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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	pcnB
Gene Synonym(s)	ECK0142, b0143, JW5808^[1], JW5808
Product Desc.	poly(A) polymerase I^[2]^[3] Poly(A) polymerase; controls plasmid copy number; rare AUU start codon, growth-rate regulated; monomeric^[4]
Product Synonyms(s)	poly(A) polymerase I^[1], B0143^[2]^[1], PcnB^[2]^[1], PAP I^[2]^[1] , ECK0142, JW5808, b0143
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pcnB-folK^[2]
Regulation/Activity
Quick Links
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Notes

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AUU start proven by mutagenesis analysis. PcnB can polyadenylate many mRNAs and it is proposed that Rho-independent transcription terminators serve as polyadenylation signals (Mohanty, 2006).^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	pcnB
Mnemonic	Plasmid copy number
Synonyms	ECK0142, b0143, JW5808^[1], JW5808
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	3.4 minutes	MG1655: 159126..157729 <gbrowseImage> name=NC_000913:157729..159126 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 161944..160580 <gbrowseImage> name=NC_012967:160580..161944 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 157728..159125 <gbrowseImage> name=NC_012759:157728..159125 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 159126..157729 <gbrowseImage> name=NC_007779:157729..159126 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 133230..131833 <gbrowseImage> name=NC_010473:131833..133230 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	157732	Edman degradation	PMID:1438224
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
pcnB(del) (Keio:JW5808)	deletion	deletion			PMID:16738554	Shigen
pcnB80						CGSC:7757
pcnB90(del)::kan						CGSC:85727
pcnB overexpression				overexpression causes increased polyadenylation which leads to decrease in half-life of total pulse-labelled RNA and decrease in half life of transcripts, such as trxA, rpsO, Ipp and ompA, table 1, as a function of poly(A) level, figure 5. Results demonstrate direct correlation between poly(A) levels and mRNA decay.	PMID:10594833		strain history: pBMK11
pcnB(del)	deletion	thyamine deletion	Growth Phenotype	elimination stops transcription of poly (A) polymerase I which dramatically stabilizes the lpp, ompA, trxA transcripts.	PMID:7534403		Strain History: MG1693 (thy A715)
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW5808	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTTACCCGAGTCGCTAATTT Primer 2:CCTGCGGTACCCTCACGACGTGG
11C5	Kohara Phage	Genobase	PMID:3038334
15A7	Kohara Phage	Genobase	PMID:3038334
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[5]	est. P1 cotransduction: 73% ^[6]
yafC502::Tn10	Linked marker	CAG18436 = CGSC7328^[5]	est. P1 cotransduction: 1% ^[6] Synonyms:zae-502::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10690	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10690	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000683	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947318	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0684	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000493	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	PcnB
Synonyms	poly(A) polymerase I^[1], B0143^[2]^[1], PcnB^[2]^[1], PAP I^[2]^[1] , ECK0142, JW5808, b0143
Product description	poly(A) polymerase I^[2]^[3] Poly(A) polymerase; controls plasmid copy number; rare AUU start codon, growth-rate regulated; monomeric^[4]
EC number (for enzymes)	2.7.7.19^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0004652	polynucleotide adenylyltransferase activity	PMID:10361280	IDA: Inferred from Direct Assay		F		complete
	GO:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002646	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010206	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0694	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004652	polynucleotide adenylyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010206	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009451	RNA modification	PMID:10361280	IDA: Inferred from Direct Assay		P		complete
	GO:0004652	polynucleotide adenylyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.7.19	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006397	mRNA processing	PMID:10361280	IDA: Inferred from Direct Assay		P		complete
	GO:0006276	plasmid maintenance	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0615	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006276	plasmid maintenance	PMID:2537812	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006378	mRNA polyadenylation	PMID:17040898	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0006378	mRNA polyadenylation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010206	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009451	RNA modification	PMID:17040898	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0003723	RNA binding	PMID:10361280	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0009451	RNA modification	PMID:9435023	IGI: Inferred from Genetic Interaction	EcoliWiki:cca\|EcoliWiki:pnp	P		complete
	GO:0005737	cytoplasm	PMID:10361280	IDA: Inferred from Direct Assay		C		complete
	GO:0005737	cytoplasm	PMID:1438224	IDA: Inferred from Direct Assay		C		complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	gltA	PMID:19402753	LCMS(ID Probability):99.6
Protein	dps	PMID:19402753	MALDI(Z-score):28.075216
Protein	rplE	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplM	PMID:19402753	MALDI(Z-score):24.173218
Protein	rlmL	PMID:19402753	MALDI(Z-score):18.794422
Protein	rplB	PMID:19402753	MALDI(Z-score):29.552366
Protein	rpsC	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):32.827078
Protein	rpsD	PMID:19402753	MALDI(Z-score):34.875026
Protein	pssA	PMID:19402753	MALDI(Z-score):24.386749
Protein	rplD	PMID:19402753	MALDI(Z-score):24.466084
Protein	yfiF	PMID:19402753	MALDI(Z-score):30.740581
Protein	rluB	PMID:19402753	MALDI(Z-score):32.442766
Protein	rsmC	PMID:19402753	LCMS(ID Probability):99.6
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MLSREESEAE QAVARPQVTV IPREQHAISR KDISENALKV MYRLNKAGYE AWLVGGGVRD LLLGKKPKDF DVTTNATPEQ VRKLFRNCRL VGRRFRLAHV MFGPEIIEVA TFRGHHEGNV SDRTTSQRGQ NGMLLRDNIF GSIEEDAQRR DFTINSLYYS VADFTVRDYV GGMKDLKDGV IRLIGNPETR YREDPVRMLR AVRFAAKLGM RISPETAEPI PRLATLLNDI PPARLFEESL KLLQAGYGYE TYKLLCEYHL FQPLFPTITR YFTENGDSPM ERIIEQVLKN TDTRIHNDMR VNPAFLFAAM FWYPLLETAQ KIAQESGLTY HDAFALAMND VLDEACRSLA IPKRLTTLTR DIWQLQLRMS RRQGKRAWKL LEHPKFRAAY DLLALRAEVE RNAELQRLVK WWGEFQVSAP PDQKGMLNEL DEEPSPRRRT RRPRKRAPRR EGTA
Length	454
Mol. Wt	52.549 kDa
pI	9.9 (calculated)
Extinction coefficient	53,860 - 54,235 (calc based on 14 Y, 6 W, and 3 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Domain	62..193	PF01743 Poly A polymerase head domain		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=pcnB taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:162135892	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947318	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000493	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ABF1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10690	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10690	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947318	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000683	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0684	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MC4100	1.92E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	26.676+/-0.453	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.155332856	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	1518	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	422	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	775	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
pcnB-folK
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:159106..159146 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b0143 (EcoliWiki Page)	NCBI GEO profiles for pcnB
microarray	GenExpDB:b0143 (EcoliWiki Page)	Summary of data for pcnB from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (159010..159248) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:D7^[7]
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Notes

Accessions Related to pcnB Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10690	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0684	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0143
EcoGene	EcoGene:EG10690	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000683	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000493	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000010598 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000021198 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT2G17580 (score: 1.000; bootstrap: 100%) AT1G28090 (score: 0.143) AT5G23690 (score: 0.136) AT3G48830 (score: 0.111)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040625-176 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040625-254 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000027999 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000005380 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000025112 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YER168C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000156703 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00014142001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PCNB	From SHIGELLACYC
E. coli O157	PCNB	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Panther (EcoliWiki Page)	PTHR13734:SF5
Superfamily (EcoliWiki Page)	SUPERFAMILY:81301
Superfamily (EcoliWiki Page)	SUPERFAMILY:81891
Pfam (EcoliWiki Page)	PF01743 Poly A polymerase head domain
EcoCyc	EcoCyc:EG10690	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10690	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000683	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0684	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000493	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

pcnB:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to pcnB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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