Skip to main content

From conformational chaos to robust regulation: the structure and function of the multi-enzyme RNA degradosome

  • Maria W. Górna (a1), Agamemnon J. Carpousis (a2) and Ben F. Luisi (a1)

The RNA degradosome is a massive multi-enzyme assembly that occupies a nexus in RNA metabolism and post-transcriptional control of gene expression in Escherichia coli and many other bacteria. Powering RNA turnover and quality control, the degradosome serves also as a machine for processing structured RNA precursors during their maturation. The capacity to switch between destructive and processing modes involves cooperation between degradosome components and is analogous to the process of RNA surveillance in other domains of life. Recruitment of components and cellular compartmentalisation of the degradosome are mediated through small recognition domains that punctuate a natively unstructured segment within a scaffolding core. Dynamic in conformation, variable in composition and non-essential under certain laboratory conditions, the degradosome has nonetheless been maintained throughout the evolution of many bacterial species, due most likely to its diverse contributions in global cellular regulation. We describe the role of the degradosome and its components in RNA decay pathways in E. coli, and we broadly compare these pathways in other bacteria as well as archaea and eukaryotes. We discuss the modular architecture and molecular evolution of the degradosome, its roles in RNA degradation, processing and quality control surveillance, and how its activity is regulated by non-coding RNA. Parallels are drawn with analogous machinery in organisms from all life domains. Finally, we conjecture on roles of the degradosome as a regulatory hub for complex cellular processes.

Corresponding author
*Author for correspondence: Ben F. Luisi, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK. Email:
Hide All
Afonyushkin, T., Vecerek, B., Moll, I., Bläsi, U. & Kaberdin, V. R. (2005). Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB. Nucleic Acids Research 33, 16781689.
Ait-Bara, S. & Carpousis, A. J. (2010). Characterization of the RNA degradosome of Pseudoalteromonas haloplanktis: conservation of the RNase E–RhlB interaction in the gammaproteobacteria. Journal of Bacteriology 192, 54135423.
Anantharaman, V., Koonin, E. V. & Aravind, L. (2002). Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Research 30, 14271464.
Andrade, J. M. & Arraiano, C. M. (2008). PNPase is a key player in the regulation of small RNAs that control the expression of outer membrane proteins. RNA 14, 543551.
Andrade, J. M., Pobre, V., Silva, I. J., Domingues, S. & Arraiano, C. M. (2009). The role of 3′–5′ exoribonucleases in RNA degradation. Progress in Molecular Biology and Translational Science 85, 187229.
Argaman, L., Hershberg, R., Vogel, J., Bejerano, G., Wagner, E. G., Margalit, H. & Altuvia, S. (2001). Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Current Biology 11, 941950.
Arnold, T. E., Yu, J. & Belasco, J. G. (1998). mRNA stabilization by the ompA 5′ untranslated region: two protective elements hinder distinct pathways for mRNA degradation. RNA 4, 319330.
Babitzke, P. & Romeo, T. (2007). CsrB sRNA family: sequestration of RNA-binding regulatory proteins. Current Opinion in Microbiology 10, 156163.
Barak, I., Muchova, K., Wilkinson, A. J., O'Toole, P. J. & Pavlendova, N. (2008). Lipid spirals in Bacillus subtilis and their role in cell division. Molecular Microbiology 68, 13151327.
Basturea, G. N., Zundel, M. A. & Deutscher, M. P. (2011). Degradation of ribosomal RNA during starvation: comparison to quality control during steady-state growth and a role for RNase PH. RNA 17, 338345.
Beich-Frandsen, M., Vecerek, B., Konarev, P. V., Sjoblom, B., Kloiber, K., Hammerle, H., Rajkowitsch, L., Miles, A. J., Kontaxis, G., Wallace, B. A., Svergun, D. I., Konrat, R., Blasi, U. & Djinovic-Carugo, K. (2011). Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq. Nucleic Acids Research 39, 49004915.
Beisel, C. L. & Storz, G. (2011). The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Molecular Cell 41, 286297.
Bernstein, J. A., Lin, P. H., Cohen, S. N. & Lin-Chao, S. (2004). Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proceedings of the National Academy of Sciences of the United States of America 101, 27582763.
Blum, E., Py, B., Carpousis, A. J. & Higgins, C. F. (1997). Polyphosphate kinase is a component of the Escherichia coli RNA degradosome. Molecular Microbiology 26, 387398.
Bohn, C., Rigoulay, C., Chabelskaya, S., Sharma, C. M., Marchais, A., Skorski, P., Borezee-Durant, E., Barbet, R., Jacquet, E., Jacq, A., Gautheret, D., Felden, B., Vogel, J. & Bouloc, P. (2010). Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Research 38, 66206636.
Bonneau, F., Basquin, J., Ebert, J., Lorentzen, E. & Conti, E. (2009). The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Cell 139, 547559.
Bouvier, M. & Carpousis, A. J. (2011). A tale of two mRNA degradation pathways mediated by RNase E. Molecular Microbiology. doi:10.1111/j.1365-2958.2011.07894.x.
Bouvier, M., Sharma, C. M., Mika, F., Nierhaus, K. H. & Vogel, J. (2008). Small RNA binding to 5′ mRNA coding region inhibits translational initiation. Molecular Cell 32, 827837.
Brandt, F., Etchells, S. A., Ortiz, J. O., Elcock, A. H., Hartl, F. U. & Baumeister, W. (2009). The native 3D organization of bacterial polysomes. Cell 136, 261271.
Brennan, R. G. & Link, T. M. (2007). Hfq structure, function and ligand binding. Current Opinion in Microbiology 10, 125133.
Briant, D. J., Hankins, J. S., Cook, M. A. & Mackie, G. A. (2003). The quaternary structure of RNase G from Escherichia coli. Molecular Microbiology 50, 13811390.
Britton, R. A., Wen, T., Schaefer, L., Pellegrini, O., Uicker, W. C., Mathy, N., Tobin, C., Daou, R., Szyk, J. & Condon, C. (2007). Maturation of the 5′ end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Molecular Microbiology 63, 127138.
Brown, J. W. & Reeve, J. N. (1985). Polyadenylated, noncapped RNA from the archaebacterium Methanococcus vannielii. Journal of Bacteriology 162, 909917.
Butland, G., Peregrin-Alvarez, J. M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., Greenblatt, J. & Emili, A. (2005). Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531537.
Callaghan, A. J., Aurikko, J. P., Ilag, L. L., Grossmann, J. G., Chandran, V., Kühnel, K., Poljak, L., Carpousis, A. J., Robinson, C. V., Symmons, M. F. & Luisi, B. F. (2004). Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. Journal of Molecular Biology 340, 965979.
Callaghan, A. J., Grossmann, J. G., Redko, Y. U., Ilag, L. L., Moncrieffe, M. C., Symmons, M. F., Robinson, C. V., Mcdowall, K. J. & Luisi, B. F. (2003). Quaternary structure and catalytic activity of the Escherichia coli ribonuclease E amino-terminal catalytic domain. Biochemistry 42, 1384813855.
Callaghan, A. J., Marcaida, M. J., Stead, J. A., Mcdowall, K. J., Scott, W. G. & Luisi, B. F. (2005a). Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover. Nature 437, 11871191.
Callaghan, A. J., Redko, Y., Murphy, L. M., Grossmann, J. G., Yates, D., Garman, E., Ilag, L. L., Robinson, C. V., Symmons, M. F., Mcdowall, K. J. & Luisi, B. F. (2005b). “Zn-link”: a metal-sharing interface that organizes the quaternary structure and catalytic site of the endoribonuclease, RNase E. Biochemistry 46674675.
Callebaut, I., Moshous, D., Mornon, J. P. & De Villartay, J. P. (2002). Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family. Nucleic Acids Research 30, 35923601.
Carabetta, V. J., Silhavy, T. J. & Cristea, I. M. (2010). The response regulator SprE (RssB) is required for maintaining poly(A) polymerase I-degradosome association during stationary phase. Journal of Bacteriology 192, 37133721.
Carpousis, A. J. (2007). The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annual Review of Microbiology 61, 7187.
Carpousis, A. J., Luisi, B. F. & Mcdowall, K. J. (2009). Endonucleolytic initiation of mRNA decay in Escherichia coli. Progress in Molecular Biology and Translational Science 85, 91135.
Carpousis, A. J., Van Houwe, G., Ehretsmann, C. & Krisch, H. M. (1994). Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell 76, 889900.
Caruthers, J. M., Feng, Y. N., Mckay, D. B. & Cohen, S. N. (2006). Retention of core catalytic functions by a conserved minimal ribonuclease E peptide that lacks the domain required for tetramer formation. Journal of Biological Chemistry 281, 2704627051.
Celesnik, H., Deana, A. & Belasco, J. G. (2007). Initiation of RNA decay in Escherichia coli by 5′ pyrophosphate removal. Molecular Cell 27, 7990.
Chandran, V. & Luisi, B. F. (2006). Recognition of enolase in the Escherichia coli RNA degradosome. Journal of Molecular Biology 358, 815.
Chandran, V., Poljak, L., Vanzo, N. F., Leroy, A., Miguel, R. N., Fernandez-Recio, J., Parkinson, J., Burns, C., Carpousis, A. J. & Luisi, B. F. (2007). Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E. Journal of Molecular Biology 367, 113132.
Chao, Y. J. & Vogel, J. (2010). The role of Hfq in bacterial pathogens. Current Opinion in Microbiology 13, 2433.
Charollais, J., Dreyfus, M. & Iost, I. (2004). CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic Acids Research 32, 27512759.
Cheng, Z. F. & Deutscher, M. P. (2003). Quality control of ribosomal RNA mediated by polynucleotide phosphorylase and RNase R. Proceedings of the National Academy of Sciences of the United States of America 100, 63886393.
Clouet-D'orval, B., Rinaldi, D., Quentin, Y. & Carpousis, A. J. (2010). Euryarchaeal β-CASP Proteins with homology to bacterial RNase J have 5′ to 3′ exoribonuclease activity. Journal of Biological Chemistry 285, 1757417583.
Coburn, G. A., Miao, X., Briant, D. J. & Mackie, G. A. (1999). Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3′ exonuclease and a DEAD-box RNA helicase. Genes and Development 13, 25942603.
Cole, S. E., Lariviere, F. J., Merrikh, C. N. & Moore, M. J. (2009). A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay. Molecular Cell 34, 440450.
Collins, J. A., Irnov, I., Baker, S. & Winkler, W. C. (2007). Mechanism of mRNA destabilization by the glmS ribozyme. Genes and Development 21, 33563368.
Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. (2009). Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Molecular and Cellular Proteomics 8, 13501360.
Condon, C. (2003). RNA processing and degradation in Bacillus subtilis. Microbiology and Molecular Biology Reviews 67, 157174.
Condon, C., Putzer, H., Luo, D. & Grunberg-Manago, M. (1997). Processing of the Bacillus subtilis thrS leader mRNA is RNase E-dependent in Escherichia coli. Journal of Molecular Biology 268, 235242.
Cordin, O., Banroques, J., Tanner, N. K. & Linder, P. (2006). The DEAD-box protein family of RNA helicases. Gene 367, 1737.
Danchin, A. (1997). Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP. DNA Research 4, 918.
Daou-Chabo, R., Mathy, N., Benard, L. & Condon, C. (2009). Ribosomes initiating translation of the hbs mRNA protect it from 5′-to-3′ exoribonucleolytic degradation by RNase J1. Molecular Microbiology 71, 15381550.
Daran-Lapujade, P., Rossell, S., Van Gulik, W. M., Luttik, M. A., De Groot, M. J., Slijper, M., Heck, A. J., Daran, J. M., De Winde, J. H., Westerhoff, H. V., Pronk, J. T. & Bakker, B. M. (2007). The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proceedings of the National Academy of Sciences of the United States of America 104, 1575315758.
De La Sierra-Gallay, I. L., Zig, L., Jamalli, A. & Putzer, H. (2008). Structural insights into the dual activity of RNase J. Nature Structural & Molecular Biology 15, 206212.
Deana, A., Celesnik, H. & Belasco, J. G. (2008). The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451, 355358.
Del Favero, M., Mazzantini, E., Briani, F., Zangrossi, S., Tortora, P. & Deho, G. (2008). Regulation of Escherichia coli polynucleotide phosphorylase by ATP. Journal of Biological Chemistry 283, 2735527359.
Depristo, M. A., Weinreich, D. M. & Hartl, D. L. (2005). Missense meanderings in sequence space: a biophysical view of protein evolution. Nature Reviews Genetics 6, 678687.
Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J. F., Guindon, S., Lefort, V., Lescot, M., Claverie, J. M. & Gascuel, O. (2008). robust phylogenetic analysis for the non-specialist. Nucleic Acids Research 36, W465W469.
Deutscher, M. P. (2006). Degradation of RNA in bacteria: comparison of mRNA and stable RNA. Nucleic Acids Research 34, 659666.
Deutscher, M. P. (2009). Maturation and degradation of ribosomal RNA in bacteria. Progress in Molecular Biology and Translational Science 85, 369391.
Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N. P., Trave, G. & Gibson, T. J. (2008). Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Frontiers in Bioscience 13, 65806603.
Dominguez-Escobar, J., Chastanet, A., Crevenna, A. H., Fromion, V., Wedlich-Soldner, R. & Carballido-Lopez, R. (2011). Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria. Science 333, 225228.
Dunker, A. K., Silman, I., Uversky, V. N. & Sussman, J. L. (2008). Function and structure of inherently disordered proteins. Current Opinion in Structural Biology 18, 756764.
Dziembowski, A., Piwowarski, J., Hoser, R., Minczuk, M., Dmochowska, A., Siep, M., Van Der Spek, H., Grivell, L. & Stepien, P. P. (2003). The yeast mitochondrial degradosome. Its composition, interplay between RNA helicase and RNase activities and the role in mitochondrial RNA metabolism. Journal of Biological Chemistry 278, 16031611.
Ehretsmann, C. P., Carpousis, A. J. & Krisch, H. M. (1992). Specificity of Escherichia coli endoribonuclease Rnase-E – in vivo and in vitro analysis of mutants in a bacteriophage-T4 messenger-RNA processing site. Genes and Development 6, 149159.
Erce, M. A., Low, J. K. K., March, P. E., Wilkins, M. R. & Takayama, K. M. (2009). Identification and functional analysis of RNase E of Vibrio angustum S14 and two-hybrid analysis of its interaction partners. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms 1794, 11071114.
Erce, M. A., Low, J. K. K. & Wilkins, M. R. (2010). Analysis of the RNA degradosome complex in Vibrio angustum S14. FEBS Journal 277, 51615173.
Even, S., Pellegrini, O., Zig, L., Labas, V., Vinh, J., Brechemmier-Baey, D. & Putzer, H. (2005). Ribonucleases J1 and J2: two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Research 33, 21412152.
Evguenieva-Hackenberg, E. & Klug, G. (2009). RNA degradation in Archaea and Gram-negative bacteria different from Escherichia coli. Progress in Molecular Biology and Translational Science 85, 275317.
Fozo, E. M., Hemm, M. R. & Storz, G. (2008). Small toxic proteins and the antisense RNAs that repress them. Microbiology and Molecular Biology Review 72, 579589.
Frank, D. N. & Pace, N. R. (1998). Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annual Review of Biochemistry 67, 153180.
French, S. L., Santangelo, T. J., Beyer, A. L. & Reeve, J. N. (2007). Transcription and translation are coupled in Archaea. Molecular Biology and Evolution 24, 893895.
Gao, J., Lee, K., Zhao, M., Qiu, J., Zhan, X., Saxena, A., Moore, C. J., Cohen, S. N. & Georgiou, G. (2006). Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Molecular Microbiology 61, 394406.
Garneau, N. L., Wilusz, J. & Wilusz, C. J. (2007). The highways and byways of mRNA decay. Nature Reviews Molecular and Cell Biology 8, 113126.
Garrey, S. M., Blech, M., Riffell, J. L., Hankins, J. S., Stickney, L. M., Diver, M., Hsu, Y. H. R., Kunanithy, V. & Mackie, G. A. (2009). Substrate binding and active site residues in RNases E and G: role of the 5′-sensor. Journal of Biological Chemistry 284, 3184331850.
Garrey, S. M. & Mackie, G. A. (2011). Roles of the 5′-phosphate sensor domain in RNase E. Molecular Microbiology 80, 16131624.
Gatewood, M. L. & Jones, G. H. (2010). (p)ppGpp inhibits polynucleotide phosphorylase from Streptomyces but not from Escherichia coli and increases the stability of bulk mRNA in Streptomyces coelicolor. Journal of Bacteriology 192, 42754280.
Gibson, T. J. (2009). Cell regulation: determined to signal discrete cooperation. Trends in Biochemical Sciences 34, 471482.
Giorgi, C., Yeo, G. W., Stone, M. E., Katz, D. B., Burge, C., Turrigiano, G. & Moore, M. J. (2007). The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. Cell 130, 179191.
Görke, B. & Vogel, J. (2008). Noncoding RNA control of the making and breaking of sugars. Genes and Development 22, 29142925.
Górna, M. W. (2010). Structural and functional studies of the Escherichia coli RNA degradosome. PhD thesis, University of Cambridge.
Górna, M. W., Pietras, Z., Tsai, Y. C., Callaghan, A. J., Hernandez, H., Robinson, C. V. & Luisi, B. F. (2010). The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome. RNA 16, 553562.
Gottesman, S. (2005). Micros for microbes: non-coding regulatory RNAs in bacteria. Trends Genet 21, 399404.
Gottesman, S. & Storz, G. (2010). Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harbor Perspectives in Biology doi:10.1101/cshperspect.a003798.
Grunberg-Manago, M. (1999). Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annual Review of Genetics 33, 193227.
Gualerzi, C. O., Giuliodori, A. M. & Pon, C. L. (2003). Transcriptional and post-transcriptional control of cold-shock genes. Journal of Molecular Biology 331, 527539.
Gunasekaran, K., Tsai, C. J., Kumar, S., Zanuy, D. & Nussinov, R. (2003). Extended disordered proteins: targeting function with less scaffold. Trends in Biochemical Sciences 28, 8185.
Hardiman, T., Lemuth, K., Keller, M. A., Reuss, M. & Siemann-Herzberg, M. (2007). Topology of the global regulatory network of carbon limitation in Escherichia coli. Journal of Biotechnology 132, 359374.
Hardwick, S. W., Chan, V. S. Y., Broadhurst, R. W. & Luisi, B. F. (2010). An RNA degradosome assembly in Caulobacter crescentus. Nucleic Acids Research 39, 14491459.
Hasenohrl, D., Lombo, T., Kaberdin, V., Londei, P. & Blasi, U. (2008). Translation initiation factor a/eIF2(-gamma) counteracts 5′ to 3′ mRNA decay in the archaeon Sulfolobus solfataricus. Proceedings of the National Academy of Sciences of the United States of America 105, 21462150.
Henkin, T. M. (2008). Riboswitch RNAs: using RNA to sense cellular metabolism. Genes and Development 22, 33833390.
Houseley, J. & Tollervey, D. (2009). The many pathways of RNA degradation. Cell 136, 763776.
Hu, W., Sweet, T. J., Chamnongpol, S., Baker, K. E. & Coller, J. (2009). Co-translational mRNA decay in Saccharomyces cerevisiae. Nature 461, 225229.
Hunt, A., Rawlins, J. P., Thomaides, H. B. & Errington, J. (2006). Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152, 28952907.
Hunter, C. A. & Anderson, H. L. (2009). What is Cooperativity? Angewandte Chemie-International Edition 48, 74887499.
Ikeda, Y., Yagi, M., Morita, T. & Aiba, H. (2011). Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli. Molecular Microbiology 79, 419432.
Iost, I. & Dreyfus, M. (2006). DEAD-box RNA helicases in Escherichia coli. Nucleic Acids Research 34, 41894197.
Jäger, S., Fuhrmann, O., Heck, C., Hebermehl, M., Schiltz, E., Rauhut, R. & Klug, G. (2001). An mRNA degrading complex in Rhodobacter capsulatus. Nucleic Acids Research 29, 45814588.
Jain, C. (2008). The E. coli RhlE RNA helicase regulates the function of related RNA helicases during ribosome assembly. RNA 14, 381389.
Janga, S. C. & Babu, M. M. (2009). Transcript stability in the protein interaction network of Escherichia coli. Molecular BioSystems 5, 154162.
Jankowsky, E. (2011). RNA helicases at work: binding and rearranging. Trends in Biochemical Sciences 36, 1929.
Jiang, X. & Belasco, J. G. (2004). Catalytic activation of multimeric RNase E and RNase G by 5′-monophosphorylated RNA. Proceedings of the National Academy of Sciences of the United States of America 101, 92119216.
Jourdan, S. S. & Mcdowall, K. J. (2008). Sensing of 5′ monophosphate by Escherichia coli RNase G can significantly enhance association with RNA and stimulate the decay of functional mRNA transcripts in vivo. Molecular Microbiology 67, 102115.
Kaberdin, V. R. & Lin-Chao, S. (2009). Unraveling new roles for minor components of the E. coli RNA degradosome. RNA Biology 6, 402405.
Kaberdin, V. R., Walsh, A. P., Jakobsen, T., Mcdowall, K. J. & Von Gabain, A. (2000). Enhanced cleavage of RNA mediated by an interaction between substrates and the arginine-rich domain of E. coli ribonuclease E. Journal of Molecular Biology 301, 257264.
Kanai, A., Oida, H., Matsuura, N. & Doi, H. (2003). Expression cloning and characterization of a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococcus furiosus. Biochemical Journal 372, 253261.
Kang, S. O., Caparon, M. G. & Cho, K. H. (2010). Virulence gene regulation by CvfA, a putative RNase: the CvfA–enolase complex in Streptococcus pyogenes links nutritional stress, growth-phase control, and virulence gene expression. Infection and Immunity 78, 27542767.
Kato, J. I. & Hashimoto, M. (2007). Construction of consecutive deletions of the Escherichia coli chromosome. Molecular Systems Biology 3, 132.
Khemici, V. & Carpousis, A. J. (2004). The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers. Molecular Microbiology 51, 777790.
Khemici, V., Poljak, L., Luisi, B. F. & Carpousis, A. J. (2008). The RNase E of Escherichia coli is a membrane-binding protein. Molecular Microbiology 70, 799813.
Khemici, V., Poljak, L., Toesca, I. & Carpousis, A. J. (2005). Evidence in vivo that the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E. Proceedings of the National Academy of Sciences of the United States of America 102, 69136918.
Khemici, V., Toesca, I., Poljak, L., Vanzo, N. F. & Carpousis, A. J. (2004). The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: functional replacement of RhlB by RhlE. Molecular Microbiology 54, 14221430.
Kido, M., Yamanaka, K., Mitani, T., Niki, H., Ogura, T. & Hiraga, S. (1996). RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli. Journal of Bacteriology 178, 39173925.
Kim, K. S. & Lee, Y. (2004). Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases. Nucleic Acids Research 32, 60576068.
Kime, L., Jourdan, S. S., Stead, J. A., Hidalgo-Sastre, A. & Mcdowall, K. J. (2010). Rapid cleavage of RNA by RNase E in the absence of 5′ monophosphate stimulation. Molecular Microbiology 76, 590604.
Koonin, E. V., Wolf, Y. I. & Aravind, L. (2001). Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Research 11, 240252.
Koslover, D. J., Callaghan, A. J., Marcaida, M. J., Garman, E. F., Martick, M., Scott, W. G. & Luisi, B. F. (2008). The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation. Structure 16, 12381244.
Kovacs, L., Csanadi, A., Megyeri, K., Kaberdin, V. R. & Miczak, A. (2005). Mycobacterial RNase E-associated proteins. Microbiology and Immunology 49, 10031007.
Lebreton, A., Tomecki, R., Dziembowski, A. & Seraphin, B. (2008). Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature 456, 993996.
Lee, K., Bernstein, J. A. & Cohen, S. N. (2002). RNase G complementation of rne null mutation identifies functional interrelationships with RNase E in Escherichia coli. Molecular Microbiology 43, 14451456.
Lee, K. & Cohen, S. N. (2003). A Streptomyces coelicolor functional orthologue of Escherichia coli RNase E shows shuffling of catalytic and PNPase-binding domains. Molecular Microbiology 48, 349360.
Lee, K., Zhan, X., Gao, J., Qiu, J., Feng, Y., Meganathan, R., Cohen, S. N. & Georgiou, G. (2003). RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli. Cell 114, 623634.
Lehnik-Habrink, M., Pfortner, H., Rempeters, L., Pietack, N., Herzberg, C. & Stulke, J. (2010). The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex. Molecular Microbiology 77, 958971.
Lehnik-Habrink, M., Newman, J., Rothe, F. M., Solovyova, A. S., Rodrigues, C., Herzberg, C., Commichau, F. M., Lewis, R. J. & Stulke, J. (2011). RNase Y in Bacillus subtilis: a natively disordered protein that is the functional equivalent to RNase E from Escherichia coli. Journal of Bacteriology 193, 54315441.
Leibundgut, M., Maier, T., Jenni, S. & Ban, N. (2008). The multienzyme architecture of eukaryotic fatty acid synthases. Current Opinion in Structural Biology 18, 714725.
Leroy, A., Vanzo, N. F., Sousa, S., Dreyfus, M. & Carpousis, A. J. (2002). Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA. Molecular Microbiology 45, 12311243.
Li, Z. & Deutscher, M. P. (2002). RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA 8, 97109.
Lin-Chao, S., Wei, C. L. & Lin, Y. T. (1999). RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity. Proceedings of the National Academy of Sciences of the United States of America 96, 1240612411.
Lin-Chao, S., Wong, T. T., Mcdowall, K. J. & Cohen, S. N. (1994). Effects of nucleotide sequence on the specificity of rne-dependent and RNase E-mediated cleavages of RNA I encoded by the pBR322 plasmid. Journal of Biological Chemistry 269, 1079710803.
Link, T. M., Valentin-Hansen, P. & Brennan, R. G. (2009). Structure of Escherichia coli Hfq bound to polyriboadenylate RNA. Proceedings of the National Academy of Sciences of the United States of America 106, 1928619291.
Liou, G. G., Chang, H. Y., Lin, C. S. & Lin-Chao, S. (2002). DEAD box RhlB RNA helicase physically associates with exoribonuclease PNPase to degrade double-stranded RNA independent of the degradosome-assembling region of RNase E. Journal of Biological Chemistry 277, 4115741162.
Liou, G. G., Jane, W. N., Cohen, S. N., Lin, N. S. & Lin-Chao, S. (2001). RNA degradosomes exist in vivo in Escherichia coli as multicomponent complexes associated with the cytoplasmic membrane via the N-terminal region of ribonuclease E. Proceedings of the National Academy of Sciences of the United States of America 98, 6368.
Lobley, A., Swindells, M. B., Orengo, C. A. & Jones, D. T. (2007). Inferring function using patterns of native disorder in proteins. PLoS Computational Biology 3, 15671579.
Lopez, P. J., Marchand, I., Joyce, S. A. & Dreyfus, M. (1999). The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo. Molecular Microbiology 33, 188199.
Lorentzen, E., Walter, P., Fribourg, S., Evguenieva-Hackenberg, E., Klug, G. & Conti, E. (2005). The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nature Structural and Molecular Biology 12, 575581.
Lundberg, U. & Altman, S. (1995). Processing of the precursor to the catalytic RNA subunit of RNase P from Escherichia coli. RNA 1, 327334.
Lykke-Andersen, S., Brodersen, D. E. & Jensen, T. H. (2009). Origins and activities of the eukaryotic exosome. Journal of Cell Science 122, 14871494.
Mackie, G. A. (1998). Ribonuclease E is a 5′-end-dependent endonuclease. Nature 395, 720723.
Mackie, G. A. (2000). Stabilization of circular rpsT mRNA demonstrates the 5′-end dependence of RNase E action in vivo. Journal of Biological Chemistry 275, 2506925072.
Majdalani, N., Vanderpool, C. K. & Gottesman, S. (2005). Bacterial small RNA regulators. Critical Reviews in Biochemistry and Molecular Biology 40, 93113.
Malecki, M., Jedrzejczak, R., Stepien, P. P. & Golik, P. (2007). In vitro reconstitution and characterization of the yeast mitochondrial degradosome complex unravels tight functional interdependence. Journal of Molecular Biology 372, 2336.
Marcaida, M. J., Depristo, M. A., Chandran, V., Carpousis, A. J. & Luisi, B. F. (2006). The RNA degradosome: life in the fast lane of adaptive molecular evolution. Trends in Biochemical Sciences 31, 359365.
Massé, E., Escorcia, F. E. & Gottesman, S. (2003). Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes and Development 17, 23742383.
Massé, E., Salvail, H., Desnoyers, G. & Arguin, M. (2007). Small RNAs controlling iron metabolism. Current Opinion in Microbiology 10, 140145.
Mathy, N., Benard, L., Pellegrini, O., Daou, R., Wen, T. & Condon, C. (2007). 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129, 681692.
Mcdowall, K. J. & Cohen, S. N. (1996). The N-terminal domain of the rne gene product has RNase E activity and is non-overlapping with the arginine-rich RNA-binding site. Journal of Molecular Biology 255, 349355.
Mcdowall, K. J., Kaberdin, V. R., Wu, S. W., Cohen, S. N. & Lin-Chao, S. (1995). Site-specific RNase E cleavage of oligonucleotides and inhibition by stem-loops. Nature 374, 287290.
Mcdowall, K. J., Lin-Chao, S. & Cohen, S. N. (1994). A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. Journal of Biological Chemistry 269, 1079010796.
Miczak, A., Kaberdin, V. R., Wei, C. L. & Lin-Chao, S. (1996). Proteins associated with RNase E in a multicomponent ribonucleolytic complex. Proceedings of the National Academy of Sciences of the United States of America 93, 38653869.
Miczak, A., Srivastava, R. A. & Apirion, D. (1991). Location of the RNA-processing enzymes RNase III, RNase E and RNase P in the Escherichia coli cell. Molecular Microbiology 5, 18011810.
Milner-White, E. J., Pietras, Z. & Luisi, B. F. (2010). An ancient anion-binding structural module in RNA and DNA helicases. Proteins 78, 19001908.
Mohanty, B. K. & Kushner, S. R. (2000). Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli. Molecular Microbiology 36, 982994.
Montero Llopis, P., Jackson, A. F., Sliusarenko, O., Surovtsev, I., Heinritz, J., Emonet, T. & Jacobs-Wagner, C. (2010). Spatial organization of the flow of genetic information in bacteria. Nature 466, 7781.
Morita, T., Kawamoto, H., Mizota, T., Inada, T. & Aiba, H. (2004). Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli. Molecular Microbiology 54, 10631075.
Morita, T., Maki, K. & Aiba, H. (2005). RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes and Development 19, 21762186.
Mudd, E. A., Sullivan, S., Gisby, M. F., Mironov, A., Kwon, C. S., Chung, W. I. & Day, A. (2008). A 125 kDa RNase E/G-like protein is present in plastids and is essential for chloroplast development and autotrophic growth in Arabidopsis. Journal of Experimental Botany 59, 25972610.
Nevo-Dinur, K., Nussbaum-Shochat, A., Ben-Yehuda, S. & Amster-Choder, O. (2011). Translation-independent localization of mRNA in E. coli. Science 331, 10811084.
Newbury, S. F., Smith, N. H. & Higgins, C. F. (1987a). Differential mRNA stability controls relative gene expression within a polycistronic operon. Cell 51, 11311143.
Newbury, S. F., Smith, N. H., Robinson, E. C., Hiles, I. D. & Higgins, C. F. (1987b). Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell 48, 297310.
Nurmohamed, S., Mckay, A. R., Robinson, C. V. & Luisi, B. F. (2010). Molecular recognition between Escherichia coli enolase and ribonuclease E. Acta crystallographica. Section D, Biological Crystallography 66, 10361040.
Nurmohamed, S., Vaidialingam, B., Callaghan, A. J. & Luisi, B. F. (2009). Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly. Journal of Molecular Biology 389, 1733.
Nurmohamed, S., Vincent, H. A., Titman, C. M., Chandran, V., Pears, M. R., Du, D., Griffin, J. L., Callaghan, A. J. & Luisi, B. F. (2011). Polynucleotide phosphorylase activity may be modulated by metabolites in Escherichia coli. Journal of Biological Chemistry 286, 1431514323.
Opdyke, J. A., Kang, J. G. & Storz, G. (2004). GadY, a small-RNA regulator of acid response genes in Escherichia coli. Journal of Bacteriology 186, 66986705.
Ow, M. C. & Kushner, S. R. (2002). Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Genes and Development 16, 11021115.
Ow, M. C., Liu, Q. & Kushner, S. R. (2000). Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly. Molecular Microbiology 38, 854866.
Papenfort, K., Said, N., Welsink, T., Lucchini, S., Hinton, J. C. D. & Vogel, J. (2009). Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA. Molecular Microbiology 74, 139158.
Pechmann, S., Levy, E. D., Tartaglia, G. G. & Vendruscolo, M. (2009). Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins. Proceedings of the National Academy of Sciences of the United States of America 106, 1015910164.
Peil, L., Virumae, K. & Remme, J. (2008). Ribosome assembly in Escherichia coli strains lacking the RNA helicase DeaD/CsdA or DbpA. The FEBS Journal 275, 37723782.
Pfeiffer, V., Papenfort, K., Lucchini, S., Hinton, J. C. D. & Vogel, J. (2009). Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nature Structural and Molecular Biology 16, 840843.
Pichon, C. & Felden, B. (2007). Proteins that interact with bacterial small RNA regulators. FEMS Microbiology Reviews 31, 614625.
Portnoy, V. & Schuster, G. (2006). RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R. Nucleic Acids Research 34, 59235931.
Prévost, K., Salvail, H., Desnoyers, G., Jacques, J. F., Phaneuf, E. & Massé, E. (2007). The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis. Molecular Microbiology 64, 12601273.
Prud'Homme-généreux, A., Beran, R. K., Iost, I., Ramey, C. S., Mackie, G. A. & Simons, R. W. (2004). Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a ‘cold shock degradosome’. Molecular Microbiology 54, 14091421.
Purusharth, R. I., Klein, F., Sulthana, S., Jäger, S., Jagannadham, M. V., Evguenieva-Hackenberg, E., Ray, M. K. & Klug, G. (2005). Exoribonuclease R interacts with endoribonuclease E and an RNA helicase in the psychrotrophic bacterium Pseudomonas syringae Lz4W. Journal of Biological Chemistry 280, 1457214578.
Py, B., Causton, H., Mudd, E. A. & Higgins, C. F. (1994). A protein complex mediating mRNA degradation in Escherichia coli. Molecular Microbiology 14, 717729.
Py, B., Higgins, C. F., Krisch, H. M. & Carpousis, A. J. (1996). A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381, 169172.
Pyle, A. M. (2008). Translocation and unwinding mechanisms of RNA and DNA helicases. Annual Review of Biophysics 37, 317336.
Radford, H. E., Meijer, H. A. & De Moor, C. H. (2008). Translational control by cytoplasmic polyadenylation in Xenopus oocytes. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms 1779, 217229.
Redko, Y., Li De Lasierra-Gallay, I. & Condon, C. (2007). When all's zed and done: the structure and function of RNase Z in prokaryotes. Nature Reviews Microbiology 5, 278286.
Remaut, H. & Waksman, G. (2006). Protein–protein interaction through beta-strand addition. Trends in Biochemical Sciences 31, 436444.
Rissland, O. S. & Norbury, C. J. (2009). Decapping is preceded by 3′ uridylation in a novel pathway of bulk mRNA turnover. Nature Structural and Molecular Biology 16, 616U656.
Roth, A. & Breaker, R. R. (2009). The structural and functional diversity of metabolite-binding riboswitches. Annual Review of Biochemistry 78, 305334.
Roux, C. M., Demuth, J. P. & Dunman, P. M. (2011). Characterization of components of the Staphylococcus aureus messenger RNA degradosome holoenzyme-like complex. Journal of Bacteriology 193, 55205526.
Russell, R. B. & Gibson, T. J. (2008). A careful disorderliness in the proteome: sites for interaction and targets for future therapies. FEBS Letters 582, 12711275.
Sabnis, N. A., Yang, H. H. & Romeo, T. (1995). Pleiotropic regulation of central carbohydrate-metabolism in Escherichia coli via the gene csrA. Journal of Biological Chemistry 270, 2909629104.
Sauer, E. & Weichenrieder, O. (2011). Structural basis for RNA 3′-end recognition by Hfq. Proceedings of the National Academy of Sciences of the United States of America 108, 1306513070.
Schaeffer, D., Tsanova, B., Barbas, A., Reis, F. P., Dastidar, E. G., Sanchez-Rotunno, M., Arraiano, C. M. & Van Hoof, A. (2009). The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nature Structural and Molecular Biology 16, 5662.
Schein, A., Sheffy-Levin, S., Glaser, F. & Schuster, G. (2008). The RNase E/G-type endoribonuclease of higher plants is located in the chloroplast and cleaves RNA similarly to the E. coli enzyme. RNA 14, 10571068.
Schiffer, S., Rosch, S. & Marchfelder, A. (2002). Assigning a function to a conserved group of proteins: the tRNA 3′-processing enzymes. EMBO Journal 21, 27692777.
Schubert, M., Edge, R. E., Lario, P., Cook, M. A., Strynadka, N. C., Mackie, G. A. & Mcintosh, L. P. (2004). Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces. Journal of Molecular Biology 341, 3754.
Schuck, A., Diwa, A. & Belasco, J. G. (2009). RNase E autoregulates its synthesis in Escherichia coli by binding directly to a stem-loop in the rne 5′ untranslated region. Molecular Microbiology 72, 470478.
Schumacher, M. A., Pearson, R. F., Moller, T., Valentin-Hansen, P. & Brennan, R. G. (2002). Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. EMBO Journal 21, 35463556.
Shahbabian, K., Jamalli, A., Zig, L. & Putzer, H. (2009). RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO Journal 28, 25232533.
Sharpe Elles, L. M., Sykes, M. T., Williamson, J. R. & Uhlenbeck, O. C. (2009). A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Nucleic Acids Research 37, 65036514.
Shevtsov, M. B., Chen, Y. L., Gollnick, P. & Antson, A. A. (2005). Crystal structure of Bacillus subtilis anti-TRAP protein, an antagonist of TRAP/RNA interaction. Proceedings of the National Academy of Sciences of the United States of America 102, 1760017605.
Shi, Z., Yang, W. Z., Lin-Chao, S., Chak, K. F. & Yuan, H. S. (2008). Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation. RNA 14, 23612371.
Siculella, L., Damiano, F., Di Summa, R., Tredici, S. M., Alduina, R., Gnoni, G. V. & Alifano, P. (2010). Guanosine 5′-diphosphate 3′-diphosphate (ppGpp) as a negative modulator of polynucleotide phosphorylase activity in a ‘rare’ actinomycete. Molecular Microbiology 77, 716729.
Singh, D., Chang, S. J., Lin, P. H., Averina, O. V., Kaberdin, V. R. & Lin-Chao, S. (2009). Regulation of ribonuclease E activity by the L4 ribosomal protein of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 106, 864869.
Sittka, A., Lucchini, S., Papenfort, K., Sharma, C. M., Rolle, K., Binnewies, T. T., Hinton, J. C. D. & Vogel, J. (2008). Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. Plos Genetics 4, e1000163.
Stead, M. B., Marshburn, S., Mohanty, B. K., Mitra, J., Castillo, L. P., Ray, D., Van Bakel, H., Hughes, T. R. & Kushner, S. R. (2010). Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Research 39, 31883203.
Suzuki, K., Babitzke, P., Kushner, S. R. & Romeo, T. (2006). Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes and Development 20, 26052617.
Symmons, M. F., Jones, G. H. & Luisi, B. F. (2000). A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. Structure 8, 12151226.
Symmons, M. F., Williams, M. G., Luisi, B. F., Jones, G. H. & Carpousis, A. J. (2002). Running rings around RNA: a superfamily of phosphate-dependent RNases. Trends in Biochemical Sciences 27, 1118.
Szczesny, R. J., Borowski, L. S., Brzezniak, L. K., Dmochowska, A., Gewartowski, K., Bartnik, E. & Stepien, P. P. (2009). Human mitochondrial RNA turnover caught in flagranti: involvement of hSuv3p helicase in RNA surveillance. Nucleic Acids Research 38, 279298.
Taghbalout, A. & Rothfield, L. (2007). RNaseE and the other constituents of the RNA degradosome are components of the bacterial cytoskeleton. Proceedings of the National Academy of Sciences of the United States of America 104, 16671672.
Taghbalout, A. & Rothfield, L. (2008). RNaseE and RNA helicase B play central roles in the cytoskeletal organization of the RNA degradosome. Journal of Biological Chemistry 283, 1385013855.
Taghbalout, A. & Yang, Q. F. (2010). Self-assembly of the bacterial cytoskeleton-associated RNA Helicase B protein into polymeric filamentous structures. Journal of Bacteriology 192, 32223226.
Takada, A., Nagai, K. & Wachi, M. (2005). A decreased level of FtsZ is responsible for inviability of RNase E-deficient cells. Genes Cells 10, 733741.
Tang, T. H., Rozhdestvensky, T. S., D'Orval, B. C., Bortolin, M. L., Huber, H., Charpentier, B., Branlant, C., Bachellerie, J. P., Brosius, J. & Huttenhofer, A. (2002). RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Research 30, 921930.
Tokuriki, N. & Tawfik, D. S. (2009). Stability effects of mutations and protein evolvability. Current Opinion in Structural Biology 19, 596604.
Toledo-Arana, A., Repoila, F. & Cossart, P. (2007). Small noncoding RNAs controlling pathogenesis. Current Opinion in Microbiology 10, 182188.
Trubetskoy, D., Proux, F., Allemand, F., Dreyfus, M. & Iost, I. (2009). SrmB, a DEAD-box helicase involved in Escherichia coli ribosome assembly, is specifically targeted to 23S rRNA in vivo. Nucleic Acids Research 37, 65406549.
Tu, K. C. & Bassler, B. L. (2007). Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi. Genes and Development 21, 221233.
Tuckerman, J. R., Gonzalez, G. & Gilles-Gonzalez, M. A. (2011). Cyclic di-GMP activation of polynucleotide phosphorylase signal-dependent RNA processing. Journal of Molecular Biology 407, 633639.
Valentin-Hansen, P., Johansen, J. & Rasmussen, A. A. (2007). Small RNAs controlling outer membrane porins. Current Opinion in Microbiology 10, 152155.
Vanzo, N. F., Li, Y. S., Py, B., Blum, E., Higgins, C. F., Raynal, L. C., Krisch, H. M. & Carpousis, A. J. (1998). Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes and Development 12, 27702781.
Vecerek, B., Rajkowitsch, L., Sonnleitner, E., Schroeder, R. & Blasi, U. (2008). The C-terminal domain of Escherichia coli Hfq is required for regulation. Nucleic Acids Research 36, 133143.
Viegas, S. C., Pfeiffer, V., Sittka, A., Silva, I. J., Vogel, J. & Arraiano, C. M. (2007). Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Research 35, 76517664.
Vogel, J. (2009). A rough guide to the non-coding RNA world of Salmonella. Molecular Microbiology 71, 111.
Vogel, J., Argaman, L., Wagner, E. G. & Altuvia, S. (2004). The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Current Biology 14, 22712276.
Vogel, J. & Luisi, B. F. (2011). Hfq and its constellation of RNA. Nature Reviews in Microbiology 9, 578589.
Vogel, J. & Papenfort, K. (2006). Small non-coding RNAs and the bacterial outer membrane. Current Opinion in Microbiology 9, 605611.
Wang, D. D., Shu, Z., Lieser, S. A., Chen, P. L. & Lee, W. H. (2009). Human mitochondrial SUV3 and PNPase form a 330 kDa heteropentamer to cooperatively degrade dsRNA with a 3′ to 5′ directionality. Journal of Biological Chemistry 284, 2081220821.
Wang, G., Chen, H. W., Oktay, Y., Zhang, J., Allen, E. L., Smith, G. M., Fan, K. C., Hong, J. S., French, S. W., Mccaffery, J. M., Lightowlers, R. N., Morse, H. C., Koehler, C. M. & Teitell, M. A. (2010). PNPase regulates RNA import into mitochondria. Cell 142, 456467.
Wassarman, K. M. (2007). 6S RNA: a small RNA regulator of transcription. Current Opinion in Microbiology 10, 164168.
Waters, L. S. & Storz, G. (2009). Regulatory RNAs in Bacteria. Cell 136, 615628.
Whitty, A. (2008). Cooperativity and biological complexity. Nature Chemical Biology 4, 435439.
Wilusz, C. J. & Wilusz, J. (2004). Bringing the role of rnRNA decay in the control of gene expression into focus. Trends in Genetics 20, 491497.
Worrall, J. A., Górna, M., Crump, N. T., Phillips, L. G., Tuck, A. C., Price, A. J., Bavro, V. N. & Luisi, B. F. (2008a). Reconstitution and analysis of the multienzyme Escherichia coli RNA degradosome. Journal of Molecular Biology 382, 870883.
Worrall, J. A., Howe, F. S., Mckay, A. R., Robinson, C. V. & Luisi, B. F. (2008b). Allosteric activation of the ATPase activity of the Escherichia coli RhlB RNA helicase. Journal of Biological Chemistry 283, 55675576.
Wright, P. E. & Dyson, H. J. (2009). Linking folding and binding. Current Opinion in Structural Biology 19, 3138.
Xiang, S., Cooper-Morgan, A., Jiao, X., Kiledjian, M., Manley, J. L. & Tong, L. (2009). Structure and function of the 5′–>3′ exoribonuclease Rat1 and its activating partner Rai1. Nature 458, 784788.
Xu, F., Lin-Chao, S. & Cohen, S. N. (1993). The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates. Proceedings of the National Academy of Sciences of the United States of America 90, 67566760.
Yang, J., Jain, C. & Schesser, K. (2008). RNase E regulates the Yersinia type 3 secretion system. Journal of Bacteriology 190, 37743778.
Yang, W., Lee, J. Y. & Nowotny, M. (2006). Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Molecular Cell 22, 513.
Yao, S. Y. & Bechhofer, D. H. (2010). Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y. Journal of Bacteriology 192, 32793286.
Zeller, M. E., Csanadi, A., Miczak, A., Rose, T., Bizebard, T. & Kaberdin, V. R. (2007). Quaternary structure and biochemical properties of mycobacterial RNase E/G. Biochemical Journal 403, 207215.
Zhang, J. & Olsen, G. J. (2009). Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii. RNA 15, 19091916.
Zundel, M. A., Basturea, G. N. & Deutscher, M. P. (2009). Initiation of ribosome degradation during starvation in Escherichia coli. RNA 15, 977983.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Quarterly Reviews of Biophysics
  • ISSN: 0033-5835
  • EISSN: 1469-8994
  • URL: /core/journals/quarterly-reviews-of-biophysics
Please enter your name
Please enter a valid email address
Who would you like to send this to? *


Altmetric attention score

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed