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MetaCyc Protein: RhlB, ATP-dependent RNA helicase of the RNA degradosome

Gene: rhlB Accession Number: EG10844 (MetaCyc)

Synonyms: mmrA?, b3780, G704, mmrA

Species: Escherichia coli K-12 substr. MG1655

Component of: degradosome (extended summary available)

Subunit composition of RhlB, ATP-dependent RNA helicase of the RNA degradosome = [RhlB]2

Summary:
RhlB is an ATP-dependent helicase that is a component of the degradosome, where it aids degradation of structured RNA by PNPase and is required for full degradosome activity [Py96, Coburn99]. RhlB is a member of the family of DEAD-box helicases, though rhlb conditional lethality is not complemented by another DEAD-box helicase, SrmB [Kalman91]. RhlB binds to the degradosome scaffold RNase E, an interaction that both makes it part of the complex and enhances its ATPase activity fifteen fold [Vanzo98]. In at least one case, rpsT mRNA, substrate polyadenylation is required following cleavage by RNase E to allow RhlB and PNPase to complete degradation [Coburn99].

RhlB forms homodimers and can bind PNPase even in the absence of RNase E. In vitro, RhlB unwinding of dsRNA allows PNPase degradation to occur [Liou02a].

Whereas uvr mutant strains show better recovery from irradiation in minimal versus rich medium, uvr mutants that also lack RhlB function recover equally well on either medium. This may be due to a delay in DNA synthesis that occurs during growth on minimal medium or on any medium when RhlB activity is absent [Sharma83, Sharma85].

RhlB has a role independent of PNPase in the RNase E-dependent cleavage of the products of T7 phage RNA polymerase. In an rhlb null, lacZ and other RNAs transcribed by T7 RNAP are stabilized. RhlB is not generally required for RNase E cleavage of non-T7 substrates, however [Khemici05]. The T7 gene 0.7 protein kinase phosphorylates RhlB, stabilizing lac and cat RNAs transcribed by T7 RNAP [Marchand01].

Locations: cytosol

Map Position: [3,962,388 <- 3,963,653]

Molecular Weight of Polypeptide: 47.126 kD (from nucleotide sequence)

Unification Links: CGSC:36971 , DIP:DIP-35644N , EcoGene:EG10844 , EcoliWiki:b3780 , Mint:MINT-8049290 , OU-Microarray:b3780 , PR:PRO_000023740 , Pride:P0A8J8 , Protein Model Portal:P0A8J8 , RefSeq:NP_418227 , SMR:P0A8J8 , String:511145.b3780 , UniProt:P0A8J8

Relationship Links: InterPro:IN-FAMILY:IPR000629 , InterPro:IN-FAMILY:IPR001650 , InterPro:IN-FAMILY:IPR011545 , InterPro:IN-FAMILY:IPR014001 , InterPro:IN-FAMILY:IPR014014 , InterPro:IN-FAMILY:IPR023554 , InterPro:IN-FAMILY:IPR027417 , Pfam:IN-FAMILY:PF00270 , Pfam:IN-FAMILY:PF00271 , Prosite:IN-FAMILY:PS00039 , Prosite:IN-FAMILY:PS51192 , Prosite:IN-FAMILY:PS51194 , Prosite:IN-FAMILY:PS51195 , Smart:IN-FAMILY:SM00487 , Smart:IN-FAMILY:SM00490

Ortholog Links: Ecol199310Cyc (Escherichia coli CFT073):C4700 , EcoO157Cyc (Escherichia coli O157:H7 str. EDL933):RHLB , ShigellaCyc (Shigella flexneri 2a str. 2457T):RHLB

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006200 - ATP catabolic process Inferred by computational analysis Inferred from experiment [Py96, GOA06, GOA01]
GO:0006401 - RNA catabolic process Inferred from experiment Inferred by computational analysis [GOA06, Coburn99]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Erce10, AitBara10, Butland05, Callaghan04, Regonesi06]
GO:0008026 - ATP-dependent helicase activity Inferred from experiment Inferred by computational analysis [GOA01, Py96]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0004004 - ATP-dependent RNA helicase activity Inferred by computational analysis [GOA06, GOA01]
GO:0004386 - helicase activity Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

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


Subunit of: degradosome

Species: Escherichia coli K-12 substr. MG1655

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 [Feng01a].

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]

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Py96, UniProt11]
UniProt: Removed.
Chain 2 -> 421
[UniProt09]
UniProt: ATP-dependent RNA helicase rhlB;
Protein-Segment 9 -> 37
[UniProt10]
UniProt: Q motif; Sequence Annotation Type: short sequence motif;
Conserved-Region 40 -> 219
[UniProt09]
UniProt: Helicase ATP-binding;
Nucleotide-Phosphate-Binding-Region 53 -> 60
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 72
[Kalman91, UniProt10]
Alternate sequence: H; UniProt: (in Ref. 1);
Protein-Segment 165 -> 168
[UniProt10]
UniProt: DEAD box; Sequence Annotation Type: short sequence motif;
Conserved-Region 245 -> 390
[UniProt09]
UniProt: Helicase C-terminal;
Sequence-Conflict 340
[Kalman91, UniProt10]
Alternate sequence: S; UniProt: (in Ref. 1);

History:
3/2/1998 (pkarp) Merged genes G704/b3780 and EG10844/rhlB
10/20/97 Gene b3780 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10844; 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

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

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

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

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

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

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

Feng01a: 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

GOA01: 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

Kalman91: Kalman M, Murphy H, Cashel M (1991). "rhlB, a new Escherichia coli K-12 gene with an RNA helicase-like protein sequence motif, one of at least five such possible genes in a prokaryote." New Biol 3(9);886-95. PMID: 1931833

Khemici04: Khemici V, Carpousis AJ (2004). "The RNA degradosome and poly(A) polymerase of Escherichia coli are required in vivo for the degradation of small mRNA decay intermediates containing REP-stabilizers." Mol Microbiol 51(3);777-90. PMID: 14731278

Khemici04a: Khemici V, Toesca I, Poljak L, Vanzo NF, Carpousis AJ (2004). "The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: functional replacement of RhlB by RhlE." Mol Microbiol 54(5);1422-30. PMID: 15554979

Khemici05: Khemici V, Poljak L, Toesca I, Carpousis AJ (2005). "Evidence in vivo that the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E." Proc Natl Acad Sci U S A 102(19);6913-8. PMID: 15867149

Kido96: Kido M, Yamanaka K, Mitani T, Niki H, Ogura T, Hiraga S (1996). "RNase E polypeptides lacking a carboxyl-terminal half suppress a mukB mutation in Escherichia coli." J Bacteriol 178(13);3917-25. PMID: 8682798

Leroy02: Leroy A, Vanzo NF, Sousa S, Dreyfus M, Carpousis AJ (2002). "Function in Escherichia coli of the non-catalytic part of RNase E: role in the degradation of ribosome-free mRNA." Mol Microbiol 45(5);1231-43. PMID: 12207692

LinChao99: Lin-Chao S, Wei CL, Lin YT (1999). "RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity." Proc Natl Acad Sci U S A 96(22);12406-11. PMID: 10535935

Liou01: Liou GG, Jane WN, Cohen SN, Lin NS, Lin-Chao S (2001). "RNA degradosomes exist in vivo in Escherichia coli as multicomponent complexes associated with the cytoplasmic membrane via the N-terminal region of ribonuclease E." Proc Natl Acad Sci U S A 98(1);63-8. PMID: 11134527

Liou02a: Liou GG, Chang HY, Lin CS, Lin-Chao S (2002). "DEAD box RhlB RNA helicase physically associates with exoribonuclease PNPase to degrade double-stranded RNA independent of the degradosome-assembling region of RNase E." J Biol Chem 277(43);41157-62. PMID: 12181321

Marchand01: Marchand I, Nicholson AW, Dreyfus M (2001). "Bacteriophage T7 protein kinase phosphorylates RNase E and stabilizes mRNAs synthesized by T7 RNA polymerase." Mol Microbiol 42(3);767-76. PMID: 11722741

Miczak96: Miczak A, Kaberdin VR, Wei CL, Lin-Chao S (1996). "Proteins associated with RNase E in a multicomponent ribonucleolytic complex." Proc Natl Acad Sci U S A 93(9);3865-9. PMID: 8632981

Morita04: Morita T, Kawamoto H, Mizota T, Inada T, Aiba H (2004). "Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli." Mol Microbiol 54(4);1063-75. PMID: 15522087

PrudhommeGenere04: Prud'homme-Genereux A, Beran RK, Iost I, Ramey CS, Mackie GA, Simons RW (2004). "Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'." Mol Microbiol 54(5);1409-21. PMID: 15554978

Py94: Py B, Causton H, Mudd EA, Higgins CF (1994). "A protein complex mediating mRNA degradation in Escherichia coli." Mol Microbiol 14(4);717-29. PMID: 7891559

Py96: Py B, Higgins CF, Krisch HM, Carpousis AJ (1996). "A DEAD-box RNA helicase in the Escherichia coli RNA degradosome." Nature 381(6578);169-72. PMID: 8610017

Regonesi06: Regonesi ME, Del Favero M, Basilico F, Briani F, Benazzi L, Tortora P, Mauri P, Deho G (2006). "Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach." Biochimie 88(2);151-61. PMID: 16139413

Sharma83: Sharma RC, Sargentini NJ, Smith KC (1983). "New mutation (mmrA1) in Escherichia coli K-12 that affects minimal medium recovery and postreplication repair after UV irradiation." J Bacteriol 154(2);743-7. PMID: 6341360

Sharma85: Sharma RC, Smith KC (1985). "A mechanism for rich-medium inhibition of the repair of daughter-strand gaps in the deoxyribonucleic acid of UV-irradiated Escherichia coli K12 uvrA." Mutat Res 146(2);177-83. PMID: 3897844

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

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

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

Vanzo98: Vanzo NF, Li YS, Py B, Blum E, Higgins CF, Raynal LC, Krisch HM, Carpousis AJ (1998). "Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome." Genes Dev 12(17);2770-81. PMID: 9732274


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Tue Nov 25, 2014, biocyc14.