Antoine Danchin

Summary

Country: France

Publications

  1. ncbi request reprint [Will we build a synthetic bacteria?]
    Antoine Danchin
    Génétique des Génomes Bactériens, URA 2171 CNRS, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris Cedex 15, France
    Med Sci (Paris) 24:533-40. 2008
  2. pmc From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later
    Valerie Barbe
    CEA, Institut de Génomique, Genoscope, 2 rue Gaston Cremieux, 91057 Evry, France
    Microbiology 155:1758-75. 2009
  3. doi request reprint Scaling up synthetic biology: Do not forget the chassis
    Antoine Danchin
    AMAbiotics SAS, Bâtiment G1, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    FEBS Lett 586:2129-37. 2012
  4. pmc Structure-based discovery of inhibitors of the YycG histidine kinase: new chemical leads to combat Staphylococcus epidermidis infections
    Zhiqiang Qin
    Key Laboratory of Medical Molecular Virology, Ministry of Education and Ministry of Public Health, Institute of Medical Microbiology, Shanghai Medical School of Fudan University, Shanghai, PR China
    BMC Microbiol 6:96. 2006
  5. pmc Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli
    Ye Jin
    Department of Biochemistry, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, PR China
    BMC Genomics 10:165. 2009
  6. pmc Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228
    Wu Wei
    Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
    BMC Genomics 7:112. 2006
  7. doi request reprint Cells need safety valves
    Antoine Danchin
    Genetics of Bacterial Genomes, Centre National de la Recherche Scientifique URA 2171, Institut Pasteur, 28 rue du Docteur Roux, Paris Cedex 15, France
    Bioessays 31:769-73. 2009
  8. ncbi request reprint A path from predation to mutualism
    Antoine Danchin
    AMAbiotics SAS, Genavenir 8, 5 rue Henri Desbrueres, 91030 Evry Cedex, France
    Mol Microbiol 77:1346-50. 2010
  9. ncbi request reprint Myopic selection of novel information drives evolution
    Antoine Danchin
    CNRS URA2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Curr Opin Biotechnol 20:504-8. 2009
  10. pmc Information of the chassis and information of the program in synthetic cells
    Antoine Danchin
    CNRS URA2171 Institut Pasteur, 28 rue du Docteur Roux, Paris Cedex 15, 75724, France
    Syst Synth Biol 3:125-34. 2009

Detail Information

Publications75

  1. ncbi request reprint [Will we build a synthetic bacteria?]
    Antoine Danchin
    Génétique des Génomes Bactériens, URA 2171 CNRS, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris Cedex 15, France
    Med Sci (Paris) 24:533-40. 2008
  2. pmc From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later
    Valerie Barbe
    CEA, Institut de Génomique, Genoscope, 2 rue Gaston Cremieux, 91057 Evry, France
    Microbiology 155:1758-75. 2009
    ..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...
  3. doi request reprint Scaling up synthetic biology: Do not forget the chassis
    Antoine Danchin
    AMAbiotics SAS, Bâtiment G1, 2 rue Gaston Cremieux, 91057 Evry Cedex, France
    FEBS Lett 586:2129-37. 2012
    ..The discussion ends with the central question of evolvability of artificial constructs and to suggest that combining in vivo Synthetic Biology with biochemical reactors might be an efficient way forward...
  4. pmc Structure-based discovery of inhibitors of the YycG histidine kinase: new chemical leads to combat Staphylococcus epidermidis infections
    Zhiqiang Qin
    Key Laboratory of Medical Molecular Virology, Ministry of Education and Ministry of Public Health, Institute of Medical Microbiology, Shanghai Medical School of Fudan University, Shanghai, PR China
    BMC Microbiol 6:96. 2006
    ..It has an urgent need to design novel antibiotics against staphylococci infections, especially those can kill cells embedded in biofilm...
  5. pmc Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli
    Ye Jin
    Department of Biochemistry, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, PR China
    BMC Genomics 10:165. 2009
    ..Acid resistance in E. coli is hierarchically controlled by numerous regulators among which are small noncoding RNAs (sncRNA)...
  6. pmc Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228
    Wu Wei
    Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Graduate School of the Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China
    BMC Genomics 7:112. 2006
    ..Traditional investigations stress differences in gene content. We focused on conserved genes that have accumulated small mutation differences during the transition...
  7. doi request reprint Cells need safety valves
    Antoine Danchin
    Genetics of Bacterial Genomes, Centre National de la Recherche Scientifique URA 2171, Institut Pasteur, 28 rue du Docteur Roux, Paris Cedex 15, France
    Bioessays 31:769-73. 2009
    ..This scenario of constraints imposed by efficient influx of metabolites provides us with a model that should be followed when constructing synthetic cells...
  8. ncbi request reprint A path from predation to mutualism
    Antoine Danchin
    AMAbiotics SAS, Genavenir 8, 5 rue Henri Desbrueres, 91030 Evry Cedex, France
    Mol Microbiol 77:1346-50. 2010
    ....
  9. ncbi request reprint Myopic selection of novel information drives evolution
    Antoine Danchin
    CNRS URA2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Curr Opin Biotechnol 20:504-8. 2009
    ..Synthetic biology faces a dilemma: it will either implement the corresponding genes, and cells will evolve in an unpredictable manner, or omit them, and cells will age and have to be reconstructed periodically...
  10. pmc Information of the chassis and information of the program in synthetic cells
    Antoine Danchin
    CNRS URA2171 Institut Pasteur, 28 rue du Docteur Roux, Paris Cedex 15, 75724, France
    Syst Synth Biol 3:125-34. 2009
    ..We suggest that the program of life codes for processes meant to trap information which comes from the context provided by the environment of the machine...
  11. pmc Natural selection and immortality
    Antoine Danchin
    Genetics of Bacterial Genomes, CNRS URA2171, Institut Pasteur, Paris, France
    Biogerontology 10:503-16. 2009
    ..This permits living systems to accumulate information over generations, but has the drawback, in multicellular organisms, to open the door for immortalisation, leading to cancer...
  12. pmc Bacteria as computers making computers
    Antoine Danchin
    Génétique des Génomes Bactériens, Institut Pasteur, Paris, France
    FEMS Microbiol Rev 33:3-26. 2009
    ..The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments...
  13. doi request reprint A challenge to vaccinology: living organisms trap information
    Antoine Danchin
    CEA Genoscope, Amabiotics, 2, rue Gaston Crémieux, 91057 Evry Cedex, France
    Vaccine 27:G13-6. 2009
    ..The consequence is that genes acquired by horizontal transfer as well as viruses will tend to perpetuate in niches where they are functional, creating recurrent conditions for emergence of diseases...
  14. pmc Three different systems participate in L-cystine uptake in Bacillus subtilis
    Pierre Burguière
    Unité de Génétique des Génomes Bactériens, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    J Bacteriol 186:4875-84. 2004
    ..The expression of the ytmI operon and the yhcL gene was regulated in response to sulfur availability, while the level of expression of the yckK gene remained low under all the conditions tested...
  15. pmc Global control of cysteine metabolism by CymR in Bacillus subtilis
    Sergine Even
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, URA CNRS 2171, 75724 Paris Cedex 15, France
    J Bacteriol 188:2184-97. 2006
    ..Transcriptome analysis of a delta cymR mutant and the wild-type strain also brought out significant changes in the expression level of a large set of genes related to stress response or to transition toward anaerobiosis...
  16. pmc Persistence drives gene clustering in bacterial genomes
    Gang Fang
    Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr, Roux, 75724 Paris Cedex 15, France
    BMC Genomics 9:4. 2008
    ..However, genomes harbor two very different categories of genes: those genes present in a majority of organisms - persistent genes - and those present in very few organisms - rare genes...
  17. doi request reprint Regulatory role of UvrY in adaptation of Photorhabdus luminescens growth inside the insect
    Evelyne Krin
    Unite de Genetique des Genomes Bacteriens URA2171, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Environ Microbiol 10:1118-34. 2008
    ..As a consequence, the uvrY-deficient strain exhibited a decreased killing of insect cells and a reduced growth on insect cells culture, suggesting a UvrY role in the adaptation of P. luminescens inside the insect...
  18. ncbi request reprint AstR-AstS, a new two-component signal transduction system, mediates swarming, adaptation to stationary phase and phenotypic variation in Photorhabdus luminescens
    Sylviane Derzelle
    Unité de Génétique des Génomes Bactériens, Département de Structure et Dynamique des Génomes, Institut Pasteur, 75724 Paris Cedex 15, France
    Microbiology 150:897-910. 2004
    ..The link between AstRS-dependent stationary-phase adaptation and phenotypic variation is discussed...
  19. pmc Conversion of methionine to cysteine in Bacillus subtilis and its regulation
    Marie Francoise Hullo
    Unité de Génétique des Génomes Bactériens, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    J Bacteriol 189:187-97. 2007
    ..The addition of O-acetyl-serine prevented the formation of this protein-DNA complex...
  20. ncbi request reprint GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli
    Florence Hommais
    Unité de Génétique des Génomes Bactériens, URA CNRS 2185, Institut Pasteur, France
    Microbiology 150:61-72. 2004
    ..These results, along with the G+C signature of the chromosomal region, support the existence of a fitness island for acid adaptation on the E. coli chromosome...
  21. ncbi request reprint The HcaR regulatory protein of Photorhabdus luminescens affects the production of proteins involved in oxidative stress and toxemia
    Sabina Chalabaev
    Unite de Genetique des Genomes Bacteriens URA2171, Institut Pasteur, Paris, France
    Proteomics 7:4499-510. 2007
    ..luminescens virulence. Our results also highlight the power of proteomic analysis for detecting unexpected links between different, concomitant processes in bacteria...
  22. pmc Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12
    Evelyne Krin
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France
    J Bacteriol 185:3139-46. 2003
    ....
  23. pmc YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity
    Undine Mechold
    Institut Pasteur, URA 2171, Unité de Génétique des Génomes Bactériens, 75724 Paris Cedex 15, France
    Nucleic Acids Res 35:4552-61. 2007
    ..coli. An ytqI mutant in B. subtilis shows impairment of growth in the absence of cysteine, a phenotype resembling that of a cysQ mutant in E. coli. Phylogenetic distribution of YtqI, Orn and CysQ supports bifunctionality of YtqI...
  24. doi request reprint RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli
    Evelyne Krin
    Institut Pasteur, Unité de Génétique des Génomes Bactériens, CNRS URA2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Res Microbiol 161:363-71. 2010
    ..In addition, we showed that H-NS positively affects motility via the flhDC master operon repression by RcsB. This substantiates the central role of RcsB in H-NS-mediated control of motility and acid stress resistance...
  25. pmc Pleiotropic role of quorum-sensing autoinducer 2 in Photorhabdus luminescens
    Evelyne Krin
    Unite de Genetique des Genomes Bacteriens URA2171, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Appl Environ Microbiol 72:6439-51. 2006
    ..Finally, we showed that the luxS-deficient strain had attenuated virulence against the lepidopteran Spodoptera littoralis. We concluded that AI-2 is involved mainly in early steps of insect invasion in P. luminescens...
  26. pmc Regulation of the Bacillus subtilis ytmI operon, involved in sulfur metabolism
    Pierre Burguière
    Unité de Génétique des Génomes Bactériens, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    J Bacteriol 187:6019-30. 2005
    ..A common motif, AT(A/T)ATTCCTAT, was found in the promoter region of the ytlI and lmo2352 genes. Deletion of part of this motif or the introduction of point mutations in this sequence confirmed its involvement in ytlI regulation...
  27. pmc Cinnamic acid, an autoinducer of its own biosynthesis, is processed via Hca enzymes in Photorhabdus luminescens
    Sabina Chalabaev
    Unité de Génétique des Membranes Bactériennes, CNRS URA 2172, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
    Appl Environ Microbiol 74:1717-25. 2008
    ..This suggests that CA is consumed via at least two separate pathways in P. luminescens: the biosynthesis of ST and a pathway involving the Hca and Mhp enzymes...
  28. pmc S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum
    Gaelle André
    Genetics of Bacterial Genomes, Pasteur Institute, CNRS URA2171, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
    Nucleic Acids Res 36:5955-69. 2008
    ..We proposed a regulatory model in which the antisense RNA controlled the expression of the ubiG operon in cis via transcriptional interference at the ubiG locus...
  29. pmc Global expression profile of Bacillus subtilis grown in the presence of sulfate or methionine
    Sandrine Auger
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, URA CNRS 2171, 75724 Paris Cedex 15, France
    J Bacteriol 184:5179-86. 2002
    ..The expression of genes encoding transporters (yhcL, ytmJKLMN, and yxeMO) was high when the sulfur source was methionine or taurine and reduced when it was sulfate...
  30. pmc Spx mediates oxidative stress regulation of the methionine sulfoxide reductases operon in Bacillus subtilis
    CongHui You
    Institut Pasteur, Unité de Génétique des Génomes Bactériens, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    BMC Microbiol 8:128. 2008
    ..Methionine sulfoxide reductases are enzymes able to regenerate methionine and restore protein function after oxidative damage...
  31. pmc Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
    Marie Touchon
    Atelier de BioInformatique, Universite Pierre et Marie Curie Paris 6, Paris, France
    PLoS Genet 5:e1000344. 2009
    ..Overall, despite a very high gene flow, genes co-exist in an organised genome...
  32. pmc Gene essentiality determines chromosome organisation in bacteria
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 28, rue du Dr Roux, 75724 Paris Cedex 15, France
    Nucleic Acids Res 31:6570-7. 2003
    ..These results indicate that essentiality plays a fundamental role in the distribution of genes in most bacterial genomes...
  33. ncbi request reprint Escherichia coli response to exogenous pyrophosphate and analogs
    Francis Biville
    Département de Biochimie et Génétique moléculaire, Institut Pasteur, Paris, France
    J Mol Microbiol Biotechnol 5:37-45. 2003
    ..The transcriptome data also indicated that processes other than iron uptake might be involved in the cellular response to exogenous pyrophosphate or methylenediphosphonic acid...
  34. ncbi request reprint Regulation of bacterial motility in response to low pH in Escherichia coli: the role of H-NS protein
    Olga A Soutourina
    Unité de Génétique des Génomes Bactériens and Génopole Plateau Protéomique, Institut Pasteur, Paris, France
    Microbiology 148:1543-51. 2002
    ..Finally, the presence of a similar regulatory region in several Gram-negative bacteria implies that this mechanism is largely conserved...
  35. pmc Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
    Claudine Medigue
    Genoscope, CNRS UMR 8030, Atelier de Génomique Comparative, 91006 Evry Cedex, France
    Genome Res 15:1325-35. 2005
    ..Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome...
  36. pmc The PhoP-PhoQ two-component regulatory system of Photorhabdus luminescens is essential for virulence in insects
    Sylviane Derzelle
    Unité de Génétique des Génomes Bactériens Laboratoire de Génomique des Microorganismes Pathogènes, Institut Pasteur, 75724 Paris, France
    J Bacteriol 186:1270-9. 2004
    ..Mg(2+)-regulated gene expression of pbgP1 was absent in the mutant and was restored when phoPQ was complemented in trans. This finding highlights the essential role played by PhoPQ in the virulence of an entomopathogen...
  37. ncbi request reprint The metNPQ operon of Bacillus subtilis encodes an ABC permease transporting methionine sulfoxide, D- and L-methionine
    Marie Francoise Hullo
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, URA CNRS 2171, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
    Res Microbiol 155:80-6. 2004
    ..Other uptake systems are therefore present for these two compounds. In contrast, the Yus ABC transporter corresponds to the sole d-methionine uptake system. We propose to rename yusC, yusB and yusA as metN, metP and metQ, respectively...
  38. ncbi request reprint 3-phenylpropionate catabolism and the Escherichia coli oxidative stress response
    Evelyne Turlin
    Unité de Génétique des Génomes Bactériens, Département de Structure et Dynamique des Génomes, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
    Res Microbiol 156:312-21. 2005
    ..The expression of hcaR was repressed in the absence of oxygen by the ArcA/ArcB two-component system...
  39. ncbi request reprint How essential are nonessential genes?
    Gang Fang
    Unité Génétique des Génomes Bactériens, Institut Pasteur, Paris Cedex, France
    Mol Biol Evol 22:2147-56. 2005
    ..They should then be regarded as truly essential genes...
  40. pmc Codon usage domains over bacterial chromosomes
    Marc Bailly-Bechet
    CNRS URA 2171, Institute Pasteur, Unité Génétique in silico, Paris, France
    PLoS Comput Biol 2:e37. 2006
    ..It is argued that a sizeable contribution to this effect comes from the dynamical compartimentalization induced by the recycling of tRNAs, leading to gene expression rates dependent on their genomic and expression context...
  41. ncbi request reprint The regulation of Enzyme IIA(Glc) expression controls adenylate cyclase activity in Escherichia coli
    Evelyne Krin
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Microbiology 148:1553-9. 2002
    ..This leads to a twofold reduction in the global amount of Enzyme IIA(Glc), the adenylate cyclase activator, responsible for the decrease in adenylate cyclase activity observed in the hns crp strain...
  42. ncbi request reprint The extant core bacterial proteome is an archive of the origin of life
    Antoine Danchin
    Génétique des Génomes Bactériens, Institut Pasteur, Paris, France
    Proteomics 7:875-89. 2007
    ..Further analysis suggests that RNA degradation, associated to the presence of iron, still plays a role in extant metabolism, including the evolution of genome structures...
  43. ncbi request reprint The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in Bacillus subtilis
    Catherine Tanous
    Institut Pasteur, UnitédeGénétique des Génomes Bactériens, Plate forme de Biophysique des Macromolecules et de leurs interactions, 75724 Paris Cedex 15, France
    J Biol Chem 283:35551-60. 2008
    ..We propose an original model, supported by the determination of the intracellular concentrations of the different partners, by which CysK positively regulates CymR in sensing the bacterial cysteine pool...
  44. ncbi request reprint The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens
    Eric Duchaud
    Laboratoire de Génomique des Microorganismes Pathogènes, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
    Nat Biotechnol 21:1307-13. 2003
    ..Moreover, newly identified insecticidal proteins may be effective alternatives for the control of insect pests...
  45. ncbi request reprint Proteome analysis of the phenotypic variation process in Photorhabdus luminescens
    Evelyne Turlin
    Unité de Génétique des Génomes Bactériens, Département de Structure et Dynamique des Génomes, Institut Pasteur, Paris, France
    Proteomics 6:2705-25. 2006
    ..The transport and binding of iron, sugars and amino acids were also affected and molecular chaperones were strongly down-regulated. A potential role for H-NS in phenotypic variation control is discussed...
  46. pmc Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC
    Stefan Engelen
    AMAbiotics SAS, Bâtiment G1, 2 rue Gaston Cremieux, 91000 Evry, France
    BMC Genomics 13:69. 2012
    ..Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase...
  47. pmc Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis
    Ming Fang
    Institut Pasteur, URA 2171, Unité de Génétique des Génomes Bactériens, 75724 Paris Cedex 15, France
    Nucleic Acids Res 37:5114-25. 2009
    ..We conclude that, unlike in E. coli, degradation of nanoRNA is performed in a redundant fashion in B. subtilis...
  48. ncbi request reprint An analysis of determinants of amino acids substitution rates in bacterial proteins
    Eduardo P C Rocha
    Unité GGB, Institut Pasteur, Paris, France
    Mol Biol Evol 21:108-16. 2004
    ..They also indicate that when a control for this variable is included, essentiality plays no significant role in the rate of protein evolution in bacteria, as is the case in eukaryotes...
  49. ncbi request reprint A Novel H-NS-like protein from an antarctic psychrophilic bacterium reveals a crucial role for the N-terminal domain in thermal stability
    Christian Tendeng
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France
    J Biol Chem 278:18754-60. 2003
    ..coli and Acinetobacter proteins, the alpha-helical domain displays weaker intermolecular interactions in the Psychrobacter protein, which may account for the low thermal stability observed at 37 degrees C...
  50. doi request reprint An updated metabolic view of the Bacillus subtilis 168 genome
    Eugeni Belda
    CEA, Institut de Génomique, Génoscope Laboratoire d Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Cremieux, Evry, France
    Microbiology 159:757-70. 2013
    ..ebi.ac.uk/chebi/). The newly annotated sequence is deposited at the International Nucleotide Sequence Data Collaboration with accession number AL009126.4...
  51. pmc Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae
    Guillaume Postic
    Unitéde Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA 2171, 75724 Paris Cedex 15, France
    RNA 18:155-65. 2012
    ..coli cysQ mutant. Here, we show that SMU.1297 can complement an E. coli orn(-) mutant, suggesting that having both pAp-phosphatase and nanoRNase activity is a common feature of NrnA homologs...
  52. pmc Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes
    Yuko Makita
    Unit of Genetics of Bacterial Genomes, Institut Pasteur, URA CNRS 2171, Cedex 15, Paris, France
    BMC Bioinformatics 8:47. 2007
    ..A further problem is that most existing methods are optimized for Escherichia coli data sets; applying these methods to newly sequenced bacterial genomes may not result in an equivalent level of accuracy...
  53. ncbi request reprint A strand-specific model for chromosome segregation in bacteria
    Eduardo P C Rocha
    Unité Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris 15, France
    Mol Microbiol 49:895-903. 2003
    ..We show that the model is consistent with the asymmetric distribution of highly expressed genes and of stress response genes in Escherichia coli and Bacillus subtilis. The model offers a framework for interpreting data from genomics...
  54. pmc Identification of Bacillus subtilis CysL, a regulator of the cysJI operon, which encodes sulfite reductase
    Isabelle Guillouard
    Unité de Génétique des Génomes Bactériens, URA CNRS 2171, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    J Bacteriol 184:4681-9. 2002
    ..This is the first report of a regulator of some of the genes involved in cysteine biosynthesis in B. subtilis...
  55. pmc Identification, characterization, and regulation of a cluster of genes involved in carbapenem biosynthesis in Photorhabdus luminescens
    Sylviane Derzelle
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France
    Appl Environ Microbiol 68:3780-9. 2002
    ..The importance of this carbapenem production in the ecology of P. luminescens is discussed...
  56. pmc 3'-5' phosphoadenosine phosphate is an inhibitor of PARP-1 and a potential mediator of the lithium-dependent inhibition of PARP-1 in vivo
    Elie Toledano
    Institut Pasteur, CNRS UMR 3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Strucurale et Chimie, Paris, France
    Biochem J 443:485-90. 2012
    ..From these results, we propose that pAp might be a physiological regulator of PARP-1 activity...
  57. pmc Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli
    Evelyne Krin
    Unité de Plasticité du Génome Bactérien, Institut Pasteur, France
    BMC Microbiol 10:273. 2010
    ..H-NS regulates the acid stress resistance. The present study aimed to characterize the H-NS-dependent cascade governing the acid stress resistance pathways and to define the interplay between the different regulators...
  58. ncbi request reprint The logic of metabolism and its fuzzy consequences
    Antoine Danchin
    Building G1, AMAbiotics SAS, 2 rue Gaston Cremieux, Evry, 91000, France
    Environ Microbiol 16:19-28. 2014
    ..A second type of denouement uses a process where protecting/deprotecting unwanted metabolites - conceptually similar to the procedure used in the laboratory of an organic chemist - is used to enter a completely new catabolic pathway...
  59. ncbi request reprint Effect of mild acid pH on the functioning of bacterial membranes in Vibrio cholerae
    Florence Hommais
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, Paris, France
    Proteomics 2:571-9. 2002
    ..Our results suggest that V. cholerae is able to sense a moderate decrease in pH and to modify accordingly its structure and physiology...
  60. pmc SubtiList: the reference database for the Bacillus subtilis genome
    Ivan Moszer
    Unité de Génétique des Génomes Bactériens and Logiciels et Banques de Données, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Nucleic Acids Res 30:62-5. 2002
    ..SubtiList is accessible at http://genolist.pasteur.fr/SubtiList/. Similar bacterial databases are accessible at http://genolist.pasteur.fr/...
  61. pmc Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells
    Undine Mechold
    Institut Pasteur, URA 2171, Unité de Génétique des Génomes Bactériens, 75724 Paris Cedex 15, France
    Nucleic Acids Res 34:2364-73. 2006
    ..Our findings point to remarkable conservation of the connection between sulfur- and RNA metabolism between E.coli and humans...
  62. ncbi request reprint Essentiality, not expressiveness, drives gene-strand bias in bacteria
    Eduardo P C Rocha
    Unité GGB, URA 2171, Institut Pasteur, 28 rue Dr Roux, 75015 Paris, France
    Nat Genet 34:377-8. 2003
    ..Here we show, however, that in Bacillus subtilis and Escherichia coli, essentiality (the transcript product), not expressiveness (the collision rate), selectively drives the biased gene distribution...
  63. ncbi request reprint UMP kinase from the Gram-positive bacterium Bacillus subtilis is strongly dependent on GTP for optimal activity
    Cristina Gagyi
    Laboratoire de Chimie Structurale des Macromolecules, Institut Pasteur, Paris, France
    Eur J Biochem 270:3196-204. 2003
    ..subtilis and E. coli enzymes...
  64. ncbi request reprint Genomes and evolution
    Antoine Danchin
    Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Curr Issues Mol Biol 5:37-42. 2003
    ..Such rules could aid the understanding of common properties and essential differences corresponding to elusive functions, or of still unknown bacterial biotopes...
  65. pmc Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"
    Etienne Larsabal
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, URA CNRS 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    BMC Bioinformatics 6:206. 2005
    ..This bias is present throughout a given genome, both in coding and non-coding sequences. Until now this bias remained of unknown origin...
  66. doi request reprint A phylogenetic view of bacterial ribonucleases
    Antoine Danchin
    Institut Pasteur, Docteur Roux, Paris Cedex 15, France
    Prog Mol Biol Transl Sci 85:1-41. 2009
    ..The recent identification of novel activities in these organisms, stresses the (underestimated) importance of degradation of very short RNAs, as well as 5'-3' degradative processes in Bacteria...
  67. doi request reprint Linking selenium biogeochemistry to the sulfur-dependent biological detoxification of arsenic
    Raoul Marie Couture
    Ecohydrology, Department of Earth and Environmental Sciences, University of Waterloo, 200 University Ave W, Waterloo, Canada
    Environ Microbiol 14:1612-23. 2012
    ..This hypothesis is discussed in terms of the relative geochemical distribution of Se and As...
  68. ncbi request reprint The metIC operon involved in methionine biosynthesis in Bacillus subtilis is controlled by transcription antitermination
    Sandrine Auger
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, URA CNRS 2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Microbiology 148:507-18. 2002
    ..When methionine levels were limiting, the amount of the full-length transcript increased. These results substantiate a model of regulation by transcription antitermination...
  69. pmc Specialized microbial databases for inductive exploration of microbial genome sequences
    Gang Fang
    HKU Pasteur Research Centre, Dexter HC Man Building, 8, Sassoon Road, Pokfulam, Hong Kong, China
    BMC Genomics 6:14. 2005
    ..The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects...
  70. pmc A tale of two oxidation states: bacterial colonization of arsenic-rich environments
    Daniel Muller
    Genetique Moleculaire, Génomique et Microbiologie, UMR7156 CNRS and Université Louis Pasteur, Strasbourg, France
    PLoS Genet 3:e53. 2007
    ..Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth...
  71. ncbi request reprint Universal biases in protein composition of model prokaryotes
    Geraldine Pascal
    Genoscope CNRS UMR 8030, Atelier de Génomique Comparative, Evry, France
    Proteins 60:27-35. 2005
    ..A remarkable role of aromatic amino acids was uncovered. Expressed orphan proteins are enriched in these residues, suggesting that they might participate in a process of gain of function during evolution...
  72. ncbi request reprint Cytosine methylation is not the major factor inducing CpG dinucleotide deficiency in bacterial genomes
    Yong Wang
    Department of Zoology, University of Hong Kong, Pokfulam, Hong Kong SAR, China
    J Mol Evol 58:692-700. 2004
    ..This suggests the existence of alternative mechanisms contributing to CpG deficiency in bacteria...
  73. ncbi request reprint Base composition bias might result from competition for metabolic resources
    Eduardo P C Rocha
    Atelier de BioInformatique, Universite Pierre et Marie Curie, 12, rue Cuvier, 75005 Paris, France
    Trends Genet 18:291-4. 2002
    ..We suggest that the higher energy cost and limited availability of G and C over A and T/U could be a basis for the understanding of these differences...
  74. ncbi request reprint Persistent biases in the amino acid composition of prokaryotic proteins
    Geraldine Pascal
    Genoscope CNRS UMR 8030, Atelier de Génomique Comparative, Evry, France
    Bioessays 28:726-38. 2006
    ..Some allow identification of species-specific functions or localisation such as surface or exported proteins. Errors in genome annotations are also revealed by correspondence analysis, making it useful for quality control and correction...
  75. ncbi request reprint The DNA secondary structure of the Bacillus subtilis genome
    Valentina Tosato
    Microbiology Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, Padriciano 99, 34012, Trieste, Italy
    FEMS Microbiol Lett 218:23-30. 2003
    ..Given the increasing biological relevance of secondary DNA structures, these findings should facilitate further studies on the evolution, dynamics and expression of the genetic information stored in bacterial genomes...