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Escherichia coli K-12 substr. MG1655 Enzyme: polynucleotide phosphorylase



Gene: pnp Accession Numbers: EG10743 (EcoCyc), b3164, ECK3152

Synonyms: bfl, PNPase

Regulation Summary Diagram: ?

Component of: degradosome (extended summary available)

Subunit composition of polynucleotide phosphorylase = [Pnp]3
         polynucleotide phosphorylase monomer = Pnp

Summary:
Polynucleotide phosphorylase (PNPase) is a 3' to 5' exonuclease and a 3'-terminal oligonucleotide polymerase. It degrades various mRNAs, is involved in cold shock regulation, is a part of tRNA maturation and degradation, adds heteropolymeric tails to some RNAs and is a component of the degradosome, a multienzyme complex that carries out RNA degradation.

PNPase is involved in general mRNA degradation. Loss of PNPase leads to an increase in steady-state levels of mRNA, as well as increasing mRNA half lives in the absence of the 3' exonuclease RNase II [Mohanty03, Kinscherf75]. PNPase also has a role in mRNA degradation during carbon starvation, where it may be required for breakdown of small rRNA fragments produced by other RNases [Kaplan74, Kaplan75].

A number of specific PNPase substrates have been identified. PNPase is involved in degradation of lac mRNA, rnb mRNA, mRNA coding for ribosomal protein S20, and the RNA-OUT antisense RNA [HarEl79, Pepe94, Mackie89, Zilhao96]. It also degrades sok antisense RNA and thrS and rpsO mRNA following cleavage by RNase E [Dam97, Nogueira01, Braun96, Hajnsdorf94]. PNPase binds to but does not degrade RNA containing 8-oxoguanine [Hayakawa01].

PNPase-mediated degradation is required for regulation of the cold shock response. PNPase degrades a number of mRNAs induced by cold shock, including those coding for CspA, RbfA, CsdA, RpoE, RseA, Rnr and many others [Yamanaka01, Cairrao03, Polissi03]. The isolated PNPase S1 RNA-binding domain can complement a deletion in four cold-shock genes [Xia01].

The 3' to 5' processive cleavage of RNA by PNPase depends on the composition and structure of the 3' end of the substrate [Plamann90, Cisneros96]. RhlB and poly(A) polymerase I (PAP I) in concert with the degradosome are required for PNPase-mediated degradation of cistrons with 3' REP-stabilizers [Khemici04].

Binding of the protein Hfq to poly(A) tracts prevents PNPase degradation of these tails in vitro [Folichon03]. RNA with 3' stem-loops are resistant to degradation by pure PNPase or whole degradosome in vitro, but addition of even a short poly(A) or mixed nucleotide tail overcomes this block [Causton94, Blum99, Lisitsky99]. Polyadenylation similarly destabilizes rpsO mRNA against degradation by RNase E, RNase II and PNPase, and is required for sok RNA degradation [Hajnsdorf95, Hajnsdorf96, Dam97]. Both 3' adenylation and 5' phosphorylation affect the rate of degradation of RNA I [Xu95a]. PNPase itself modulates polyadenylation of several RNAs [Mohanty00].

PNPase is involved in tRNA processing and maintenance. Though purified PNPase is incapable of completely processing tRNA in vitro, it is effective, along with RNase II, in trimming long 3' trailing sequences to yield 2-4 nucleotide intermediates which will be trimmed by RNases T and PH [Deutscher88, Li94a]. PNPase is also partially required for repair of 3'-terminal CCA sequences in tRNAs in the absence of tRNA nucleotidyltransferase [Reuven97]. PNPase is also involved in the degradation of mutant tRNA, in a process that is enhanced by polyadenylation by PAP I [Li02].

PNPase also catalyzes the "reverse" reaction, converting nucleoside diphosphates into polyribonucleotides [Littauer57, Gillam78, Gillam80]. PNPase generates heteropolymeric tails on RNA and is responsible for residual polyadenylation detected in PAP I deficient strains [Mohanty00a]. Hfq, which binds to the 3' end of RNA and prevents PNPase-mediated degradation, also prevents PNPase-mediated addition of nucleosides to bound RNA, while promoting PAP I activity [Folichon05].

PNPase is a trimer of Pnp monomers [Portier75, Soreq77]. Each Pnp monomer has two RNA-binding sites, KH and S1, that are dispensible for strict catalytic function but are required for Pnp autoregulation, growth at low temperature, and the generation of oligonucleotides [Jarrige02, MatusOrtega07, Guissani76]. The S1 domain is a five-stranded antiparallel β barrel with conserved residues on one face forming the RNA binding site [Bycroft97].

PNPase binds the signaling molecule c-di-GMP; binding enhances several PNPase activities, including ADP/Pi phosphoryl exchange and poly(A) synthesis [Tuckerman11].

PNPase is subject to autoregulation at the mRNA level. RNase III cleaves a stem-loop in the pnp mRNA leader sequence, following which PNPase binds and degrades the 5' half of the cleaved duplex [Portier87, Takata89, Jarrige01, RobertLe92, Takata87, Carzaniga09]. PNPase autoregulation also decreases as general RNA polyadenylation increases and following a shift to cold temperatures [Mohanty02, Mathy01, Zangrossi00, Beran01].

Strains lacking both PNPase and RNase II activity are inviable and collect mRNA fragments 100-1,500 nucleotides long [Donovan86]. In a triple mutant in pnp, rnb and rne, mRNA degradation slows three- to fourfold and the length and number of poly(A) tails increases [Arraiano88, OHara95]. In a pnp mutant lacking RNase PH function, the 50S ribosomal subunit and 23S rRNA is degraded [Zhou97].

Even in the absence of the degradosome scaffold RNase E, PNPase and the helicase RhlB interact. In vitro, RhlB unwinding of dsRNA allows PNPase degradation to occur [Liou02].

PNPase is required to prevent phage P4 superinfection. This prevention requires binding of CI antisense RNA to sequences on nascent P4 transcripts; PNPase processes CI RNA [Piazza96].

pnp shows differential codon adaptation, resulting in differential translation efficiency signatures, in thermophilic microbes. It was therefore predicted to play a role in the heat shock response. A pnp deletion mutant was shown to be more sensitive than wild-type specifically to heat shock, but not other stresses [Krisko14].

Gene Citations: [Regnier86, Sands88, Nakamura85]

Locations: cytosol, membrane

Map Position: [3,307,055 <- 3,309,190] (71.28 centisomes)
Length: 2136 bp / 711 aa

Molecular Weight of Polypeptide: 77.101 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010397 , CGSC:379 , DIP:DIP-10522N , EchoBASE:EB0736 , EcoGene:EG10743 , EcoliWiki:b3164 , Mint:MINT-244786 , ModBase:P05055 , OU-Microarray:b3164 , PortEco:pnp , PR:PRO_000023561 , Pride:P05055 , Protein Model Portal:P05055 , RefSeq:NP_417633 , RegulonDB:EG10743 , SMR:P05055 , String:511145.b3164 , UniProt:P05055

Relationship Links: InterPro:IN-FAMILY:IPR001247 , InterPro:IN-FAMILY:IPR003029 , InterPro:IN-FAMILY:IPR004087 , InterPro:IN-FAMILY:IPR004088 , InterPro:IN-FAMILY:IPR009019 , InterPro:IN-FAMILY:IPR012162 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR015847 , InterPro:IN-FAMILY:IPR015848 , InterPro:IN-FAMILY:IPR020568 , InterPro:IN-FAMILY:IPR022967 , InterPro:IN-FAMILY:IPR027408 , Panther:IN-FAMILY:PTHR11252 , PDB:Structure:1SRO , PDB:Structure:3CDI , PDB:Structure:3CDJ , PDB:Structure:3GCM , PDB:Structure:3GLL , PDB:Structure:3GME , PDB:Structure:3H1C , Pfam:IN-FAMILY:PF00013 , Pfam:IN-FAMILY:PF00575 , Pfam:IN-FAMILY:PF01138 , Pfam:IN-FAMILY:PF03725 , Pfam:IN-FAMILY:PF03726 , Prosite:IN-FAMILY:PS50084 , Prosite:IN-FAMILY:PS50126 , Smart:IN-FAMILY:SM00316 , Smart:IN-FAMILY:SM00322

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009408 - response to heat Inferred from experiment [Krisko14]
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic Inferred by computational analysis Inferred from experiment [Li94a, GOA01a]
GO:0006396 - RNA processing Inferred by computational analysis [GOA01a]
GO:0006402 - mRNA catabolic process Inferred by computational analysis [GOA06, GOA01a]
GO:0006950 - response to stress Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000175 - 3'-5'-exoribonuclease activity Inferred from experiment Inferred by computational analysis [GOA01a, Li94a]
GO:0004654 - polyribonucleotide nucleotidyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Littauer57]
GO:0005515 - protein binding Inferred from experiment [Erce10, AitBara10, Regonesi06, Butland05, Callaghan04]
GO:0035438 - cyclic-di-GMP binding Inferred from experiment [Tuckerman11]
GO:0042802 - identical protein binding Inferred from experiment [Lasserre06, Callaghan04]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016779 - nucleotidyltransferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07, LopezCampistrou05, Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: information transfer RNA related RNA degradation
metabolism degradation of macromolecules RNA

Essentiality data for pnp knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Enzymatic reaction of: polynucleotide phosporylase (polynucleotide phosphorylase)

EC Number: 3.1.13.1

a tRNA precursor with a 5' extension and a long 3' trailer + n H2O <=> a tRNA precursor with a 5' extension and a short 3' extension + n a nucleoside 5'-monophosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is irreversible in the direction shown.

In Pathways: tRNA processing


Enzymatic reaction of: polynucleotide phosphorylase

EC Number: 2.7.7.8

a single-stranded RNA + phosphate <=> a single-stranded RNA + a nucleoside diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

Cofactors or Prosthetic Groups: Mg2+ [Kimhi68, Littauer57]

Inhibitors (Unknown Mechanism): 6-azauridine diphosphate [Skoda59]


Subunit of: degradosome

Subunit composition of degradosome = [(Ppk)2][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2]
         polyphosphate kinase = (Ppk)2 (extended summary available)
         ribonuclease E = (Rne)4 (extended summary available)
                 RNase E = Rne
         RhlB, ATP-dependent RNA helicase of the RNA degradosome = (RhlB)2 (extended summary available)
         polynucleotide phosphorylase = (Pnp)3 (extended summary available)
                 polynucleotide phosphorylase monomer = Pnp
         enolase = (Eno)2 (extended summary available)

Summary:
The degradosome is a large, multiprotein complex involved in RNA degradation. It consists of the RNA degradation enzymes RNase E and PNPase, as well as the ATP-dependent RNA helicase RhlB and the metabolic enzyme enolase [Py94, Carpousis94, Py96]. Polyphosphate kinase and the chaperone protein DnaK are also associated with and may be components of the degradosome [Blum97, Miczak96]. A "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible for this test case, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur [Coburn99]. Based on immunogold labeling studies, RhlB and RNase E are present in equimolar quantities in the degradosome, which is tethered to the cytoplasmic membrane via the amino-terminus of RNase E [Liou01].

RNase E provides the organizational structure for the degradosome. Its carboxy-terminal half binds PNPase, RhlB and enolase, and the loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I [Kido96, Vanzo98, Morita04]. This scaffold region is flexible, with isolated segments of increased structure that may be involved in binding other degradosome constituents [Callaghan04]. RNase E binding to partner proteins can be selectively disrupted. Loss of RhlB and enolase binding results in reduced degradosome activity. Conversely, disrupted PNPase binding yields increased activity. Strains any alteration in RNase E binding do not grow as well as wild type [Leroy02]. The amino-terminal half of RNase E contains sequences involved in oligomerization [Vanzo98].

In vitro purified degradosome generates 147-nucleotide RNase E cleavage intermediates from rpsT mRNA. Continuous cycles of polyadenylation and PNPase cleavage are necessary and sufficient to break down these intermediates, though RNase II can block this second degradation step [Coburn98]. RNAs with 3' REP stabilizers or stem loops must be polyadenylated to allow breakdown by the degradosome [Khemici04, Blum99]. Poly(G) and poly(U) tails do not allow degradation, though addition of a stretch of mixed nucleotides copied from within a coding region has stimulated degradation of a test substrate [Blum99].

The degradosome copurifies with fragments from its RNA substrates, including rRNA fragments derived from cleavage of 16S and 23S rRNA by RNase E, 5S rRNA and ssrA RNA [Bessarab98, LinChao99].

The DEAD-box helicases SrmB, RhlE and CsdA bind RNase E in vitro at a different site than RhlB. RhlE and CsdA can both replace RhlB in promoting PNPase activity in vitro [Khemici04a]. CsdA is induced by cold shock, and following a shift to 15 degrees C it copurifies with the degradosome [PrudhommeGenere04].

At least two poly(A)-binding proteins interact with the degradosome. The cold-shock protein CspE inhibits internal cleavage and breakdown of polyadenylated RNA by RNase E and PNPase by blocking digestion through the poly(A) tail. S1, a component of the 30S ribosome, binds to RNase E and PNPase without apparent effect on their activities [Feng01].

The global effects of mutations in degradeosome constituents on mRNA levels have been evaluated using microarrays [Bernstein04].

Locations: inner membrane

GO Terms:

Cellular Component: GO:0005886 - plasma membrane [Liou01]


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 77 -> 80
[UniProt14]
UniProt: FFRR loop; important for RNA binding; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 79 -> 80
[UniProt14]
Alternate sequence: RR → AA; UniProt: Strongly reduces RNA binding. Reduces RNA degradation.
Mutagenesis-Variant 83
[Shi08, UniProt14]
Alternate sequence: R → A; UniProt: No effect on RNA-binding. No effect on degradation of long RNA molecules. Impairs degradation of short RNA molecules.
Mutagenesis-Variant 100
[Jarrige02, UniProt14]
Alternate sequence: R → D; UniProt: Abolishes enzyme activity.
Acetylation-Modification 302
[Yu08]
 
Mutagenesis-Variant 319
[Jarrige02, UniProt14]
Alternate sequence: R → A; UniProt: Abolishes enzyme activity.
Protein-Segment 327 -> 331
[UniProt14]
UniProt: Interaction with RNase E; Sequence Annotation Type: region of interest.
Sequence-Conflict 357
[Regnier87, UniProt10]
Alternate sequence: G → R; UniProt: (in Ref. 1; AAA83905);
Mutagenesis-Variant 398 -> 399
[UniProt14]
Alternate sequence: RR → DD; UniProt: Abolishes enzyme activity.
Mutagenesis-Variant 428
[Jarrige02, UniProt14]
Alternate sequence: V → P; UniProt: Abolishes enzyme activity.
Mutagenesis-Variant 444
[Jarrige02, UniProt14]
Alternate sequence: C → W; UniProt: Abolishes enzyme activity.
Sequence-Conflict 450
[Regnier87, UniProt10]
Alternate sequence: L → S; UniProt: (in Ref. 1; AAA83905);
Metal-Binding-Site 486
[UniProt14]
UniProt: Magnesium.
Mutagenesis-Variant 492
[Jarrige02, UniProt14]
Alternate sequence: D → G; UniProt: Abolishes enzyme activity.
Metal-Binding-Site 492
[UniProt14]
UniProt: Magnesium.
Conserved-Region 553 -> 612
[UniProt09]
UniProt: KH;
Conserved-Region 622 -> 690
[UniProt09]
UniProt: S1 motif;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Ingrid Keseler on Fri Jun 8, 2007:
Corrected start site based on [Link97 ].
10/20/97 Gene b3164 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10743; confirmed by SwissProt match.


References

AitBara10: Ait-Bara S, Carpousis AJ (2010). "Characterization of the RNA degradosome of Pseudoalteromonas haloplanktis: conservation of the RNase E-RhlB interaction in the gammaproteobacteria." J Bacteriol 192(20);5413-23. PMID: 20729366

Arraiano88: Arraiano CM, Yancey SD, Kushner SR (1988). "Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12." J Bacteriol 170(10);4625-33. PMID: 2459106

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Beran01: Beran RK, Simons RW (2001). "Cold-temperature induction of Escherichia coli polynucleotide phosphorylase occurs by reversal of its autoregulation." Mol Microbiol 39(1);112-25. PMID: 11123693

Bernstein04: Bernstein JA, Lin PH, Cohen SN, Lin-Chao S (2004). "Global analysis of Escherichia coli RNA degradosome function using DNA microarrays." Proc Natl Acad Sci U S A 101(9);2758-63. PMID: 14981237

Bessarab98: Bessarab DA, Kaberdin VR, Wei CL, Liou GG, Lin-Chao S (1998). "RNA components of Escherichia coli degradosome: evidence for rRNA decay." Proc Natl Acad Sci U S A 95(6);3157-61. PMID: 9501232

Blum97: Blum E, Py B, Carpousis AJ, Higgins CF (1997). "Polyphosphate kinase is a component of the Escherichia coli RNA degradosome." Mol Microbiol 1997;26(2);387-98. PMID: 9383162

Blum99: Blum E, Carpousis AJ, Higgins CF (1999). "Polyadenylation promotes degradation of 3'-structured RNA by the Escherichia coli mRNA degradosome in vitro." J Biol Chem 274(7);4009-16. PMID: 9933592

Braun96: Braun F, Hajnsdorf E, Regnier P (1996). "Polynucleotide phosphorylase is required for the rapid degradation of the RNase E-processed rpsO mRNA of Escherichia coli devoid of its 3' hairpin." Mol Microbiol 19(5);997-1005. PMID: 8830280

Butland05: Butland G, Peregrin-Alvarez JM, 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(7025);531-7. PMID: 15690043

Bycroft97: Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG (1997). "The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold." Cell 88(2);235-42. PMID: 9008164

Cairrao03: Cairrao F, Cruz A, Mori H, Arraiano CM (2003). "Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA." Mol Microbiol 50(4);1349-60. PMID: 14622421

Callaghan04: Callaghan AJ, Aurikko JP, Ilag LL, Gunter Grossmann J, Chandran V, Kuhnel K, Poljak L, Carpousis AJ, Robinson CV, Symmons MF, Luisi BF (2004). "Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E." J Mol Biol 340(5);965-79. PMID: 15236960

Carpousis94: Carpousis AJ, Van Houwe G, Ehretsmann C, Krisch HM (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(5);889-900. PMID: 7510217

Carzaniga09: Carzaniga T, Briani F, Zangrossi S, Merlino G, Marchi P, Deho G (2009). "Autogenous regulation of Escherichia coli polynucleotide phosphorylase expression revisited." J Bacteriol. PMID: 19136586

Causton94: Causton H, Py B, McLaren RS, Higgins CF (1994). "mRNA degradation in Escherichia coli: a novel factor which impedes the exoribonucleolytic activity of PNPase at stem-loop structures." Mol Microbiol 14(4);731-41. PMID: 7534370

Cisneros96: Cisneros B, Court D, Sanchez A, Montanez C (1996). "Point mutations in a transcription terminator, lambda tI, that affect both transcription termination and RNA stability." Gene 181(1-2);127-33. PMID: 8973320

Coburn98: Coburn GA, Mackie GA (1998). "Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes." J Mol Biol 279(5);1061-74. PMID: 9642084

Coburn99: Coburn GA, Miao X, Briant DJ, Mackie GA (1999). "Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3' exonuclease and a DEAD-box RNA helicase." Genes Dev 13(19);2594-603. PMID: 10521403

Dam97: Dam Mikkelsen N, Gerdes K (1997). "Sok antisense RNA from plasmid R1 is functionally inactivated by RNase E and polyadenylated by poly(A) polymerase I." Mol Microbiol 26(2);311-20. PMID: 9383156

Deutscher88: Deutscher MP, Marshall GT, Cudny H (1988). "RNase PH: an Escherichia coli phosphate-dependent nuclease distinct from polynucleotide phosphorylase." Proc Natl Acad Sci U S A 85(13);4710-4. PMID: 2455297

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Donovan86: Donovan WP, Kushner SR (1986). "Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12." Proc Natl Acad Sci U S A 83(1);120-4. PMID: 2417233

Erce10: Erce MA, Low JK, Wilkins MR (2010). "Analysis of the RNA degradosome complex in Vibrio angustum S14." FEBS J 277(24);5161-73. PMID: 21126315

Feng01: Feng Y, Huang H, Liao J, Cohen SN (2001). "Escherichia coli poly(A)-binding proteins that interact with components of degradosomes or impede RNA decay mediated by polynucleotide phosphorylase and RNase E." J Biol Chem 276(34);31651-6. PMID: 11390393

Folichon03: Folichon M, Arluison V, Pellegrini O, Huntzinger E, Regnier P, Hajnsdorf E (2003). "The poly(A) binding protein Hfq protects RNA from RNase E and exoribonucleolytic degradation." Nucleic Acids Res 31(24);7302-10. PMID: 14654705

Folichon05: Folichon M, Allemand F, Regnier P, Hajnsdorf E (2005). "Stimulation of poly(A) synthesis by Escherichia coli poly(A)polymerase I is correlated with Hfq binding to poly(A) tails." FEBS J 272(2);454-63. PMID: 15654883

Gillam78: Gillam S, Jahnke P, Smith M (1978). "Enzymatic synthesis of oligodeoxyribonucleotides of defined sequence." J Biol Chem 253(8);2532-9. PMID: 632285

Gillam80: Gillam S, Smith M (1980). "Use of E. coli polynucleotide phosphorylase for the synthesis of oligodeoxyribonucleotides of defined sequence." Methods Enzymol 65(1);687-701. PMID: 6990191

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Guissani76: Guissani A, Portier C (1976). "Study on the structure-function relationship of polynucleotide phosphorylase: model of a proteolytic degraded polynucleotide phosphorylase." Nucleic Acids Res 3(11);3015-24. PMID: 794831

Hajnsdorf94: Hajnsdorf E, Steier O, Coscoy L, Teysset L, Regnier P (1994). "Roles of RNase E, RNase II and PNPase in the degradation of the rpsO transcripts of Escherichia coli: stabilizing function of RNase II and evidence for efficient degradation in an ams pnp rnb mutant." EMBO J 13(14);3368-77. PMID: 7519147

Hajnsdorf95: Hajnsdorf E, Braun F, Haugel-Nielsen J, Regnier P (1995). "Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli." Proc Natl Acad Sci U S A 92(9);3973-7. PMID: 7732015

Hajnsdorf96: Hajnsdorf E, Braun F, Haugel-Nielsen J, Le Derout J, Regnier P (1996). "Multiple degradation pathways of the rpsO mRNA of Escherichia coli. RNase E interacts with the 5' and 3' extremities of the primary transcript." Biochimie 78(6);416-24. PMID: 8915531

HarEl79: Har-El R, Silberstein A, Kuhn J, Tal M (1979). "Synthesis and degradation of lac mRNA in E. coli depleted of 30S ribosomal subunits." Mol Gen Genet 173(2);135-44. PMID: 386032

Hayakawa01: Hayakawa H, Kuwano M, Sekiguchi M (2001). "Specific binding of 8-oxoguanine-containing RNA to polynucleotide phosphorylase protein." Biochemistry 40(33);9977-82. PMID: 11502194

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jarrige01: Jarrige AC, Mathy N, Portier C (2001). "PNPase autocontrols its expression by degrading a double-stranded structure in the pnp mRNA leader." EMBO J 20(23);6845-55. PMID: 11726520

Jarrige02: Jarrige A, Brechemier-Baey D, Mathy N, Duche O, Portier C (2002). "Mutational analysis of polynucleotide phosphorylase from Escherichia coli." J Mol Biol 321(3);397-409. PMID: 12162954

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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Other References Related to Gene Regulation

Caldara06: Caldara M, Charlier D, Cunin R (2006). "The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation." Microbiology 152(Pt 11);3343-54. PMID: 17074904

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Krin03: Krin E, Laurent-Winter C, Bertin PN, Danchin A, Kolb A (2003). "Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12." J Bacteriol 185(10);3139-46. PMID: 12730174

Makarova01: Makarova KS, Mironov AA, Gelfand MS (2001). "Conservation of the binding site for the arginine repressor in all bacterial lineages." Genome Biol 2(4);RESEARCH0013. PMID: 11305941

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Shimada13: Shimada T, Yoshida H, Ishihama A (2013). "Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli." J Bacteriol 195(10);2212-9. PMID: 23475967


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