All aerobically grown living cells are exposed to oxidative damage by reactive oxygen species (ROS). A major damage by ROS to proteins is caused by covalent modifications of...
Genomics of an extreme psychrophile, Psychromonas ingrahamii (2008)
Riley, Monica, Staley, James T, Danchin, Antoine, Wang, Ting Zhang, Brettin, Thomas S, Hauser, Loren J, ...
Abstract Background The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile...
Genomics of an extreme psychrophile, Psychromonas ingrahamii (2008)
Riley, Monica, Staley, James T., Danchin, Antoine, Wang, Ting Zhang, Brettin, Thomas S., Hauser, Loren J., ...
© 2008 Riley et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any...
Persistence drives gene clustering in bacterial genomes (2008)
Fang, Gang, Rocha, Eduardo PC, Danchin, Antoine
Abstract Background Gene clustering plays an important role in the organization of the bacterial chromosome and several mechanisms have been proposed to explain its extent. However, the controversies...
Ménard, Armelle, Danchin, Antoine, Dupouy, Sandrine, Mégraud, Francis, Lehours, Philippe
The present study concerns the identification of a novel coding sequence in a region of the Helicobacter pylori genome, located between JHP1069/HP1141 and JHP1071/HP1143 according to the numbering of...
Ashida, Hiroki, Saito, Yohtaro, Nakano, Toshihiro, Tandeau De Marsac, Nicole, Sekowska, Agnieszka, Danchin, Antoine, ...
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme in the fixation of CO2 in the Calvin cycle of plants. Many genome projects have revealed that bacteria, including Bacillus...
André, Gaëlle, Even, Sergine, Putzer, Harald, Burguière, Pierre, Croux, Christian, Danchin, Antoine, ...
The ubiGmccBA operon of Clostridium acetobutylicum is involved in methionine to cysteine conversion. We showed that its expression is controlled by a complex regulatory system combining several...
Potent and selective inhibitors of Staphylococcus epidermidis tryptophanyl-tRNA synthetase (2007)
Wu, Yang, Yu, Kunqian, Xu, Bin, Chen, Lili, Chen, Xianglong, Mao, Jialing, ...
Objectives The skin commensal and opportunistic pathogen Staphylococcus epidermidis is one of the leading causes of nosocomial and biofilm-associated infections, which urgently requires discovery of...
YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity (2007)
Mechold, Undine, Fang, Gang, Ngo, Saravuth, Ogryzko, Vasily, Danchin, Antoine
Oligoribonuclease is the only RNase in Escherichia coli that is able to degrade RNA oligonucleotides five residues and shorter in length. Firmicutes including Bacillus subtilis do not have an...
A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments (2007)
Daniel Muller, Claudine Médigue, Sandrine Koechler, Valérie Barbe, Mohamed Barakat, Emmanuel Talla, ...
Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural...
A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments (2007)
Daniel Muller, Claudine Médigue, Sandrine Koechler, Valérie Barbe, Mohamed Barakat, Emmanuel Talla, ...
Microbial biotransformations have a major impact on the contamination by toxic elements, threatening public health in developing and industrial countries. Finding means of preserving natural...
Bacteria are not Lamarckian (2007)
Instructive influence of environment on heredity has been a debated topic for centuries. Darwin's identification of natural selection coupled to chance variation as the driving force for evolution,...
Makita, Yuko, De Hoon, Michiel JL, Danchin, Antoine
Abstract Background Computational prediction methods are currently used to identify genes in prokaryote genomes. However, identification of the correct translation initiation sites remains a...
A tale of two oxidation states: bacterial colonization of arsenic-rich environments. (2007)
Muller, Daniel, Médigue, Claudine, Koechler, Sandrine, Barbe, Valérie, Barakat, Mohamed, Talla, Emmanuel, ...
Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural...
A tale of two oxidation states: bacterial colonization of arsenic-rich environments. (2007)
Muller, Daniel, Médigue, Claudine, Koechler, Sandrine, Barbe, Valérie, Barakat, Mohamed, Talla, Emmanuel, ...
Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural...
Watt, Rory M., Wang, Jing, Leong, Meikid, Kung, Hsiang-fu, Cheah, Kathryn S.E., Liu, Depei, ...
To investigate the feasibility of conducting a genomic-scale protein labeling and localization study in Escherichia coli, a representative subset of 23 coding DNA sequences (CDSs) was selected for...
Watt, Rory M., Wang, Jing, Leong, Meikid, Kung, Hsiang-fu, Cheah, Kathryn S.E., Liu, Depei, ...
To investigate the feasibility of conducting a genomic-scale protein labeling and localization study in Escherichia coli, a representative subset of 23 coding DNA sequences (CDSs) was selected for...
Qin, Zhiqiang, Zhang, Jian, Xu, Bin, Chen, Lili, Wu, Yang, Yang, Xiaomei, ...
Abstract Background Coagulase-negative Staphylococcus epidermidis has become a major frequent cause of infections in relation to the use of implanted medical devices. The pathogenicity of S....
Wei, Wu, Cao, ZhiWei, Zhu, Yu-Li, Wang, XiaoJing, Ding, GuoHui, Xu, Hao, ...
Abstract Background Staphylococcus epidermidis , long regarded as an innocuous commensal bacterium of the human skin, is the most frequent cause of nosocomial infections associated with implanted...
Codon Usage Domains over Bacterial Chromosomes (2006)
Marc Bailly-Bechet, Antoine Danchin, Mudassar Iqbal, Matteo Marsili, Massimo Vergassola
The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information...
Yap, Yee Leng, Wei, Dong, Danchin, Antoine
The precise diagnosis of cancer type based on microarray data is of particular importance and is also a challenging task. We have devised a novel pattern recognition procedure based on independent...
You, CongHui, Lu, HongYan, Sekowska, Agnieszka, Fang, Gang, Wang, YiPing, Gilles, Anne-Marie, ...
Abstract Background Two putative methionine aminopeptidase genes, map (essential) and yflG (non-essential), were identified in the genome sequence of Bacillus subtilis . We investigated whether they...
Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns" (2005)
Larsabal, Etienne, Danchin, Antoine
Abstract Background The genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a given genome,...
Specialized microbial databases for inductive exploration of microbial genome sequences (2005)
Fang, Gang, Ho, Christine, Qiu, Yaowu, Cubas, Virginie, Yu, Zhou, Cabau, Cédric, ...
Abstract Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function...
3-phenylpropionate catabolism and the Escherichia coli oxidative stress response (2005)
Turlin, Evelyne, Sismeiro, Odile, Le Caer, Jean-Pierre, Labas, Valérie, Danchin, Antoine, Biville, Francis
How Essential are Non-essential Genes? (2005)
Fang, Gang, Rocha, Eduardo, Danchin, Antoine
Gene essentiality in bacteria has been identified in silico, focusing on gene persistence, or experimentally, focusing on the growth of knock-outs in rich media. Comparing 55 genomes of Firmicutes...
Yap, Yee Leng, Wong, Maria P., Zhang, Xue Wu, Hernandez, David, Gras, Robin, Smith, David K., ...
Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set M AD,...
How Essential Are Nonessential Genes? (2005)
Fang, Gang, Rocha, Eduardo, Danchin, Antoine
Gene essentiality in bacteria has been identified in silico, focusing on gene persistence, or experimentally, focusing on the growth of knockouts in rich media. Comparing 55 genomes of Firmicutes and...
Médigue, Claudine, Krin, Evelyne, Pascal, Géraldine, Barbe, Valérie, Bernsel, Andreas, Bertin, Philippe N., ...
A considerable fraction of life develops in the sea at temperatures lower than 15°C. Little is known about the adaptive features selected under those conditions. We present the analysis of the...
Médigue, Claudine, Krin, Evelyne, Pascal, Géraldine, Barbe, Valérie, Bernsel, Andreas, Bertin, Philippe N., ...
A considerable fraction of life develops in the sea at temperatures lower than 15°C. Little is known about the adaptive features selected under those conditions. We present the analysis of the...
How Essential are Non-essential Genes? (2005)
Fang, Gang, Rocha, Eduardo, Danchin, Antoine
Gene essentiality in bacteria has been identified in silico, focusing on gene persistence, or experimentally, focusing on the growth of knock-outs in rich media. Comparing 55 genomes of Firmicutes...
The bag or the spindle: the cell factory at the time of systems' biology (2004)
Abstract Genome programs changed our view of bacteria as cell factories, by making them amenable to systematic rational improvement. As a first step, isolated genes (including those of the...
Classification between normal and tumor tissues based on the pair-wise gene expression ratio (2004)
Yap, YeeLeng, Zhang, XueWu, Ling, MT, Wang, XiangHong, Wong, YC, Danchin, Antoine
Abstract Background Precise classification of cancer types is critically important for early cancer diagnosis and treatment. Numerous efforts have been made to use gene expression profiles to improve...
Bacterial variations on the methionine salvage pathway (2004)
Sekowska, Agnieszka, Dénervaud, Valérie, Ashida, Hiroki, Michoud, Karine, Haas, Dieter, Yokota, Akiho, ...
Abstract Background The thiomethyl group of S-adenosylmethionine is often recycled as methionine from methylthioadenosine. The corresponding pathway has been unravelled in Bacillus subtilis . However...
An Analysis of Determinants of Amino Acids Substitution Rates in Bacterial Proteins (2004)
Rocha, Eduardo P. C., Danchin, Antoine
The variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category, essentiality, or metabolic costs of its...
Antoine Danchin, Antoine Danchin
The bag or the spindle: the cell factory at the time of systems' biology
Yap, Yee, Zhang, Xue, Danchin, Antoine
Abstract Background The exact origin of the cause of the Severe Acute Respiratory Syndrome (SARS) is still an open question. The genomic sequence relationship of SARS-CoV with 30 different...
A double epidemic model for the SARS propagation (2003)
Ng, Tuen, Turinici, Gabriel, Danchin, Antoine
Abstract Background An epidemic of a Severe Acute Respiratory Syndrome (SARS) caused by a new coronavirus has spread from the Guangdong province to the rest of China and to the world, with a puzzling...
BMC Infectious Diseases Research article A double epidemic model for the SARS propagation (2003)
Tuen Wai Ng, Gabriel Turinici, Antoine Danchin, Biomed Central
Background: An epidemic of a Severe Acute Respiratory Syndrome (SARS) caused by a new coronavirus has spread from the Guangdong province to the rest of China and to the world, with a puzzling...
An Analysis of Determinants of Amino Acids Substitution Rates in Bacterial Proteins (2003)
Rocha, Eduardo P. C., Danchin, Antoine
The variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category or essentiality, as well as the metabolic...
Gene essentiality determines chromosome organisation in bacteria (2003)
Rocha, Eduardo P. C., Danchin, Antoine
In Escherichia coli and Bacillus subtilis, essentiality, not expressivity, drives the distribution of genes between the two replicating strands. Although essential genes tend to be coded in the...
An Analysis of Determinants of Amino Acids Substitution Rates in Bacterial Proteins (2003)
Rocha, Eduardo P. C., Danchin, Antoine
The variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category or essentiality, as well as the metabolic...
The methionine salvage pathway in Bacillus subtilis (2002)
Sekowska, Agnieszka, Danchin, Antoine
Abstract Background Polyamine synthesis produces methylthioadenosine, which has to be disposed of. The cell recycles it into methionine through methylthioribose (MTR). Very little was known about MTR...
Bocs, Stéphanie, Danchin, Antoine, Médigue, Claudine
Abstract Background Analysis of any newly sequenced bacterial genome starts with the identification of protein-coding genes. Despite the accumulation of multiple complete genome sequences, which...
SubtiList: the reference database for the Bacillus subtilis genome (2002)
Moszer, Ivan, Jones, Louis M., Moreira, Sandrine, Fabry, Cécilia, Danchin, Antoine
SubtiList is the reference database dedicated to the genome of Bacillus subtilis 168, the paradigm of Gram-positive endospore-forming bacteria. Developed in the framework of the B.subtilis genome...
MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis (2001)
Sekowska, Agnieszka, Mulard, Laurence, Krogh, Susanne, Tse, Jane KS, Danchin, Antoine
Abstract Background Methylthioadenosine, the main by-product of spermidine synthesis, is degraded in Bacillus subtilis as adenine and methylthioribose. The latter is an excellent sulfur source and...
Sekowska, Agnieszka, Robin, Stephane, Daudin, Jean-Jacques, Henaut, Alain, Danchin, Antoine
Abstract Background In global gene expression profiling experiments, variation in the expression of genes of interest can often be hidden by general noise. To determine how biologically significant...
Ongoing Evolution of Strand Composition in Bacterial Genomes (2001)
Rocha, Eduardo P. C., Danchin, Antoine
We tried to identify the substitutions involved in the establishment of replication strand bias, which has been recognized as an important evolutionary factor in the evolution of bacterial genomes....
Expression profiling in reference bacteria: dreams and reality (2000)
Danchin, Antoine, Sekowska, Agnieszka
Abstract Profiling of gene expression in bacteria is now being used to uncover unknown genes expressed in particular genetic backgrounds or environmental conditions. Obtaining the best possible...
A brief history of genome research and bioinformatics in France (2000)
The development of in silico genomics has progressed slowly in France for a number of political reasons. Two administrative organizations, the Groupement de Recherche sur les Ge´nomes (GREG) and the...
Identification of yrrU as the Methylthioadenosine Nucleosidase Gene in Bacillus subtilis (1999)
Sekowska, Agnieszka, Danchin, Antoine
Taking trimethoprim as the selective agent in the presence of thymine, we adapted to Bacillus subtilis a selection procedure depending on the peculiar organisation of the one-carbon metabolism. The...
Guerdoux-Jamet, Pascale, Hénaut, Alain, Nitschké, Patrick, Danchin, Antoine
Analysis of the codon usage of genes coding for the structural components of the outer membrane in Escherichia coli, is consistent with the requirement for high expression of these genes. Because...
Genome comparison permits identification of chromosome regions conserved during evolution. Bacillus subtilis and Escherichia coli are so distant that there exists veryfew conserved landmarks in their...
Detection of new genes in a bacterial genome using Markov models for three gene classes (1995)
Borodovsky, Mark, Mclninch, James D., Koonin, Eugene V., Rudd, Kenneth E., Médigue, Claudine, Danchin, Antoine
We further investigated the statistical features of the three classes of Escherichia coli genes that have been previously delineated by factorial correspondence analysis and dynamic clustering...
Bacteria are not Lamarckian (1993)
Instructive influence of environment on heredity has been a debated topic for centuries. Darwin's identification of natural selection coupled to chance variation as the driving force for evolution,...
Bacteria are not Lamarckian (1993)
Instructive influence of environment on heredity has been a debated topic for centuries. Darwin's identification of natural selection coupled to chance variation as the driving force for evolution,...
Rouxel, Thierry, Danchin, Antoine, Henaut, Alain
The table of ‘biochemical pathways’ published by Boehringer is considered as the most exhaustive document dealing with intermediary metabolism. The present work consisted of constructing a...
The complete nucleotide sequence of the adenylate cyclase gene of Escherichia coli (1984)
Aiba, Hiroji, Mori, Kazuyasu, Tanaka, Minoru, Ooi, Tatsuo, Roy, Anne, Danchin, Antoine
The complete nucleotide sequence of the cya gene from E. coli was determined. The gene encodes a polypeptide consisting of 848 amino acid residues with a calculated molecular weight of 97,542. The...
Thesis (doctoral)--Faculté des sciences de Paris, 1971.
MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis
Sekowska, Agnieszka, Mulard, Laurence, Krogh, Susanne, Tse, Jane KS, Danchin, Antoine
Immunochemical Analysis of UMP Kinase from Escherichia coli
Landais, Stéphanie, Gounon, Pierre, Laurent-Winter, Christine, Mazié, Jean-Claude, Danchin, Antoine, Bârzu, Octavian, ...
Mono- and polyclonal antibodies directed against UMP kinase from Escherichia coli were tested with the intact protein or with fragments obtained by deletion mutagenesis. As detected in enzyme-linked...
Catabolite Regulation of the pta Gene as Part of Carbon Flow Pathways in Bacillus subtilis
Presecan-Siedel, Elena, Galinier, Anne, Longin, Robert, Deutscher, Josef, Danchin, Antoine, Glaser, Philippe, ...
In Bacillus subtilis, the products of the pta and ackA genes, phosphotransacetylase and acetate kinase, play a crucial role in the production of acetate, one of the most abundant by-products of...
CotA of Bacillus subtilis Is a Copper-Dependent Laccase
Hullo, Marie-Françoise, Moszer, Ivan, Danchin, Antoine, Martin-Verstraete, Isabelle
The spore coat protein CotA of Bacillus subtilis displays similarities with multicopper oxidases, including manganese oxidases and laccases. B. subtilis is able to oxidize manganese, but neither CotA...
SubtiList: the reference database for the Bacillus subtilis genome
Moszer, Ivan, Jones, Louis M., Moreira, Sandrine, Fabry, Cécilia, Danchin, Antoine
SubtiList is the reference database dedicated to the genome of Bacillus subtilis 168, the paradigm of Gram-positive endospore-forming bacteria. Developed in the framework of the B.subtilis genome...
Isolation and Characterization of vicH, Encoding a New Pleiotropic Regulator in Vibrio cholerae
Tendeng, Christian, Badaut, Cyril, Krin, Evelyne, Gounon, Pierre, Ngo, Saravuth, Danchin, Antoine, ...
During the last decade, the hns gene and its product, the H-NS protein, have been extensively studied in Escherichia coli. H-NS-like proteins seem to be widespread in gram-negative bacteria. However,...
Mutational Analysis of UMP Kinase from Escherichia coli
Bucurenci, Nadia, Serina, Lidia, Zaharia, Cristina, Landais, Stéphanie, Danchin, Antoine, Bârzu, Octavian
UMP kinase from Escherichia coli is one of the four regulatory enzymes involved in the de novo biosynthetic pathway of pyrimidine nucleotides. This homohexamer, with no counterpart in eukarya, might...
Sismeiro, Odile, Trotot, Pascale, Biville, Francis, Vivares, Christian, Danchin, Antoine
Complementation of an Escherichia coli cya mutant with a genomic library from Aeromonas hydrophila allowed isolation of clones containing two different cya genes. Whereas one of these genes (cyaA)...
Derzelle, Sylviane, Duchaud, Eric, Kunst, Frank, Danchin, Antoine, Bertin, Philippe
The luminescent entomopathogenic bacterium Photorhabdus luminescens produces several yet-uncharacterized broad-spectrum antibiotics. We report the identification and characterization of a cluster of...
The secE Gene of Helicobacter pylori
Médigue, Claudine, Wong, Benjamin Chun-Yu, Lin, Marie Chia-Mi, Bocs, Stéphanie, Danchin, Antoine
Despite extensive annotation by two independent teams, the Helicobacter pylori genome appeared to lack a complete secretion machinery. The use of clinical isolates to substantiate in silico...
Guillouard, Isabelle, Auger, Sandrine, Hullo, Marie-Françoise, Chetouani, Farid, Danchin, Antoine, Martin-Verstraete, Isabelle
The way in which the genes involved in cysteine biosynthesis are regulated is poorly characterized in Bacillus subtilis. We showed that CysL (formerly YwfK), a LysR-type transcriptional regulator,...
Global Expression Profile of Bacillus subtilis Grown in the Presence of Sulfate or Methionine
Auger, Sandrine, Danchin, Antoine, Martin-Verstraete, Isabelle
DNA arrays were used to investigate the global transcriptional profile of Bacillus subtilis grown in the presence of sulfate or methionine as the sole sulfur source. The expression of at least 56...
Expression profiling in reference bacteria: dreams and reality
Danchin, Antoine, Sekowska, Agnieszka
Profiling of gene expression in bacteria is now being used to uncover unknown genes expressed in particular genetic backgrounds or environmental conditions. Obtaining the best possible information...
Transcription Regulation Coupling of the Divergent argG and metY Promoters in Escherichia coli K-12
Krin, Evelyne, Laurent-Winter, Christine, Bertin, Philippe N., Danchin, Antoine, Kolb, Annie
The cAMP-catabolite activator protein (CAP) complex is a pleiotropic regulator that regulates a vast number of Escherichia coli genes, including those involved in carbon metabolism. We identified two...
Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
Gene essentiality determines chromosome organisation in bacteria
Rocha, Eduardo P. C., Danchin, Antoine
In Escherichia coli and Bacillus subtilis, essentiality, not expressivity, drives the distribution of genes between the two replicating strands. Although essential genes tend to be coded in the...
Médigue, Claudine, Rose, Matthias, Viari, Alain, Danchin, Antoine
During the determination of a DNA sequence, the introduction of artifactual frameshifts and/or in-frame stop codons in putative genes can lead to misprediction of gene products. Detection of such...
Derzelle, Sylviane, Turlin, Evelyne, Duchaud, Eric, Pages, Sylvie, Kunst, Frank, Givaudan, Alain, ...
Photorhabdus luminescens is a symbiont of entomopathogenic nematodes. Analysis of the genome sequence of this organism revealed a homologue of PhoP-PhoQ, a two-component system associated with...
Bacterial variations on the methionine salvage pathway
Sekowska, Agnieszka, Dénervaud, Valérie, Ashida, Hiroki, Michoud, Karine, Haas, Dieter, Yokota, Akiho, ...
A Theory of the Epigenesis of Neuronal Networks by Selective Stabilization of Synapses
Changeux, Jean-Pierre, Courrége, Philippe, Danchin, Antoine
A formalism is introduced to represent the connective organization of an evolving neuronal network and the effects of environment on this organization by stabilization or degeneration of labile...
Three Different Systems Participate in l-Cystine Uptake in Bacillus subtilis
Burguière, Pierre, Auger, Sandrine, Hullo, Marie-Françoise, Danchin, Antoine, Martin-Verstraete, Isabelle
The symporter YhcL and two ATP binding cassette transporters, YtmJKLMN and YckKJI, were shown to mediate l-cystine uptake in Bacillus subtilis. A triple ΔyhcL ΔytmJKLMN ΔyckK mutant was unable to...
Classification between normal and tumor tissues based on the pair-wise gene expression ratio
Yap, YeeLeng, Zhang, XueWu, Ling, MT, Wang, XiangHong, Wong, YC, Danchin, Antoine
The bag or the spindle: the cell factory at the time of systems' biology
Genome programs changed our view of bacteria as cell factories, by making them amenable to systematic rational improvement. As a first step, isolated genes (including those of the metagenome), or...
Yap, Yee Leng, Wong, Maria P., Zhang, Xue Wu, Hernandez, David, Gras, Robin, Smith, David K., ...
Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set MAD,...
Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human
Song, Huai-Dong, Tu, Chang-Chun, Zhang, Guo-Wei, Wang, Sheng-Yue, Zheng, Kui, Lei, Lian-Cheng, ...
The genomic sequences of severe acute respiratory syndrome coronaviruses from human and palm civet of the 2003/2004 outbreak in the city of Guangzhou, China, were nearly identical. Phylogenetic...
Specialized microbial databases for inductive exploration of microbial genome sequences
Fang, Gang, Ho, Christine, Qiu, Yaowu, Cubas, Virginie, Yu, Zhou, Cabau, Cédric, ...
Regulation of the Bacillus subtilis ytmI Operon, Involved in Sulfur Metabolism
Burguière, Pierre, Fert, Juliette, Guillouard, Isabelle, Auger, Sandrine, Danchin, Antoine, Martin-Verstraete, Isabelle
The YtlI regulator of Bacillus subtilis activates the transcription of the ytmI operon encoding an l-cystine ABC transporter, a riboflavin kinase, and proteins of unknown function. The expression of...
The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis
You, CongHui, Lu, HongYan, Sekowska, Agnieszka, Fang, Gang, Wang, YiPing, Gilles, Anne-Marie, ...
As diseases have evolved to exploit the holes in our defences, including weaknesses in society, we have to reconsider our way of life, otherwise they will continue to haunt us
Médigue, Claudine, Krin, Evelyne, Pascal, Géraldine, Barbe, Valérie, Bernsel, Andreas, Bertin, Philippe N., ...
A considerable fraction of life develops in the sea at temperatures lower than 15°C. Little is known about the adaptive features selected under those conditions. We present the analysis of the...
Global Control of Cysteine Metabolism by CymR in Bacillus subtilis†
Even, Sergine, Burguière, Pierre, Auger, Sandrine, Soutourina, Olga, Danchin, Antoine, Martin-Verstraete, Isabelle
YrzC has previously been identified as a repressor controlling ytmI expression via its regulation of YtlI activator synthesis in Bacillus subtilis. We identified YrzC as a master regulator of sulfur...
Codon Usage Domains over Bacterial Chromosomes
Bailly-Bechet, Marc, Danchin, Antoine, Iqbal, Mudassar, Marsili, Matteo, Vergassola, Massimo
The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information...
Mechold, Undine, Ogryzko, Vasily, Ngo, Saravuth, Danchin, Antoine
We identified Oligoribonuclease (Orn), an essential Escherichia coli protein and the only exonuclease degrading small ribonucleotides (5mer to 2mer) and its human homologue, small fragment nuclease...
Xia, Xuhua, Wei, Ting, Xie, Zheng, Danchin, Antoine
We used 94 RAPD primers of different nucleotide composition to probe the genomic differences between a highly virulent P. multocida strain and an attenuated vaccine strain derived from the virulent...
MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis
Sekowska, Agnieszka, Mulard, Laurence, Krogh, Susanne, Tse, Jane KS, Danchin, Antoine
Immunochemical Analysis of UMP Kinase from Escherichia coli
Landais, Stéphanie, Gounon, Pierre, Laurent-Winter, Christine, Mazié, Jean-Claude, Danchin, Antoine, Bârzu, Octavian, ...
Mono- and polyclonal antibodies directed against UMP kinase from Escherichia coli were tested with the intact protein or with fragments obtained by deletion mutagenesis. As detected in enzyme-linked...
Catabolite Regulation of the pta Gene as Part of Carbon Flow Pathways in Bacillus subtilis
Presecan-Siedel, Elena, Galinier, Anne, Longin, Robert, Deutscher, Josef, Danchin, Antoine, Glaser, Philippe, ...
In Bacillus subtilis, the products of the pta and ackA genes, phosphotransacetylase and acetate kinase, play a crucial role in the production of acetate, one of the most abundant by-products of...
CotA of Bacillus subtilis Is a Copper-Dependent Laccase
Hullo, Marie-Françoise, Moszer, Ivan, Danchin, Antoine, Martin-Verstraete, Isabelle
The spore coat protein CotA of Bacillus subtilis displays similarities with multicopper oxidases, including manganese oxidases and laccases. B. subtilis is able to oxidize manganese, but neither CotA...
SubtiList: the reference database for the Bacillus subtilis genome
Moszer, Ivan, Jones, Louis M., Moreira, Sandrine, Fabry, Cécilia, Danchin, Antoine
SubtiList is the reference database dedicated to the genome of Bacillus subtilis 168, the paradigm of Gram-positive endospore-forming bacteria. Developed in the framework of the B.subtilis genome...
Isolation and Characterization of vicH, Encoding a New Pleiotropic Regulator in Vibrio cholerae
Tendeng, Christian, Badaut, Cyril, Krin, Evelyne, Gounon, Pierre, Ngo, Saravuth, Danchin, Antoine, ...
During the last decade, the hns gene and its product, the H-NS protein, have been extensively studied in Escherichia coli. H-NS-like proteins seem to be widespread in gram-negative bacteria. However,...
Mutational Analysis of UMP Kinase from Escherichia coli
Bucurenci, Nadia, Serina, Lidia, Zaharia, Cristina, Landais, Stéphanie, Danchin, Antoine, Bârzu, Octavian
UMP kinase from Escherichia coli is one of the four regulatory enzymes involved in the de novo biosynthetic pathway of pyrimidine nucleotides. This homohexamer, with no counterpart in eukarya, might...
Sismeiro, Odile, Trotot, Pascale, Biville, Francis, Vivares, Christian, Danchin, Antoine
Complementation of an Escherichia coli cya mutant with a genomic library from Aeromonas hydrophila allowed isolation of clones containing two different cya genes. Whereas one of these genes (cyaA)...
Derzelle, Sylviane, Duchaud, Eric, Kunst, Frank, Danchin, Antoine, Bertin, Philippe
The luminescent entomopathogenic bacterium Photorhabdus luminescens produces several yet-uncharacterized broad-spectrum antibiotics. We report the identification and characterization of a cluster of...
The secE Gene of Helicobacter pylori
Médigue, Claudine, Wong, Benjamin Chun-Yu, Lin, Marie Chia-Mi, Bocs, Stéphanie, Danchin, Antoine
Despite extensive annotation by two independent teams, the Helicobacter pylori genome appeared to lack a complete secretion machinery. The use of clinical isolates to substantiate in silico...
Guillouard, Isabelle, Auger, Sandrine, Hullo, Marie-Françoise, Chetouani, Farid, Danchin, Antoine, Martin-Verstraete, Isabelle
The way in which the genes involved in cysteine biosynthesis are regulated is poorly characterized in Bacillus subtilis. We showed that CysL (formerly YwfK), a LysR-type transcriptional regulator,...
Global Expression Profile of Bacillus subtilis Grown in the Presence of Sulfate or Methionine
Auger, Sandrine, Danchin, Antoine, Martin-Verstraete, Isabelle
DNA arrays were used to investigate the global transcriptional profile of Bacillus subtilis grown in the presence of sulfate or methionine as the sole sulfur source. The expression of at least 56...
Expression profiling in reference bacteria: dreams and reality
Danchin, Antoine, Sekowska, Agnieszka
Profiling of gene expression in bacteria is now being used to uncover unknown genes expressed in particular genetic backgrounds or environmental conditions. Obtaining the best possible information...
Transcription Regulation Coupling of the Divergent argG and metY Promoters in Escherichia coli K-12
Krin, Evelyne, Laurent-Winter, Christine, Bertin, Philippe N., Danchin, Antoine, Kolb, Annie
The cAMP-catabolite activator protein (CAP) complex is a pleiotropic regulator that regulates a vast number of Escherichia coli genes, including those involved in carbon metabolism. We identified two...
Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
Gene essentiality determines chromosome organisation in bacteria
Rocha, Eduardo P. C., Danchin, Antoine
In Escherichia coli and Bacillus subtilis, essentiality, not expressivity, drives the distribution of genes between the two replicating strands. Although essential genes tend to be coded in the...
Médigue, Claudine, Rose, Matthias, Viari, Alain, Danchin, Antoine
During the determination of a DNA sequence, the introduction of artifactual frameshifts and/or in-frame stop codons in putative genes can lead to misprediction of gene products. Detection of such...
Derzelle, Sylviane, Turlin, Evelyne, Duchaud, Eric, Pages, Sylvie, Kunst, Frank, Givaudan, Alain, ...
Photorhabdus luminescens is a symbiont of entomopathogenic nematodes. Analysis of the genome sequence of this organism revealed a homologue of PhoP-PhoQ, a two-component system associated with...
Bacterial variations on the methionine salvage pathway
Sekowska, Agnieszka, Dénervaud, Valérie, Ashida, Hiroki, Michoud, Karine, Haas, Dieter, Yokota, Akiho, ...
A Theory of the Epigenesis of Neuronal Networks by Selective Stabilization of Synapses
Changeux, Jean-Pierre, Courrége, Philippe, Danchin, Antoine
A formalism is introduced to represent the connective organization of an evolving neuronal network and the effects of environment on this organization by stabilization or degeneration of labile...
Three Different Systems Participate in l-Cystine Uptake in Bacillus subtilis
Burguière, Pierre, Auger, Sandrine, Hullo, Marie-Françoise, Danchin, Antoine, Martin-Verstraete, Isabelle
The symporter YhcL and two ATP binding cassette transporters, YtmJKLMN and YckKJI, were shown to mediate l-cystine uptake in Bacillus subtilis. A triple ΔyhcL ΔytmJKLMN ΔyckK mutant was unable to...
Classification between normal and tumor tissues based on the pair-wise gene expression ratio
Yap, YeeLeng, Zhang, XueWu, Ling, MT, Wang, XiangHong, Wong, YC, Danchin, Antoine
The bag or the spindle: the cell factory at the time of systems' biology
Genome programs changed our view of bacteria as cell factories, by making them amenable to systematic rational improvement. As a first step, isolated genes (including those of the metagenome), or...
Yap, Yee Leng, Wong, Maria P., Zhang, Xue Wu, Hernandez, David, Gras, Robin, Smith, David K., ...
Gene transcription in a set of 49 human primary lung adenocarcinomas and 9 normal lung tissue samples was examined using Affymetrix GeneChip technology. A total of 3442 genes, called the set MAD,...
Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human
Song, Huai-Dong, Tu, Chang-Chun, Zhang, Guo-Wei, Wang, Sheng-Yue, Zheng, Kui, Lei, Lian-Cheng, ...
The genomic sequences of severe acute respiratory syndrome coronaviruses from human and palm civet of the 2003/2004 outbreak in the city of Guangzhou, China, were nearly identical. Phylogenetic...
Specialized microbial databases for inductive exploration of microbial genome sequences
Fang, Gang, Ho, Christine, Qiu, Yaowu, Cubas, Virginie, Yu, Zhou, Cabau, Cédric, ...
Regulation of the Bacillus subtilis ytmI Operon, Involved in Sulfur Metabolism
Burguière, Pierre, Fert, Juliette, Guillouard, Isabelle, Auger, Sandrine, Danchin, Antoine, Martin-Verstraete, Isabelle
The YtlI regulator of Bacillus subtilis activates the transcription of the ytmI operon encoding an l-cystine ABC transporter, a riboflavin kinase, and proteins of unknown function. The expression of...
Médigue, Claudine, Krin, Evelyne, Pascal, Géraldine, Barbe, Valérie, Bernsel, Andreas, Bertin, Philippe N., ...
A considerable fraction of life develops in the sea at temperatures lower than 15°C. Little is known about the adaptive features selected under those conditions. We present the analysis of the...
The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis
You, CongHui, Lu, HongYan, Sekowska, Agnieszka, Fang, Gang, Wang, YiPing, Gilles, Anne-Marie, ...
As diseases have evolved to exploit the holes in our defences, including weaknesses in society, we have to reconsider our way of life, otherwise they will continue to haunt us
Global Control of Cysteine Metabolism by CymR in Bacillus subtilis†
Even, Sergine, Burguière, Pierre, Auger, Sandrine, Soutourina, Olga, Danchin, Antoine, Martin-Verstraete, Isabelle
YrzC has previously been identified as a repressor controlling ytmI expression via its regulation of YtlI activator synthesis in Bacillus subtilis. We identified YrzC as a master regulator of sulfur...
Codon Usage Domains over Bacterial Chromosomes
Bailly-Bechet, Marc, Danchin, Antoine, Iqbal, Mudassar, Marsili, Matteo, Vergassola, Massimo
The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information...
Mechold, Undine, Ogryzko, Vasily, Ngo, Saravuth, Danchin, Antoine
We identified Oligoribonuclease (Orn), an essential Escherichia coli protein and the only exonuclease degrading small ribonucleotides (5mer to 2mer) and its human homologue, small fragment nuclease...
Xia, Xuhua, Wei, Ting, Xie, Zheng, Danchin, Antoine
We used 94 RAPD primers of different nucleotide composition to probe the genomic differences between a highly virulent P. multocida strain and an attenuated vaccine strain derived from the virulent...
Pleiotropic Role of Quorum-Sensing Autoinducer 2 in Photorhabdus luminescens†
Krin, Evelyne, Chakroun, Nesrine, Turlin, Evelyne, Givaudan, Alain, Gaboriau, François, Bonne, Isabelle, ...
Bacterial virulence is an integrative process that may involve quorum sensing. In this work, we compared by global expression profiling the wild-type entomopathogenic Photorhabdus luminescens subsp....
A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments
Muller, Daniel, Médigue, Claudine, Koechler, Sandrine, Barbe, Valérie, Barakat, Mohamed, Talla, Emmanuel, ...
Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural...
Conversion of Methionine to Cysteine in Bacillus subtilis and Its Regulation▿
Hullo, Marie-Françoise, Auger, Sandrine, Soutourina, Olga, Barzu, Octavian, Yvon, Mireille, Danchin, Antoine, ...
Bacillus subtilis can use methionine as the sole sulfur source, indicating an efficient conversion of methionine to cysteine. To characterize this pathway, the enzymatic activities of CysK, YrhA and...
Watt, Rory M., Wang, Jing, Leong, Meikid, Kung, Hsiang-fu, Cheah, Kathryn S.E., Liu, Depei, ...
To investigate the feasibility of conducting a genomic-scale protein labeling and localization study in Escherichia coli, a representative subset of 23 coding DNA sequences (CDSs) was selected for...
YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity
Mechold, Undine, Fang, Gang, Ngo, Saravuth, Ogryzko, Vasily, Danchin, Antoine
Oligoribonuclease is the only RNase in Escherichia coli that is able to degrade RNA oligonucleotides five residues and shorter in length. Firmicutes including Bacillus subtilis do not have an...
Genomics of an extreme psychrophile, Psychromonas ingrahamii
Riley, Monica, Staley, James T, Danchin, Antoine, Wang, Ting Zhang, Brettin, Thomas S, Hauser, Loren J, ...
Chalabaev, Sabina, Turlin, Evelyne, Bay, Sylvie, Ganneau, Christelle, Brito-Fravallo, Emma, Charles, Jean-François, ...
Photorhabdus luminescens, an entomopathogenic bacterium and nematode symbiont, has homologues of the Hca and Mhp enzymes. In Escherichia coli, these enzymes catalyze the degradation of the aromatic...
You, CongHui, Sekowska, Agnieszka, Francetic, Olivera, Martin-Verstraete, Isabelle, Wang, YiPing, Danchin, Antoine
André, Gaëlle, Even, Sergine, Putzer, Harald, Burguière, Pierre, Croux, Christian, Danchin, Antoine, ...
The ubiGmccBA operon of Clostridium acetobutylicum is involved in methionine to cysteine conversion. We showed that its expression is controlled by a complex regulatory system combining several...
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
Touchon, Marie, Hoede, Claire, Tenaillon, Olivier, Barbe, Valérie, Baeriswyl, Simon, Bidet, Philippe, ...
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We...
Ménard, Armelle, Danchin, Antoine, Dupouy, Sandrine, Mégraud, Francis, Lehours, Philippe
The present study concerns the identification of a novel coding sequence in a region of the Helicobacter pylori genome, located between JHP1069/HP1141 and JHP1071/HP1143 according to the numbering of...
Natural selection and immortality
Genomes replicate while the host cells reproduce. I explore the reproduction/replication dialogue, based on a deep analysis of bacterial genomes, in relation to ageing. Making young structures from...
Bacteria as computers making computers
Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we...
Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis
Fang, Ming, Zeisberg, Wencke-Maria, Condon, Ciaran, Ogryzko, Vasily, Danchin, Antoine, Mechold, Undine
Escherichia coli possesses only one essential oligoribonuclease (Orn), an enzyme that can degrade oligoribonucleotides of five residues and shorter in length (nanoRNA). Firmicutes including Bacillus...
Information of the chassis and information of the program in synthetic cells
Synthetic biology aims at reconstructing life to put to the test the limits of our understanding. It is based on premises similar to those which permitted invention of computers, where a machine,...