rne:Gene

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Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

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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

rne

Mnemonic

RNase E

Synonyms

ECK1069, b1084, JW1071, ams, hmp1, rne_1, smbB[1], smbB

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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

24.58 minutes 

MG1655: 1143590..1140405
<gbrowseImage> name=NC_000913:1140405..1143590 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1158936..1155751
<gbrowseImage> name=NC_012967:1155751..1158936 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1044330..1047515
<gbrowseImage> name=NC_012759:1044330..1047515 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1145944..1142759
<gbrowseImage> name=NC_007779:1142759..1145944 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1199035..1195850
<gbrowseImage> name=NC_010473:1195850..1199035 source=DH10B preset=GeneLocation </gbrowseImage>

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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

1140405

Edman degradation

PMID:2011493[2]


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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

rne-3071(ts)

temperature sensitive

PMID:8320240[3] PMID:1846032[4]

CGSC:7537

rne3071

mRNA degredation

RNase E deficient mutation causes accumulation of P1-t1 in strain due to lack of RNase E cleave of 3' terminal hairpin stricture, Figure 4.

PMID:7519147[5]

rne3071

mRNA degredation

This temperature sensitive mutation up regulates mutL-miaA which are co transcribed, and promoters Pmia and P1hfq by a factor of 3, 7 and 8 fold. Table 2.

PMID:7748952[6]

Strain:N3431


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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

JW1071

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:gccAAAAGAATGTTAATCAACGCAACTCAG

Primer 2:cctTCAACAGGTTGCGGACGCGCAGGAGCG

E3G11

Kohara Phage

Genobase

PMID:3038334[8]

14C1

Kohara Phage

Genobase

PMID:3038334[8]

zcc-282::Tn10

Linked marker

CAG18466 = CGSC7359[9]

est. P1 cotransduction: % [10]

zce-726::Tn10

Linked marker

CAG12078 = CGSC7361[9]

est. P1 cotransduction: 59% [10]

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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:EG10859

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10859

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000850

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945641

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0852

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003668

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. Chauhan, AK et al. (1991) Sequencing and expression of the rne gene of Escherichia coli. Nucleic Acids Res. 19 125-9 PubMed
  3. McDowall, KJ et al. (1993) The ams-1 and rne-3071 temperature-sensitive mutations in the ams gene are in close proximity to each other and cause substitutions within a domain that resembles a product of the Escherichia coli mre locus. J. Bacteriol. 175 4245-9 PubMed
  4. Babitzke, P & Kushner, SR (1991) The Ams (altered mRNA stability) protein and ribonuclease E are encoded by the same structural gene of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 88 1-5 PubMed
  5. Hajnsdorf, E et al. (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 3368-77 PubMed
  6. Tsui, HC & Winkler, ME (1994) Transcriptional patterns of the mutL-miaA superoperon of Escherichia coli K-12 suggest a model for posttranscriptional regulation. Biochimie 76 1168-77 PubMed
  7. Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  8. 8.0 8.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  9. 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. 10.0 10.1 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).

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