Transcriptionnal and post-transcriptionnal control of genetic expression

Head : Harald Putzer

Publications de l'équipe



  1. Marcos-Viquez J, Rodríguez-Hernández A, Álvarez-Añorve LI, Medina-García A, Plumbridge J, Calcagno ML, Rodríguez-Romero A, Bustos-Jaimes I. (2023) Substrate binding in the allosteric site mimics homotropic cooperativity in the SIS-fold glucosamine-6-phosphate deaminases. Protein Sci. Jun;32(6):e4651. doi: 10.1002/pro.4651.

  2. Korobeinikova A, Laalami S, Berthy C, Putzer H. (2023) “RNase Y Autoregulates Its Synthesis in Bacillus subtilis.” Microorganisms. 11(6):1374. doi: 10.3390/microorganisms11061374.

  3. Wiegard JC, Damm K, Lechner M, Thölken C, Ngo S, Putzer H, Hartmann RK (2023) Processing and decay of 6S-1 and 6S-2 RNAs in Bacillus subtilis. RNA. doi: 10.1261/rna.079666.123.

  4. Bronchain O, Ducos B, Putzer H, Delagrange M, Laalami S, Philippe-Caraty L, Saroul K, Ciapa B (2023) Presenilin natural antisense transcription in the sea urchin: a general control of gene expression during development? J Cell Sci. doi: 10.1242/jcs.261284

  5. Lejars, M., Caillet, J., Solchaga-Flores, E., Guillier, M., Plumbridge, J. & Hajnsdorf, E.. (2022) "Regulatory interplay between RNase III and asRNAs in E. coli; the case of AsflhD and FlhD, component of master regulator of motility" mBio, 13 doi.org/10.1128/mbio.00981-22.

  6. Laalami S, Cavaiuolo M., Roque S., Chagneau C. and H. Putzer (2021). Escherichia coli RNase E can efficiently replace RNase Y in Bacillus subtilis. Nucl Acids Res., 49, 4643-4654. doi: 10.1093/nar/gkab216 https://doi.org/10.1093/nar/gkab216

  7. Cavaiuolo M, Chagneau C., Laalami S. and H. Putzer (2020). Impact of RNase E and RNase J on global mRNA metabolism in the Cyanobacterium Synechocystis PCC6803. Front. Microbiol., 11:1055 doi: 10.3389/fmicb.2020.01055 https://doi.org/10.3389/fmicb.2020.01055

  8. Hamouche L, Billaudeau C, Rocca A, Chastanet A, Ngo S, Laalami S, Putzer H. (2020). Dynamic membrane localization of RNase Y in Bacillus subtilis. mBio, 11(1). pii: e03337-19. doi: 10.1128/mBio.03337-19. https://mbio.asm.org/content/11/1/e03337-19

  9. Hardouin P., Velours C., Bou-Nader C., Assrir N., Laalami S., Putzer H., Durand D., B. Golinelli-Pimpaneau (2018). Dissociation of the dimer of the intrinsically disordered domain of RNase Y upon antibody binding. Biophysical J., 115, 2102-2113. https://www.cell.com/biophysj/fulltext/S0006-3495(18)31164-0

  10. Lamrabet O, Plumbridge J, Martin M, Lenski RE, Schneider D, Hindré T (2019). Plasticity of Promoter-Core Sequences Allows Bacteria to Compensate for the Loss of a Key Global Regulatory Gene. Mol Biol Evol. 36(6):1121-1133. https://doi.org/10.1093/molbev/msz042

  11. Fernandez M, Plumbridge J (2019). Complex synergistic amino acid-nucleotide interactions contribute to the specificity of NagC operator recognition and induction. Microbiology. 2019 Jul;165(7):792-803. https://doi.org/10.1099/mic.0.000814.

  12. Plumbridge J. Deutscher J (2019). Regulation of Carbon Assimilation in Bacteria in Encyclopedia of Microbiology 4th Edition. Edited by Schmidt TM. Published by Elsevier. doi.org/10.1016/B978-0-12-801238-3.02454-5

  13. Mora L., Ngo S., Laalami S. and H. Putzer (2018). In vitro study of the major Bacillus subtilis ribonucleases Y and J. Methods in Enzymology, 612, 343-359. https://doi.org/10.1016/bs.mie.2018.08.004

  14. Liponska A., Jamalli A., Kuras R., Suay L., Garbe E., Wollman F.A., Laalami S. and H. Putzer (2018). Tracking the elusive 5’ exonuclease activity of Chlamydomonas reinhartdii RNase J. Plant Mol Biol, 96, 641-653. doi: 10.1007/s11103-018-0720-2

  15. Hamouche L., Laalami S., Daerr A., Song S., Holland I.B., Séror S.J., Hamze K. and H. Putzer (2017). Bacillus subtilis swarmer cells lead, multiply and generate a trail of ‘quiescent’ descendants. MBio 8, e02102-16. doi: 10.1128/mBio.02102-16

  16. Álvarez-Añorve L.I., Gaugué, I., Link H., Marcos-Viquez J., Diaz-Jimenez D.M., Zonzein S., Bustos-Jaimes I., Schmitz-Afonso I., Calcagno M. and Plumbridge J (2016). Allosteric activation of Escherichia coli glucosamine-6-phosphate deaminase (NagB) in vivo justified by intracellular amino sugar metabolite concentrations J. Bacteriol 198: 1610-1620 doi: 10.1128/JB.00870-15

  17. Hamouche L., Laalami S., Lakkis G., Kobaissi A., Chokr A., Putzer H. and K. Hamze (2015). The Effect of Chemotaxis on the Swarming Ability of Bacillus subtilis: Critical Effect of Glutamic Acid and Lysine. Int J Sci Tec Res 4: 14-21

  18. Bréchemier-Baey D, Domínguez-Ramírez L, Oberto J, Plumbridge J. (2015) Operator recognition by the ROK transcription factor family members, NagC and Mlc. Nucleic Acids Res. 43: 361-372

  19. Plumbridge J. (2015) Regulation of the use of amino sugars by E. coli and B. subtilis: same genes different control. J. Mol. Microbiol. Biotechnol. 50th PTS Anniversary Symposium volume 25: 154-167.

  20. Bréchemier-Baey D, Pennetier C, Plumbridge J. (2015) Dual Inducer recognition by an Mlc homologue. Microbiology 161: 1694-1706

  21. Laalami S., Zig L. and H. Putzer (2014). Initiation of mRNA decay in bacteria. Cell Mol Life Sci, doi: 10.1007/s00018-013-1472-4.

  22. Jamalli A., Hébert A., Zig L. and H. Putzer (2014). Control of expression of the ribonucleases J1 and J2 in B. subtilis. J. Bacteriol., 196, 318-324. doi: 10.1128/JB.01053-13

  23. Gaugué I, Oberto J, Plumbridge J. (2014) Regulation of amino sugar utilisation in Bacillus subtilis by the GntR family regulators, NagR and GamR. Mol. Microbiol. 92(1): 100-115

  24. Plumbridge J., Bossi L. Oberto J. Wade JT. Figueroa-Bossi N. (2014) Interplay of transcriptional and small RNA-dependent control mechanisms regulates chitosugar uptake in Escherichia coli andSalmonella. Mol. Microbiol. 92(4): 648-658

  25. Schroeter R., Hoffmann T., Voigt B., Meyer H., Bleisteiner M., Muntel J., Jürgen B., Albrecht D., Becher D., Lalk M., Evers S., Bongaerts J.,lMaurer K., Putzer H., Hecker M., Schweder T. and E. Bremer (2013). Stress responses of the industrial workhorse Bacillus licheniformis to osmotic challenges. PloS ONE 8(11) : e80956. doi: 10.1371/journal.pone.0080956

  26. Gaugué I., Oberto J., Putzer H. and J. Plumbridge (2013). The Use of Amino Sugars by Bacillus subtilis: Presence of a Unique Operon for the Catabolism of Glucosamine. PLoS ONE 8(5) : e63025. doi: 10.1371/journal.pone.0063025

  27. Laalami S., Bessières P., Rocca A., Zig L., Nicolas P. and H. Putzer (2013). Bacillus subtilis RNase Y activity in vivo analysed by tiling microarrays. PLoS ONE 8(1) : e54062. doi: 10.1371/journal.pone.0054062

  28. Cournac A, Plumbridge J. (2013) DNA looping in prokaryotes:experimental and theoretical approaches. J. Bacteriol. 195: 1109-1119

  29. Bréchemier-Baey D, Domínguez-Ramírez L, Plumbridge J. (2012) The linker sequence, joining the DNA binding domain of the homologous transcription factors Mlc and NagC, to the rest of the protein determines the specificity of their target recognition in Escherichia coli. Mol. Microbiol. 85(5):1007-1.

  30. Taverniti V., Forti F., Ghisotti D. and H. Putzer (2011). Mycobacterium smegmatis RNase J is a 5’-3’ exo-/endoribonuclease and both RNase J and RNase E are involved in ribosomal RNA maturation. Mol. Microbiol., 82, 1260-1276. doi: 10.1111/j.1365-2958.2011.07888.x

  31. Laalami S. and H. Putzer (2011). mRNA degradation and maturation in prokaryotes : the global players. Biomolecular Concepts,2, 491-506. doi: 10.1515/BMC.2011.042

  32. Álvarez-Añorve LI, Alonzo DA, Mora-Lugo R, Lara-González S, Bustos-Jaimes I, Plumbridge J, Calcagno ML. (2011) Allosteric kinetics of the isoform 1 of human glucosamine-6-phosphate deaminase. Biochim Biophys Acta. 1814(12):1846-53.

  33. Bruscella P., Shahbabian K., Laalami S. and H. Putzer (2011). RNase Y is responsible for uncoupling the expression of translation factor IF3 from that of the ribosomal proteins L35 and L20 in Bacillus subtilis Mol. Microbiol., 81, 1526-154. doi: 10.1111/j.1365-2958.2011.07793.x

  34. Dorléans A., Li de la Sierra Gallay I., Piton J., Zig L., Winieski L., Putzer H. and C. Condon (2011). Molecular basis for the recognition and cleavage of RNA by the bifunctional 5'-3' exo/endoribonuclease RNase J. Structure, 19, 1252-1261. doi: 10.1016/j.str.2011.06.018

  35. Hamze K., Autret S., Hinc K., Julkowska D., Laalami S., Briandet R., Renault M., Absalon C., Holland I.B., Putzer H. & S.J. Séror (2011). Single cell in situ analysis in a B. subtilis swarming community identifies three subpopulations differentially expressing hag (flagellin), including specialized swarmers. Microbiology, 157, 2456-2469. doi: 10.1099/mic.0.047159-0

  36. Brill J., Hoffmann T., Putzer H. and E. Bremer (2011). T-box-mediated control of the anabolic proline biosynthetic genes of Bacillus subtilis. Microbiology, 157, 977-987. doi: 10.1099/mic.0.047357-0

  37. Mathy N, Hébert A., Mervelet P., Bénard L., Dorléans A., Li de la Sierra-Gallay I., Noirot P., Putzer H. and C. Condon (2010). Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol. Microbiol., 75, 489-498. doi: 10.1111/j.1365-2958.2009.07004.x

  38. McVicker G, Sun L, Sohanpal BK, Gashi K, Williamson RA, Plumbridge J, (2011) Blomfield IC. SlyA protein activates fimB gene expression and type 1 fimbriation in Escherichia coli K-12. J Biol Chem. 286(37):32026-35.

  39. Pennetier C, Oberto J, Plumbridge J. (2010) An Antisense Transcript from within the ptsG Promoter Region in Escherichia coli. J Mol Microbiol Biotechnol. 18(4):230-240.

  40. Shahbabian K., Jamalli A., Zig L. and H. Putzer (2009). RNase Y, a novel endoribonuclease, initiates riboswitch turnover in B. subtilis. EMBO J., 28, 3523-3533. doi: 10.1038/emboj.2009.283

  41. Álvarez-Añorve LI, Bustos-Jaimes I, Calcagno ML, Plumbridge J. (2009) Allosteric regulation of glucosamine-6-phosphate deaminase (NagB) and growth of Escherichia coli on glucosamine. J Bacteriol. 191(20):6401-7.

  42. El Qaidi S, Allemand F, Oberto J, Plumbridge J. (2009) Repression of galP, the galactose transporter in Escherichia coli, requires the specific regulator of N-acetylglucosamine metabolism. Mol Microbiol. 71(1):146-57.

  43. Plumbridge J. (2009) An alternative route for recycling of N-acetylglucosamine from peptidoglycan involves the N-acetylglucosamine phosphotransferase system in Escherichia coli. J Bacteriol. 191(18):5641-7.

  44. El Qaidi S, Plumbridge J. (2008) Switching control of expression of ptsG from the Mlc regulon to the NagC regulon. J Bacteriol. 190(13):4677-86. May Erratum in: J Bacteriol. 190(16):5733.

  45. Mäder U., Zig L., Kretschmer J., Homuth G. and H. Putzer (2008). mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene expression on a global scale. Mol. Microbiol., 70, 183-196. doi: 10.1111/j.1365-2958.2008.06400.x

  46. Li de la Sierra-Gallay I., Zig L., Jamalli A. and H. Putzer (2008). Structural insights into the dual activity of RNase J. Nat. Struct. Mol. Biol., 15, 206-212.

  47. Pennetier C, Domínguez-Ramírez L, Plumbridge J. (2008) Different regions of Mlc and NagC, homologous transcriptional repressors controlling expression of the glucose and N-acetylglucosamine phosphotransferase systems in Escherichia coli, are required for inducer signal recognition. Mol Microbiol. Jan;67(2):364-77.

  48. Choonee N., Even S., Zig L. and H. Putzer (2007). Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism. Nucleic Acids Res., 35, 1578-1588.

  49. Sohanpal BK, Friar S, Roobol J, Plumbridge JA, Blomfield IC. (2007) Multiple co-regulatory elements and IHF are necessary for the control of fimB expression in response to sialic acid and N-acetylglucosamine in Escherichia coli K-12. Mol Microbiol. 2007 Feb;63(4):1223-36.

  50. Álvarez-Añorve LI, Calcagno ML, Plumbridge J. Why does Escherichia coli grow more slowly on glucosamine than on N-acetylglucosamine? Effects of enzyme levels and allosteric activation of GlcN6P deaminase (NagB) on growth rates. J Bacteriol. 187(9):2974-82.

  51. Even S., Pellegrini O., Zig L., Labas V., Vinh J., Brechemier-Baey D. and H. Putzer (2005). Ribonucleases J1 and J2 : two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Res., 33, 2141-2152.

  52. Condemine G, Berrier C, Plumbridge J, Ghazi A. (2005) Function and expression of an N-acetylneuraminic acid-inducible outer membrane channel in Escherichia coli. J Bacteriol. 187(6):1959-65.

  53. Sohanpal BK, El-Labany S, Lahooti M, Plumbridge JA, Blomfield IC. (2004) Integrated regulatory responses of fimB to N-acetylneuraminic (sialic) acid and GlcNAc in Escherichia coli K-12. Proc Natl Acad Sci U S A.101(46):16322-7.

  54. Plumbridge J, Pellegrini O. (2004) Expression of the chitobiose operon of Escherichia coli is regulated by three transcription factors: NagC, ChbR and CAP. Mol Microbiol. 52(2):437-49.

  55. Even S., Brito R., Condon C. and H. Putzer (2003). Aminoacyl-tRNA synthetase gene regulation in bacteria. Rec. Res. Dev. Biol., Vol. 1, p. 201-218.

  56. Pellegrini O., Nezzar J., Marchfelder A., Putzer H. and C. Condon (2003). Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis. EMBO J., 22, 4534-4543.

  57. Soupene E, van Heeswijk WC, Plumbridge J, Stewart V, Bertenthal D, Lee H, Prasad G, Paliy O, Charernnoppakul P, Kustu S. Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J Bacteriol. 185(18):5611-26.

  58. Seitz S, Lee SJ, Pennetier C, Boos W, Plumbridge J. (2003) Analysis of the interaction between the global regulator Mlc and EIIBGlc of the glucose-specific phosphotransferase system in Escherichia coli. J Biol Chem. 278(12):10744-51.

  59. Kalivoda KA, Steenbergen SM, Vimr ER, Plumbridge J. (2003) Regulation of sialic acid catabolism by the DNA binding protein NanR in Escherichia coli. J Bacteriol.185(16):4806-15.

  60. Condon C. and H. Putzer (2002). The phylogenetic distribution of bacterial ribonucleases. Nucleic Acids Res., 30, 5339-5346.

  61. Putzer H., Condon C., Brechemier-Baey D., Brito R. and M. Grunberg-Manago (2002). Transfer RNA mediated antitermination in vitro. Nucleic Acids Res., 30, 3026-3033.

  62. Condon C., Rourera J. Brechemier-Baey D. and H. Putzer (2002). Ribonuclease M5 has few, if any, mRNA substrates in Bacillus subtilis. J. Bacteriol., 184, 2845-2849.

  63. Plumbridge J. Regulation of gene expression in the PTS in Escherichia coli: the role and interactions of Mlc. Curr Opin Microbiol. 5(2):187-93. Review.

  64. Putzer H. and S. Laalami (2002). Regulation of the expression of aminoacyl-tRNA synthetases and translational factors, p. 388-415. In: J. Lapointe and L. Brakier-Gingras (eds.), Translational Mechanisms. Landes Bioscience, Georgetown, Tx.

  65. Condon C., Brechemier-Baey D., Beltchev B., Grunberg-Manago M. and H. Putzer (2001). Identification of the gene encoding the 5S ribosomal RNA maturase in Bacillus subtilis: mature 5S rRNA is dispensable for ribosome function. RNA, 7, 1-12.

  66. Montero-Morán GM, Lara-González S, Álvarez-Añorve LI, Plumbridge JA, Calcagno ML. (2001) On the multiple functional roles of the active site histidine in catalysis and allosteric regulation of Escherichia coli glucosamine 6-phosphate deaminase. Biochemistry. 40(34):10187-96.

  67. Plumbridge J. (2001) Regulation of PTS gene expression by the homologous transcriptional regulators, Mlc and NagC, in Escherichia coli (or how two similar repressors can behave differently). J Mol Microbiol Biotechnol. 3(3):371-80.

  68. Plumbridge J. (2001) DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli. Nucleic Acids Res. 29(2):506-14.

  69. Lee SJ, Boos W, Bouché JP, Plumbridge J. (2000) Signal transduction between a membrane-bound transporter, PtsG, and a soluble transcription factor, Mlc, of Escherichia coli. EMBO J.19(20):5353-61.

  70. Plumbridge J. (2000) A mutation which affects both the specificity of PtsG sugar transport and the regulation of ptsG expression by Mlc in Escherichia coli. Microbiology. 146 ( Pt 10):2655-63.