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Escherichia coli K-12 substr. MG1655 Enzyme: RNase I, cleaves phosphodiester bond between any two nucleotides



Gene: rna Accession Numbers: EG10856 (EcoCyc), b0611, ECK0604

Synonyms: rnsA

Regulation Summary Diagram: ?

Summary:
Ribonuclease I (RNase I) is an endonuclease that cleaves phosphodiester bonds in RNA, yielding nucleoside 3'-phosphates and 3'-phosphooligonucleotides [Spahr61]. RNase I is partially reponsible for the degradation of total and ribosomal RNA during both normal and nutrient starvation conditions, especially during carbon starvation [Kaplan74, Kaplan75, Cohen77]. RNase I is specifically required for the breakdown of 23 S RNA, though it is not required for degradation of 16 S RNA or very small (4 S) RNA fragments that result from breakdown of larger RNA [Kaplan75a, Kaplan75]. RNase I degradation of the 50 S ribosome releases the ribosomal proteins L4, L10 and L7/12 in addition to cleaving the 23 S RNA to yield a smaller product [Raziuddin79]. Polyamines stimulate the activity of RNase I against synthetic polynucleotides in vitro [Kumagai77].

RNase I is a periplasmic protein that can be released by spheroblasting or treatment of cells with N-dodecyldiethanolamine. This release allows subsequent enhanced breakdown of rRNA by RNase I [Neu64, Neu64a, Neu64b, Neu65, Abrell71a, Lambert76]. RNase I appears to remain with the membrane fraction in disrupted cells [Kaplan76].

Some structural analysis of RNase I has been completed. Its conformation energy is 11.5 kcal/mol at pH 7.5, and its T(m) is 64 degrees C at pH 4.0 [Padmanabhan01]. It has a 23-residue amino-terminal signal sequence which is cleaved and likely allows its transport to the periplasm [Meador90]. Preliminary crystallization of RNase I has been done, with visualization of the structure at greater than three angstrom resolution [Lim93].

Mutants lacking RNase I or other ribonuclease activities have reduced DNA degradation, possibly due to interaction between excess RNA and DNA endonuclease I [Wright71]. RNase I is also required for full recovery from starvation, as cell viability studies show a direct correlation between recovery from starvation and the ability to degrade RNA [Kaplan75a]. A method has been developed to screen for mutants in RNase I by checking for a delay in β-galactosidase expression during amino acid starvation [Kaplan73a].

Citations: [Gesteland66, KivityVogel67, Durwald68, Cammack70, Reiner69]

Locations: periplasmic space, cytosol

Map Position: [643,420 <- 644,226] (13.87 centisomes)
Length: 807 bp / 268 aa

Molecular Weight of Polypeptide: 29.618 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002107 , CGSC:273 , DIP:DIP-10723N , EchoBASE:EB0849 , EcoGene:EG10856 , EcoliWiki:b0611 , Mint:MINT-1292710 , ModBase:P21338 , OU-Microarray:b0611 , PortEco:rna , PR:PRO_000023786 , Pride:P21338 , Protein Model Portal:P21338 , RefSeq:NP_415144 , RegulonDB:EG10856 , SMR:P21338 , String:511145.b0611 , UniProt:P21338

Relationship Links: InterPro:IN-FAMILY:IPR001568 , InterPro:IN-FAMILY:IPR018188 , Panther:IN-FAMILY:PTHR11240 , PDB:Structure:2EA1 , PDB:Structure:2PQX , PDB:Structure:2PQY , PDB:Structure:2Z70 , Pfam:IN-FAMILY:PF00445 , Prosite:IN-FAMILY:PS00530 , Prosite:IN-FAMILY:PS00531

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006401 - RNA catabolic process Inferred from experiment [Kaplan75]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis Inferred from experiment [Wright71, UniProtGOA11a]
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic Inferred by computational analysis [GOA01, GOA01a]
Molecular Function: GO:0004519 - endonuclease activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Wright71]
GO:0003723 - RNA binding Inferred by computational analysis [GOA01a]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a]
GO:0008847 - Enterobacter ribonuclease activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0033897 - ribonuclease T2 activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0030288 - outer membrane-bounded periplasmic space [Neu64]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

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

Essentiality data for rna knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, 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 [Baba06, Comment 2]

Credits:
Revised 25-May-2011 by Brito D


Enzymatic reaction of: RNase I endoribonuclease (RNase I, cleaves phosphodiester bond between any two nucleotides)

EC Number: 3.1.27.6

rRNA[periplasmic space] <=> 2 a single-stranded RNA[periplasmic space]

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.

Inhibitors (Unknown Mechanism): Ca2+ [Loskot78] , Mg2+ [Raziuddin79]


Enzymatic reaction of: RNase I endoribonuclease (RNase I, cleaves phosphodiester bond between any two nucleotides)

EC Number: 3.1.27.6

23S rRNA[periplasmic space] + H2O[periplasmic space] <=> 2 a single-stranded RNA[periplasmic space]

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

The reaction is physiologically favored in the direction shown.


Enzymatic reaction of: RNase I endoribonuclease (RNase I, cleaves phosphodiester bond between any two nucleotides)

EC Number: 3.1.27.6

an mRNA[periplasmic space] + H2O[periplasmic space] <=> 2 a single-stranded RNA[periplasmic space]

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

The reaction is physiologically favored in the direction shown.

Inhibitors (Unknown Mechanism): Ca2+ [Loskot78] , Mg2+ [Raziuddin79, Loskot78]


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 23
[Meador90]
 
Chain 24 -> 268
[UniProt09]
UniProt: Ribonuclease I;
Active-Site 78
[UniProt10a]
UniProt: Non-Experimental Qualifier: by similarity;
Disulfide-Bond-Site 159, 103
[UniProt10a]
UniProt: Non-Experimental Qualifier: by similarity;
Active-Site 152
[UniProt10a]
UniProt: Non-Experimental Qualifier: by similarity;
Active-Site 156
[UniProt10a]
UniProt: Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0611 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10856; confirmed by SwissProt match.


References

Abrell71a: Abrell JW (1971). "Ribonuclease I released from Escherichia coli by osmotic shock." Arch Biochem Biophys 142(2);693-700. PMID: 4994433

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

Cammack70: Cammack KA, Miller DS, Grinstead KH (1970). "Physical properties of ribosomal ribonucleic acid isolated from bacteria deficient in ribonuclease I." Biochem J 117(4);745-55. PMID: 4915439

Cohen77: Cohen L, Kaplan R (1977). "Accumulation of nucleotides by starved Escherichia coli cells as a probe for the involvement of ribonucleases in ribonucleic acid degradation." J Bacteriol 129(2);651-7. PMID: 320188

Durwald68: Durwald H, Hoffmann-Berling H (1968). "Endonuclease-I-deficient and ribonuclease I-deficient Escherichia coli mutants." J Mol Biol 34(2);331-46. PMID: 4938550

Gerdes03: 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

Gesteland66: Gesteland RF (1966). "Isolation and characterization of ribonuclease I mutants of Escherichia coli." J Mol Biol 16(1);67-84. PMID: 5331244

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."

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

Kaplan73a: Kaplan S (1973). "Screening procedure for Escherichia coli mutants deficient in ribonuclease I." J Bacteriol 113(2);1081-3. PMID: 4570595

Kaplan74: Kaplan R, Apirion D (1974). "The involvement of ribonuclease I, ribonuclease II, and polynucleotide phosphorylase in the degradation of stable ribonucleic acid during carbon starvation in Escherichia coli." J Biol Chem 249(1);149-51. PMID: 4358625

Kaplan75: Kaplan R, Apirion D (1975). "Decay of ribosomal ribonucleic acid in Escherichia coli cells starved for various nutrients." J Biol Chem 250(8);3174-8. PMID: 1091648

Kaplan75a: Kaplan R, Apirion D (1975). "The fate of ribosomes in Escherichia coli cells starved for a carbon source." J Biol Chem 250(5);1854-63. PMID: 1089666

Kaplan76: Kaplan R, Hartstein E (1976). "The site of ribosome degradation in starved Escherichia coli cells." J Biol Chem 251(4);1147-53. PMID: 765338

KivityVogel67: Kivity-Vogel T, Elson D (1967). "On the metabolic inactivation of messenger RNA in Escherichia coli: ribonuclease I and polynucleotide phosphorylase." Biochim Biophys Acta 138(1);66-75. PMID: 4860430

Kumagai77: Kumagai H, Igarashi K, Yoshikawa M, Hirose S (1977). "Effects of polyamines on the activities of Escherichia coli ribonuclease I and II." J Biochem (Tokyo) 81(2);381-8. PMID: 321440

Lambert76: Lambert PA, Smith AR (1976). "Antimicrobial action of dodecyldiethanolamine: activation of ribonuclease I in Escherichia coli." Microbios 17(67);35-49. PMID: 801034

Lim93: Lim LW, Mathur S, Cannistraro VJ, Kennell D (1993). "Preliminary X-ray crystallographic studies of ribonuclease I from Escherichia coli." J Mol Biol 234(2);499-501. PMID: 8230230

Loskot78: Loskot F, Bauer U (1978). "[Treatment of ventricular extrasystole with mexiletine and Neo-gilurytmal in myocardial infarct patients]." Adv Clin Pharmacol 16;75-80. PMID: 80103

Meador90: Meador J, Kennell D (1990). "Cloning and sequencing the gene encoding Escherichia coli ribonuclease I: exact physical mapping using the genome library." Gene 95(1);1-7. PMID: 2253883

Neu64: Neu HC, Heppel LA (1964). "The release of ribonuclease into the medium when E. coli cells are converted to spheroplasts." Biochem Biophys Res Commun 14;109-12. PMID: 5319839

Neu64a: Neu HC, Heppel LA (1964). "Some observations on the "latent" ribonuclease of Escherichia coli." Proc Natl Acad Sci U S A 51;1267-74. PMID: 14218066

Neu64b: Neu HC, Heppel LA (1964). "The release of ribonuclease into the medium when Escherichia coli cells are converted to spheroplasts." J Biol Chem 239;3893-900. PMID: 14257624

Neu65: Neu HC, Heppel LA (1965). "The release of enzymes from Escherichia coli by osmotic shock and during the formation of spheroplasts." J Biol Chem 240(9);3685-92. PMID: 4284300

Padmanabhan01: Padmanabhan S, Zhou K, Chu CY, Lim RW, Lim LW (2001). "Overexpression, biophysical characterization, and crystallization of ribonuclease I from Escherichia coli, a broad-specificity enzyme in the RNase T2 family." Arch Biochem Biophys 390(1);42-50. PMID: 11368513

Raziuddin79: Raziuddin , Chatterji D, Ghosh S, Burma DP (1979). "Site of action of RNase I on the 50 S ribosome of Escherichia coli and the association of the enzyme with the partially degraded subunit." J Biol Chem 254(21);10575-8. PMID: 115862

Reiner69: Reiner AM (1969). "Genetic locus for ribonuclease I in Escherichia coli." J Bacteriol 97(3);1522-3. PMID: 4887525

Spahr61: Spahr PF, Hollingworth BR (1961). "Purification and Mechanism of Action of Ribonuclease from Escherichia coli Ribosomes." J Biol Chem 236: 823-31.

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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."

Wright71: Wright M (1971). "Mutants of Escherichia coli lacking endonuclease I, ribonuclease I, or ribonuclease II." J Bacteriol 107(1);87-94. PMID: 4105037

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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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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