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Escherichia coli K-12 substr. MG1655 Enzyme: poly(A) polymerase I



Gene: pcnB Accession Numbers: EG10690 (EcoCyc), b0143, ECK0142

Synonyms: PAP I

Regulation Summary Diagram: ?

Summary:
Poly(A) polymerase I is responsible for the polyadenylation of 3' ends of RNA molecules.

Poly(A) polymerase polyadenylates the vast majority of mRNA transcripts [Mohanty & Kushner, 2006]. Unlike in eukaryotes, increased polyadenylation of mRNAs leads to decreased mRNA half-life [Mohanty99, Mohanty & Kushner, 2006]. Rho-independent transcription terminators appear to serve as targeting signals for polyadenylation [Mohanty & Kushner, 2006]. The Hfq protein appears to be involved in the recognition of 3' termini of RNA by poly(A) polymerase I [Le03].

Intracellular levels of poly(A) polymerase I as well as the level of pcnB transcription vary inversely with growth rate [Jasiecki03]. Overexpression of poly(A) polymerase I is toxic and leads to slowed growth [Mohanty99, Mohanty & Kushner, 2006]. Use of AUU as the translational start codon results in InfC discrimination (as with production of the IF-3 translation initiation factor) and results in low levels of poly(A) polymerase I in the cells [Binns02].

A his-tagged version of poly(A) polymerase I showed reduced activity following phosphorylation of its his tag. In other proteins, this sometimes correlates with the protein itself being regulated via phosphorylation [Jasiecki06].

Gene Citations: [Talarico92, Liu89b, Podkovyrov95, Cao96]

Locations: inner membrane, cytosol

Map Position: [157,729 <- 159,126] (3.4 centisomes)
Length: 1398 bp / 465 aa

Molecular Weight of Polypeptide: 53.871 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000493 , CGSC:13584 , DIP:DIP-47859N , EchoBASE:EB0684 , EcoGene:EG10690 , EcoliWiki:b0143 , ModBase:P0ABF1 , OU-Microarray:b0143 , PortEco:pcnB , PR:PRO_000023500 , Protein Model Portal:P0ABF1 , RefSeq:NP_414685 , RegulonDB:EG10690 , SMR:P0ABF1 , String:511145.b0143 , UniProt:P0ABF1

Relationship Links: InterPro:IN-FAMILY:IPR002646 , InterPro:IN-FAMILY:IPR010206 , InterPro:IN-FAMILY:IPR025866 , InterPro:IN-FAMILY:IPR026007 , Panther:IN-FAMILY:PTHR13734:SF5 , Pfam:IN-FAMILY:PF01743 , Pfam:IN-FAMILY:PF12626

In Paralogous Gene Group: 47 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006276 - plasmid maintenance Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Liu89b]
GO:0006378 - mRNA polyadenylation Inferred from experiment Inferred by computational analysis [GOA01a, Mohanty & Kushner, 2006]
GO:0006397 - mRNA processing Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Raynal99]
GO:0009451 - RNA modification Inferred from experiment [Mikiewicz97, Mohanty & Kushner, 2006, Raynal99]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006396 - RNA processing Inferred by computational analysis [GOA01a]
GO:0043631 - RNA polyadenylation Inferred by computational analysis [GOA06]
Molecular Function: GO:0003723 - RNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Raynal99]
GO:0004652 - polynucleotide adenylyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Raynal99]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016779 - nucleotidyltransferase activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, Cao92, Raynal99]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for pcnB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes et al., 2003, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba et al., 2006, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba et al., 2006, Comment 2]

Enzymatic reaction of: poly(A) polymerase

EC Number: 2.7.7.19

ATP + an mRNA <=> an mRNA + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Kinetic Parameters:

Substrate
Km (μM)
Citations
ATP
130.0
[Betat04, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Propeptide 1 -> 10
[UniProt11]
.
Chain 11 -> 465
[UniProt11]
UniProt: Poly(A) polymerase.
Active-Site 80
[UniProt, 2010]
UniProt: Non-Experimental Qualifier: by similarity;
Active-Site 82
[UniProt, 2010]
UniProt: Non-Experimental Qualifier: by similarity;
Sequence-Conflict 93
[Liu89b, UniProt10]
Alternate sequence: R → A; UniProt: (in Ref. 1);
Active-Site 162
[UniProt, 2010]
UniProt: Non-Experimental Qualifier: by similarity;
Sequence-Conflict 315
[Liu89b, UniProt10]
Alternate sequence: A → T; UniProt: (in Ref. 1);
Sequence-Conflict 332
[Liu89b, UniProt10]
Alternate sequence: K → N; UniProt: (in Ref. 1);
Sequence-Conflict 437 -> 438
[Liu89b, UniProt10]
Alternate sequence: ML → IV; UniProt: (in Ref. 1);
Sequence-Conflict 449 -> 465
[Liu89b, UniProt10]
Alternate sequence: RRTRRPRKRAPRREGTA → QSYSSSTQTRTTS; UniProt: (in Ref. 1);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
10/20/97 Gene b0143 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10690; confirmed by SwissProt match.


References

Baba et al., 2006: 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

Betat04: Betat H, Rammelt C, Martin G, Morl M (2004). "Exchange of regions between bacterial poly(A) polymerase and the CCA-adding enzyme generates altered specificities." Mol Cell 15(3);389-98. PMID: 15304219

Binns02: Binns N, Masters M (2002). "Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: a second chromosomal example of translation initiated at AUU." Mol Microbiol 44(5);1287-98. PMID: 12068810

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Cao92: Cao GJ, Sarkar N (1992). "Identification of the gene for an Escherichia coli poly(A) polymerase." Proc Natl Acad Sci U S A 89(21);10380-4. PMID: 1438224

Cao96: Cao GJ, Pogliano J, Sarkar N (1996). "Identification of the coding region for a second poly(A) polymerase in Escherichia coli." Proc Natl Acad Sci U S A 1996;93(21);11580-5. PMID: 8876178

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

Gerdes et al., 2003: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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."

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

Jasiecki03: Jasiecki J, Wegrzyn G (2003). "Growth-rate dependent RNA polyadenylation in Escherichia coli." EMBO Rep 4(2);172-7. PMID: 12612607

Jasiecki06: Jasiecki J, Wegrzyn G (2006). "Phosphorylation of Escherichia coli poly(A) polymerase I and effects of this modification on the enzyme activity." FEMS Microbiol Lett 261(1);118-22. PMID: 16842368

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

Le03: Le Derout J, Folichon M, Briani F, Deho G, Regnier P, Hajnsdorf E (2003). "Hfq affects the length and the frequency of short oligo(A) tails at the 3' end of Escherichia coli rpsO mRNAs." Nucleic Acids Res 31(14);4017-23. PMID: 12853618

Liu89b: Liu JD, Parkinson JS (1989). "Genetics and sequence analysis of the pcnB locus, an Escherichia coli gene involved in plasmid copy number control." J Bacteriol 171(3);1254-61. PMID: 2537812

Mikiewicz97: Mikiewicz D, Wrobel B, Wegrzyn G, Plucienniczak A (1997). "Isolation and characterization of a ColE1-like plasmid from Enterobacter agglomerans with a novel variant of rom gene." Plasmid 38(3);210-9. PMID: 9435023

Mohanty & Kushner, 2006: Mohanty BK, Kushner SR (2006). "The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells." Nucleic Acids Res 34(19);5695-704. PMID: 17040898

Mohanty99: Mohanty BK, Kushner SR (1999). "Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism." Mol Microbiol 34(5);1094-108. PMID: 10594833

Podkovyrov95: Podkovyrov SM, Larson TJ (1995). "A new vector-host system for construction of lacZ transcriptional fusions where only low-level gene expression is desirable." Gene 1995;156(1);151-2. PMID: 7737510

Raynal99: Raynal LC, Carpousis AJ (1999). "Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation." Mol Microbiol 32(4);765-75. PMID: 10361280

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Talarico92: Talarico TL, Ray PH, Dev IK, Merrill BM, Dallas WS (1992). "Cloning, sequence analysis, and overexpression of Escherichia coli folK, the gene coding for 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase." J Bacteriol 1992;174(18);5971-7. PMID: 1325970

UniProt, 2010: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Jasiecki06a: Jasiecki J, Wegrzyn G (2006). "Transcription start sites in the promoter region of the Escherichia coli pcnB (plasmid copy number) gene coding for poly(A) polymerase I." Plasmid 55(2):169-72. PMID: 16330100

Lacour03: Lacour S, Kolb A, Landini P (2003). "Nucleotides from -16 to -12 determine specific promoter recognition by bacterial sigmaS-RNA polymerase." J Biol Chem 278(39);37160-8. PMID: 12853450

NadratowskaWeso10: Nadratowska-Wesolowska B, Slominska-Wojewodzka M, Lyzen R, Wegrzyn A, Szalewska-Palasz A, Wegrzyn G (2010). "Transcription regulation of the Escherichia coli pcnB gene coding for poly(A) polymerase I: roles of ppGpp, DksA and sigma factors." Mol Genet Genomics 284(4);289-305. PMID: 20700605


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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