Autogenous Regulation of Escherichia coli Polynucleotide Phosphorylase Expression Revisited

ABSTRACT The Escherichia coli polynucleotide phosphorylase (PNPase; encoded by pnp), a phosphorolytic exoribonuclease, posttranscriptionally regulates its own expression at the level of mRNA stability and translation. Its primary transcript is very efficiently processed by RNase III, an endonuclease that makes a staggered double-strand cleavage about in the middle of a long stem-loop in the 5′-untranslated region. The processed pnp mRNA is then rapidly degraded in a PNPase-dependent manner. Two non-mutually exclusive models have been proposed to explain PNPase autogenous regulation. The earlier one suggested that PNPase impedes translation of the RNase III-processed pnp mRNA, thus exposing the transcript to degradative pathways. More recently, this has been replaced by the current model, which maintains that PNPase would simply degrade the promoter proximal small RNA generated by the RNase III endonucleolytic cleavage, thus destroying the double-stranded structure at the 5′ end that otherwise stabilizes the pnp mRNA. In our opinion, however, the first model was not completely ruled out. Moreover, the RNA decay pathway acting upon the pnp mRNA after disruption of the 5′ double-stranded structure remained to be determined. Here we provide additional support to the current model and show that the RNase III-processed pnp mRNA devoid of the double-stranded structure at its 5′ end is not translatable and is degraded by RNase E in a PNPase-independent manner. Thus, the role of PNPase in autoregulation is simply to remove, in concert with RNase III, the 5′ fragment of the cleaved structure that both allows translation and prevents the RNase E-mediated PNPase-independent degradation of the pnp transcript.

[1]  H. Čelešnik,et al.  The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal , 2008, Nature.

[2]  C. Condon.  Maturation and degradation of RNA in bacteria. , 2007, Current opinion in microbiology.

[3]  P. Tortora,et al.  The KH and S1 domains of Escherichia coli polynucleotide phosphorylase are necessary for autoregulation and growth at low temperature. , 2007, Biochimica et biophysica acta.

[4]  V. Kaberdin,et al.  Translation initiation and the fate of bacterial mRNAs. , 2006, FEMS microbiology reviews.

[5]  S. R. Kushner,et al.  The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells , 2006, Nucleic acids research.

[6]  P. Fisher,et al.  Polynucleotide phosphorylase: an evolutionary conserved gene with an expanding repertoire of functions. , 2006, Pharmacology & therapeutics.

[7]  G. Mackie,et al.  Function of the Conserved S1 and KH Domains in Polynucleotide Phosphorylase , 2005, Journal of bacteriology.

[8]  J. Belasco,et al.  Lost in translation: the influence of ribosomes on bacterial mRNA decay. , 2005, Genes & development.

[9]  R. Bermúdez-Cruz,et al.  Conserved domains in polynucleotide phosphorylase among eubacteria. , 2005, Biochimie.

[10]  J. Belasco,et al.  Catalytic activation of multimeric RNase E and RNase G by 5'-monophosphorylated RNA. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[11]  R. DeSalle,et al.  The origin of polynucleotide phosphorylase domains. , 2004, Molecular phylogenetics and evolution.

[12]  P. Tortora,et al.  A mutation in polynucleotide phosphorylase from Escherichia coli impairing RNA binding and degradosome stability. , 2004, Nucleic acids research.

[13]  Stanley N Cohen,et al.  The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[14]  C. Portier,et al.  Mutational analysis of polynucleotide phosphorylase from Escherichia coli. , 2002, Journal of molecular biology.

[15]  C. Portier,et al.  PNPase autocontrols its expression by degrading a double‐stranded structure in the pnp mRNA leader , 2001, The EMBO journal.

[16]  V. Kaberdin,et al.  Cleavage of poly(A) tails on the 3'-end of RNA by ribonuclease E of Escherichia coli. , 2001, Nucleic acids research.

[17]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[18]  R. Simons,et al.  Cold‐temperature induction of Escherichia coli polynucleotide phosphorylase occurs by reversal of its autoregulation †‡ , 2001, Molecular microbiology.

[19]  B. Luisi,et al.  A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. , 2000, Structure.

[20]  S. R. Kushner,et al.  Polynucleotide phosphorylase functions both as a 3′ → 5′ exonuclease and a poly(A) polymerase in Escherichia coli , 2000 .

[21]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[22]  P. Tortora,et al.  Transcriptional and post‐transcriptional control of polynucleotide phosphorylase during cold acclimation in Escherichia coli , 2000, Molecular microbiology.

[23]  J. García-Mena,et al.  A novel mutation in the KH domain of polynucleotide phosphorylase affects autoregulation and mRNA decay in Escherichia coli , 1999, Molecular microbiology.

[24]  M. Dreyfus,et al.  The C‐terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo , 1999, Molecular microbiology.

[25]  R. Favaro,et al.  Photometric assay for polynucleotide phosphorylase. , 1999, Analytical biochemistry.

[26]  E. Hajnsdorf,et al.  E. coli RpsO mRNA decay: RNase E processing at the beginning of the coding sequence stimulates poly(A)-dependent degradation of the mRNA. , 1999, Journal of molecular biology.

[27]  G. Mackie.  Ribonuclease E is a 5′-end-dependent endonuclease , 1998, Nature.

[28]  Mark Proctor,et al.  The Solution Structure of the S1 RNA Binding Domain: A Member of an Ancient Nucleic Acid–Binding Fold , 1997, Cell.

[29]  C. Higgins,et al.  A DEAD-box RNA helicase in the Escherichia coli RNA degradosome , 1996, Nature.

[30]  V. Kaberdin,et al.  Proteins associated with RNase E in a multicomponent ribonucleolytic complex. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[31]  T. Gibson,et al.  Three-Dimensional Structure and Stability of the KH Domain: Molecular Insights into the Fragile X Syndrome , 1996, Cell.

[32]  L. Corcoran,et al.  Expression and Purification of Glutathione‐S‐Transferase Fusion Proteins , 1994, Current protocols in molecular biology.

[33]  A. J. Carpousis,et al.  Nucleolytic inactivation and degradation of the RNase III processed pnp message encoding polynucleotide phosphorylase of Escherichia coli. , 1994, Journal of molecular biology.

[34]  H. Krisch,et al.  Copurification of E. coli RNAase E and PNPase: Evidence for a specific association between two enzymes important in RNA processing and degradation , 1994, Cell.

[35]  C. Portier,et al.  Polynucleotide phosphorylase of Escherichia coli induces the degradation of its RNase III processed messenger by preventing its translation. , 1994, Nucleic acids research.

[36]  L. Shapiro,et al.  Three-step PCR mutagenesis for 'linker scanning'. , 1993, Nucleic acids research.

[37]  S. R. Kushner,et al.  Analysis of mRNA decay and rRNA processing in Escherichia coli multiple mutants carrying a deletion in RNase III , 1993, Journal of bacteriology.

[38]  P. Sabbattini,et al.  Bacteriophage P4 immunity controlled by small RNAs via transcription termination , 1992, Molecular microbiology.

[39]  F. Forti,et al.  Genetic analysis of the immunity region of phage‐plasmid P4 , 1992, Molecular microbiology.

[40]  C. Portier,et al.  E.coli polynucleotide phosphorylase expression is autoregulated through an RNase III‐dependent mechanism. , 1992, The EMBO journal.

[41]  R. Lurz,et al.  Dissection of IncP conjugative plasmid transfer: definition of the transfer region Tra2 by mobilization of the Tra1 region in trans , 1992, Journal of bacteriology.

[42]  M. Izuhara,et al.  Processing in the 5' region of the pnp transcript facilitates the site-specific endonucleolytic cleavages of mRNA. , 1992, Nucleic acids research.

[43]  C. Gualerzi,et al.  Identification of a cold shock transcriptional enhancer of the Escherichia coli gene encoding nucleoid protein H-NS. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[44]  E. Hajnsdorf,et al.  Decay of mRNA encoding ribosomal protein S15 of Escherichia coli is initiated by an RNase E-dependent endonucleolytic cleavage that removes the 3' stabilizing stem and loop structure. , 1991, Journal of molecular biology.

[45]  M. Grunberg‐Manago,et al.  RNase III cleavages in non-coding leaders of Escherichia coli transcripts control mRNA stability and genetic expression. , 1990, Biochimie.

[46]  M. Izuhara,et al.  Differential degradation of the Escherichia coli polynucleotide phosphorylase mRNA. , 1989, Nucleic acids research.

[47]  M. Grunberg‐Manago,et al.  The first step in the functional inactivation of the Escherichia coli polynucleotide phosphorylase messenger is a ribonuclease III processing at the 5′ end. , 1987, The EMBO journal.

[48]  M. Grunberg‐Manago,et al.  Nucleotide sequence of the pnp gene of Escherichia coli encoding polynucleotide phosphorylase. Homology of the primary structure of the protein with the RNA-binding domain of ribosomal protein S1. , 1987, The Journal of biological chemistry.

[49]  C. Portier,et al.  Initiation, attenuation and RNase III processing of transcripts from the Escherichia coli operon encoding ribosomal protein S15 and polynucleotide phosphorylase. , 1986, Journal of molecular biology.

[50]  T. Mukai,et al.  Attenuation and processing of RNA from the rpsO-pnp transcription unit of Escherichia coli. , 1985, Nucleic acids research.

[51]  C. Portier,et al.  Expression of the rpsO and pnp genes: structural analysis of a DNA fragment carrying their control regions. , 1984, Nucleic acids research.

[52]  D. Apirion,et al.  Structural analysis and in vitro processing to p5 rRNA of a 9S RNA molecule isolated from an rne mutant of E. coli , 1978, Cell.

[53]  J. Chou,et al.  Deoxyadenosine diphosphate as a substrate and inhibitor of polynucleotide phosphorylase of Micrococcus luteus. 3. Copolymerization of adenosine diphosphate and deoxyadenosine diphosphate. , 1971, The Journal of biological chemistry.

[54]  U. K. Laemmli,et al.  Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4 , 1970, Nature.

[55]  M. Grunberg‐Manago,et al.  Kinetics of polymerization and phosphorolysis reactions of E. coli polynucleotide phosphorylase. Role of oligonucleotides in polymerization. , 1970, European journal of biochemistry.

[56]  M. Grunberg‐Manago,et al.  An altered polynucleotide phosphorylase in E. coli mutant Q13. , 1967, Biochemical and biophysical research communications.

[57]  H. Wade,et al.  Magnesium ion-independent ribonucleic acid depolymerases in bacteria. , 1966, The Biochemical journal.

[58]  G. Bertani,et al.  Growth abnormalities in Hfr derivatives of Escherichia coli strain C. , 1965, Journal of general microbiology.

[59]  L. De Gioia,et al.  Genetic analysis of polynucleotide phosphorylase structure and functions. , 2007, Biochimie.

[60]  M. Grunberg‐Manago,et al.  Cloning of E. coli pnp gene from an episome , 2004, Molecular and General Genetics MGG.

[61]  Michael Zuker,et al.  Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide , 1999 .

[62]  Jan Barciszewski,et al.  RNA Biochemistry and Biotechnology , 1999 .

[63]  J. Chou,et al.  Deoxyadenosine Diphosphate as a Substrate and Inhibitor of Polynucleotide Phosphorylase of Micrococcus Zuteus , 1998 .

[64]  S. R. Kushner,et al.  Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. , 1986, Proceedings of the National Academy of Sciences of the United States of America.