Antoine Danchin

Summary

Affiliation: Institut Pasteur
Country: France

Publications

  1. pmc The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis
    CongHui You
    National Laboratory of Protein Engineering and Plant Genetic Engineering, The College of Life Sciences, Peking University, 100871, Beijing, PR China
    BMC Microbiol 5:57. 2005
  2. pmc A double epidemic model for the SARS propagation
    Tuen Wai Ng
    Department of Mathematics, The University of Hong Kong, Hong Kong, China
    BMC Infect Dis 3:19. 2003
  3. pmc Genomics of an extreme psychrophile, Psychromonas ingrahamii
    Monica Riley
    Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    BMC Genomics 9:210. 2008
  4. pmc Classification between normal and tumor tissues based on the pair-wise gene expression ratio
    YeeLeng Yap
    HKU Pasteur Research Centre, Dexter H, C, Man Building, 8 Sassoon Road Pokfulam, Hongkong, China
    BMC Cancer 4:72. 2004
  5. ncbi request reprint From protein sequence to function
    A Danchin
    Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Curr Opin Struct Biol 9:363-7. 1999
  6. 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
  7. ncbi request reprint Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP
    A Danchin
    Institut Pasteur, Département de Biochimie et Génétique moléculaire, Paris, France
    DNA Res 4:9-18. 1997
  8. pmc Mapping the bacterial cell architecture into the chromosome
    A Danchin
    Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Philos Trans R Soc Lond B Biol Sci 355:179-90. 2000
  9. ncbi request reprint A brief history of genome research and bioinformatics in France
    A Danchin
    Regulation of Gene Expression, Institut Pasteur, Paris, France
    Bioinformatics 16:65-75. 2000
  10. 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

Detail Information

Publications140 found, 100 shown here

  1. pmc The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis
    CongHui You
    National Laboratory of Protein Engineering and Plant Genetic Engineering, The College of Life Sciences, Peking University, 100871, Beijing, PR China
    BMC Microbiol 5:57. 2005
    ..We investigated whether they can function as methionine aminopeptidases and further explored possible reasons for their essentiality or dispensability in B. subtilis...
  2. pmc A double epidemic model for the SARS propagation
    Tuen Wai Ng
    Department of Mathematics, The University of Hong Kong, Hong Kong, China
    BMC Infect Dis 3:19. 2003
    ..It is important both for predicting the future of the present outbreak and for implementing effective prophylactic measures, to identify the causes of this behavior...
  3. pmc Genomics of an extreme psychrophile, Psychromonas ingrahamii
    Monica Riley
    Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    BMC Genomics 9:210. 2008
    ..Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles...
  4. pmc Classification between normal and tumor tissues based on the pair-wise gene expression ratio
    YeeLeng Yap
    HKU Pasteur Research Centre, Dexter H, C, Man Building, 8 Sassoon Road Pokfulam, Hongkong, China
    BMC Cancer 4:72. 2004
    ..Numerous efforts have been made to use gene expression profiles to improve precision of tumor classification. However, reliable cancer-related signals are generally lacking...
  5. ncbi request reprint From protein sequence to function
    A Danchin
    Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Curr Opin Struct Biol 9:363-7. 1999
    ..Inductive reasoning, based on the integration of biological and sequence knowledge, should enable sequence and functional data to be combined in a productive way...
  6. 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...
  7. ncbi request reprint Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP
    A Danchin
    Institut Pasteur, Département de Biochimie et Génétique moléculaire, Paris, France
    DNA Res 4:9-18. 1997
    ..This article briefly discusses the availability of cytosine nucleotides in eukaryotes, and suggests that they are derived from phospholipids turnover. Finally, the GC content of genomes is discussed in this new light...
  8. pmc Mapping the bacterial cell architecture into the chromosome
    A Danchin
    Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Philos Trans R Soc Lond B Biol Sci 355:179-90. 2000
    ....
  9. ncbi request reprint A brief history of genome research and bioinformatics in France
    A Danchin
    Regulation of Gene Expression, Institut Pasteur, Paris, France
    Bioinformatics 16:65-75. 2000
    ..These organizations have created the dynamics that hopefully will place France (which coordinated consortia that completed several of the first large microbial genomes) among the developed nations that support Large-Scale Biology...
  10. 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...
  11. pmc Infection of society. 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
    Antoine Danchin
    Unit of Genetics of Bacterial Genomes at the Institut Pasteur in Paris, France
    EMBO Rep 4:333-5. 2003
  12. pmc Not every truth is good. The dangers of publishing knowledge about potential bioweapons
    Antoine Danchin
    HKU Pasteur Research Centre, Hong Kong
    EMBO Rep 3:102-4. 2002
  13. 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...
  14. 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...
  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. 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...
  17. 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...
  18. 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...
  19. 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...
  20. 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
    ....
  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. 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...
  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. 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...
  25. 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...
  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 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...
  28. 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...
  29. 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...
  30. 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...
  31. 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...
  32. 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...
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. 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...
  38. doi 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...
  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. 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...
  41. 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...
  42. 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...
  43. 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...
  44. 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...
  45. ncbi request reprint The structural and functional organization of H-NS-like proteins is evolutionarily conserved in gram-negative bacteria
    P Bertin
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Mol Microbiol 31:319-29. 1999
    ..sphaeroides, XrvA in Xanthomonas oryzae and VicH in Vibrio cholerae. These results demonstrate that proteins structurally and functionally related to H-NS are widespread in Gram-negative bacteria...
  46. pmc Multiple control of flagellum biosynthesis in Escherichia coli: role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the flhDC master operon
    O Soutourina
    Unité de Régulation de l Expression Génétique, Institut Pasteur, 75724 Paris Cedex 15, France
    J Bacteriol 181:7500-8. 1999
    ....
  47. 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...
  48. 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...
  49. 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...
  50. 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...
  51. 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...
  52. 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...
  53. 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...
  54. 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...
  55. 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...
  56. 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...
  57. 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...
  58. 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...
  59. ncbi request reprint Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS
    F Hommais
    Unité de Régulation de l Expression Génétique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris, France
    Mol Microbiol 40:20-36. 2001
    ..These results suggest that there is a strong relationship between the H-NS regulon and the maintenance of intracellular homeostasis...
  60. pmc Bacillus subtilis F0F1 ATPase: DNA sequence of the atp operon and characterization of atp mutants
    M Santana
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    J Bacteriol 176:6802-11. 1994
    ..It therefore appears that B. subtilis and E. coli respond in similar ways to the absence of oxidative phosphorylation...
  61. pmc Bacterial variations on the methionine salvage pathway
    Agnieszka Sekowska
    HKU Pasteur Research Centre, 8, Sassoon Road, Pokfulam, Hong Kong, SAR Hong Kong
    BMC Microbiol 4:9. 2004
    ..The corresponding pathway has been unravelled in Bacillus subtilis. However methylthioadenosine is subjected to alternative degradative pathways depending on the organism...
  62. 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...
  63. 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...
  64. 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...
  65. 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...
  66. doi request reprint CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulphur source utilization and plays a role in biofilm formation
    Olga Soutourina
    Unité de Génétique des Génomes Bactériens, CNRS URA 2171, France
    Mol Microbiol 73:194-211. 2009
    ..aureus via an ica-independent mechanism. These data indicate that fine-tuning of sulphur metabolism plays an important part in the physiology of this major pathogen and its adaptation to environmental conditions and survival in the host...
  67. ncbi request reprint Ongoing evolution of strand composition in bacterial genomes
    E P Rocha
    Atelier de BioInformatique, Universite Paris VI, Paris, France
    Mol Biol Evol 18:1789-99. 2001
    ..halodurans. Finally, we propose a more extended model based on the analysis of the substitution asymmetries of CHLAMYDIA: This model fits well with the data provided by bacterial genomes presenting strong strand bias...
  68. pmc Catabolite regulation of the pta gene as part of carbon flow pathways in Bacillus subtilis
    E Presecan Siedel
    , Laboratoire des Fermentations, Institut Pasteur, F 75724, Paris, France
    J Bacteriol 181:6889-97. 1999
    ..In addition to CcpA, carbon catabolite activation of the pta gene therefore requires at least two other cofactors, FBP and either HPr or Crh, phosphorylated at Ser-46 by the ATP-dependent Hpr kinase...
  69. ncbi request reprint S-adenosylmethionine decarboxylase of Bacillus subtilis is closely related to archaebacterial counterparts
    A Sekowska
    Régulation de l Expression Génétique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris, France
    Mol Microbiol 36:1135-47. 2000
    ..This observation may couple polyamine metabolism to sulphur and carbon metabolism by a so far unknown mechanism...
  70. ncbi request reprint The complete genome sequence of the gram-positive bacterium Bacillus subtilis
    F Kunst
    Institut Pasteur, Unité de Biochimie Microbienne, Paris, France
    Nature 390:249-56. 1997
    ....
  71. ncbi request reprint H-NS and H-NS-like proteins in Gram-negative bacteria and their multiple role in the regulation of bacterial metabolism
    P Bertin
    Unité de Régulation de l Expression Génétique, Institut Pasteur, 28, rue du Dr Roux, 75724 Paris Cedex 15, France
    Biochimie 83:235-41. 2001
    ..Finally, expression profiling and phenotypic analysis suggest that, unlike H-NS, its paralogous protein StpA does not play any role in these processes...
  72. pmc The ptsH, ptsI, and crr genes of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system: a complex operon with several modes of transcription
    H De Reuse
    Unité Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    J Bacteriol 170:3827-37. 1988
    ....
  73. ncbi request reprint Role of Escherichia coli histone-like nucleoid-structuring protein in bacterial metabolism and stress response--identification of targets by two-dimensional electrophoresis
    C Laurent-Winter
    Laboratoire d Electrophorèse Bidimensionnelle, Institut Pasteur, Paris, France
    Eur J Biochem 244:767-73. 1997
    ..Finally, synthesis of several proteins belonging to the heat-shock regulon, more particularly molecular chaperones, was induced in an hns mutant...
  74. pmc Control of bacterial motility by environmental factors in polarly flagellated and peritrichous bacteria isolated from Lake Baikal
    O A Soutourina
    Unité de Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15 France
    Appl Environ Microbiol 67:3852-9. 2001
    ..Thus, striking similarities observed in the two organisms suggest that these processes have evolved toward a similar regulatory mechanism in polarly flagellated and laterally flagellated (peritrichous) bacteria...
  75. ncbi request reprint Regulation of Escherichia coli adenylate cyclase activity during hexose phosphate transport
    V Dumay
    Unité de Régulation de l Expression Génétique Centre National de la Recherche Scientifique Unité Associée 1129, Institut Pasteur, Paris, France
    Microbiology 142:575-83. 1996
    ..We present data indicating that Glc6P per se or its degradation is unlikely to be responsible for the low cAMP level. It is concluded that the level of cAMP in the cell is determined by the flux of Glc6P through UhpT...
  76. pmc Anaerobic transcription activation in Bacillus subtilis: identification of distinct FNR-dependent and -independent regulatory mechanisms
    H Cruz Ramos
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    EMBO J 14:5984-94. 1995
    ..Thus induction of genes involved in anaerobic respiration requires in B.subtilis at least two levels of regulation: activation of fnr transcription and activation of FNR to induce transcription of FNR-dependent promoters...
  77. ncbi request reprint Fructose catabolism in Xanthomonas campestris pv. campestris. Sequence of the PTS operon, characterization of the fructose-specific enzymes
    V de Crecy-Lagard
    Unité de Régulation de l Expression Génétique, Institut National de la Santé et de la Recherche Médicale Unité 199, Institut Pasteur, Paris, France
    J Biol Chem 266:18154-61. 1991
    ..Several other enzymes of fructose metabolism were assayed and a potential pathway for fructose catabolism is presented...
  78. ncbi request reprint Exploring the Penicillium marneffei genome
    Kwok Yung Yuen
    HKU Pasteur Research Centre, 8 Sassoon Road, Hong Kong
    Arch Microbiol 179:339-53. 2003
    ..Furthermore, the presence of genes encoding pheromone homologues and ankyrin repeat-containing proteins of other fungi and algae strongly suggests the presence of a sexual stage that presumably exists in the environment...
  79. 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
  80. 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...
  81. 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/...
  82. pmc Identification and isolation of a gene required for nitrate assimilation and anaerobic growth of Bacillus subtilis
    P Glaser
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    J Bacteriol 177:1112-5. 1995
    ..Analysis of mutants showed that narA but not narQ is required for both nitrate assimilation and respiration...
  83. pmc Aeromonas hydrophila adenylyl cyclase 2: a new class of adenylyl cyclases with thermophilic properties and sequence similarities to proteins from hyperthermophilic archaebacteria
    O Sismeiro
    , Institut Pasteur, Paris, France
    J Bacteriol 180:3339-44. 1998
    ..The possibility of a gene transfer between such phylogenetically divergent bacteria is discussed...
  84. ncbi request reprint Characterization of polyamine synthesis pathway in Bacillus subtilis 168
    A Sekowska
    Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Mol Microbiol 29:851-8. 1998
    ..This is consistent with the level of polyamines measured in the cell...
  85. ncbi request reprint Comparative analysis of the cya locus in enterobacteria and related gram-negative facultative anaerobes
    P Trotot
    Institut Pasteur, Département de Biochimie et Génétique moléculaire, Paris, France
    Biochimie 78:277-87. 1996
    ..Finally, comparison of the different polypeptide sequences of ACs permits discussion of important features of the catalytic and regulatory centers of the protein...
  86. ncbi request reprint Filling the gap between hns and adhE in Escherichia coli K12
    A Danchin
    Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Microbiology 141:959-60. 1995
    ..We report the sequence of the hns-adh region, at 27 min on the genome...
  87. pmc Structural and functional relationships between Pasteurella multocida and enterobacterial adenylate cyclases
    M Mock
    Unité des Antigènes Bactériens Centre National de la Recherche Scientifique Unité Associée 557, Institut Pasteur, Paris, France
    J Bacteriol 173:6265-9. 1991
    ..coli enzyme III-glucose is involved in the regulation of P. multocida adenylate cyclase. It also indicates that the underlying process leading to enterobacterial adenylate cyclase activation has been conserved through evolution...
  88. ncbi request reprint Multiple IS insertion sequences near the replication terminus in Escherichia coli K-12
    I Moszer
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Biochimie 73:1361-74. 1991
    ..It was found to map at 30 min on the chromosome map and to harbour two insertion sequences (IS2 and IS30) as well as several putative coding sequences which had no feature in common with known proteins...
  89. ncbi request reprint Identification of two fructose transport and phosphorylation pathways in Xanthomonas campestris pv. campestris
    V de Crecy-Lagard
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Mol Gen Genet 227:465-72. 1991
    ..The mutant strains also failed to utilize mannose, sucrose and mannitol, suggesting the existence of a branch point between the metabolism of fructose and of these latter carbohydrates...
  90. pmc A Xanthomonas campestris pv. campestris protein similar to catabolite activation factor is involved in regulation of phytopathogenicity
    V de Crecy-Lagard
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    J Bacteriol 172:5877-83. 1990
    ..Production of xanthan gum, pigment, and extracellular enzymes was either increased or decreased, suggesting that CLP plays a role in the regulation of phytopathogenicity...
  91. ncbi request reprint Regulation of the early steps of 3-phenylpropionate catabolism in Escherichia coli
    E Turlin
    Départment de Biochimie et Génétique Moléculaire, Institut Pasteur, Paris, France
    J Mol Microbiol Biotechnol 3:127-33. 2001
    ..The expression of hcaR is strongly repressed in the presence of glucose. Glucose-dependent repression of hcaR expression could only be partially overcome by adding exogenous cAMP...
  92. ncbi request reprint Positive regulation of the expression of the Escherichia coli pts operon. Identification of the regulatory regions
    H De Reuse
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    J Mol Biol 226:623-35. 1992
    ..We finally propose that the expression of the pts operon is controlled by two alternative positive regulatory mechanisms, which are designed to allow activation of the pts operon under a great variety of growth conditions...
  93. ncbi request reprint Sulfur-limitation-regulated proteins in Bacillus subtilis: a two-dimensional gel electrophoresis study
    J Y Coppee
    Unité de Régulation de l Expression Génétique, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    Microbiology 147:1631-40. 2001
    ..This putative operon is activated by a LysR-like regulator, YTLI: This is the first regulator involved in the control of expression in response to sulfur availability to be identified in B. subtilis...
  94. ncbi request reprint A gene encoding a tyrosine tRNA synthetase is located near sacS in Bacillus subtilis
    P Glaser
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    DNA Seq 1:251-61. 1991
    ..Finally phylogenetic relationships between known tyrosine and tryptophan tRNA synthetases are discussed...
  95. pmc Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
    Yee Leng Yap
    HKU Pasteur Research Centre, Dexter H, C, Man Building, 8 Sassoon Road Pokfulam, Hong Kong
    BMC Bioinformatics 4:43. 2003
    ..In approach two, a multivariate factor analysis was performed to derive the embedded tetra-nucleotide usage patterns. These patterns were subsequently used to classify the selected viruses...
  96. 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...
  97. ncbi request reprint Cloning and sequence of the Bordetella bronchiseptica adenylate cyclase-hemolysin-encoding gene: comparison with the Bordetella pertussis gene
    F Betsou
    Unité de bactériologie moléculaire et médicale, Institut Pasteur, Paris, France
    Gene 162:165-6. 1995
    ..The deduced amino-acid sequence was compared to the AC-Hly from B. pertussis (Bp) and the main differences were found in the C-terminal repeat region of the molecule...
  98. pmc Mutations in the bglY gene increase the frequency of spontaneous deletions in Escherichia coli K-12
    P Lejeune
    Unité Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Proc Natl Acad Sci U S A 87:360-3. 1990
    ..bglY mutations are recessive and can be complemented by a DNA fragment of 900 base pairs assumed to contain the entire bglY wild-type gene. This mutator effect is recA-independent...
  99. ncbi request reprint The calmodulin-sensitive adenylate cyclase of Bordetella pertussis: cloning and expression in Escherichia coli
    P Glaser
    Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Mol Microbiol 2:19-30. 1988
    ..The enzyme expressed in E. coli is recognized in Western blots by antibodies directed against purified B. pertussis adenylate cyclase, and its activity is inhibited by these antibodies...
  100. ncbi request reprint Molecular cloning, sequencing, and physiological characterization of the qox operon from Bacillus subtilis encoding the aa3-600 quinol oxidase
    M Santana
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    J Biol Chem 267:10225-31. 1992
    ..Although several terminal oxidases are found in B. subtilis, Qox oxidase (aa3-600) is predominant during the vegetative growth and its absence leads to important alterations of the phenotype of B. subtilis...
  101. ncbi request reprint Mutations in bglY, the structural gene for the DNA-binding protein H1 of Escherichia coli, increase the expression of the kanamycin resistance gene carried by plasmid pGR71
    P Bertin
    Unité de Régulation de l Expression Génétique, Institut Pasteur, Paris, France
    Mol Gen Genet 233:184-92. 1992
    ..Assay of beta-galactosidase in wild-type and mutant strains showed that expression of the antibiotic resistance gene was directly affected by H1 protein, the bglY gene product...