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Escherichia coli K-12 substr. MG1655 Polypeptide: DeaD, DEAD-box RNA helicase



Gene: deaD Accession Numbers: EG10215 (EcoCyc), b3162, ECK3150

Synonyms: csdA, mssB, rhlD

Regulation Summary Diagram: ?

Summary:
The DeaD protein is a DEAD-box RNA helicase that participates in the assembly of the large, but not the small subunit of the ribosome [Charollais04, Kitahara09] and is involved in RNA degradation under low temperature growth conditions [PrudhommeGenere04, Awano07]. DeaD appears to destabilize mRNA secondary structures in the translation initiation region of mRNAs [Butland07]. Recent experiments showed that DeaD may destabilize inhibitory stem-loop structures in the 5' UTR of rpoS, thereby enabling annealing of the small regulatory RNA DsrA [Resch10], and that DeaD activates uvrY mRNA translation by counteracting an inhibitory secondary structure formed between the uvrY mRNA leader and coding region [Vakulskas14].

Reports differed on whether [Bizebard04, Turner07, Stampfl13] or not [Jones96, Lu99a] the RNA helicase activity of purified DeaD requires ATP hydrolysis. The measured ATP-independent unwinding activity may have been due to spontaneous base pair opening [Stampfl13]. The DEAD motif is required for efficient in vitro ATPase and helicase acivities and for in vivo function at 15°C [Turner07, Awano07]. ATP-independent activities of DeaD include stimulation of RNA strand annealing, strand displacement, and RNA chaperone activity [Zhao11b]. Kinetic analysis of the annealing and strand displacement activities of DeaD support the hypothesis that hypothesis that the unwinding activity of DeaD is largely determined by the thermodynamic stability of its substrates [Stampfl13].

DeaD is able to destabilize secondary structure in the translation initiation region of mRNAs, facilitating translation [Butland07].

The DeaD protein was found to be associated with a pre-50S ribosomal particle [Charollais04] and interacts with poly(A) polymerase I [Raynal99], ObgE [Sato05] and RNase E [PrudhommeGenere04], as well as a number of ribosomal and other proteins [Butland07]. The presence of DeaD may assist in the efficient assembly of circularly permuted rRNAs, allowing them to function in the ribosome [Kitahara09].

DeaD is able to replace the function of the RNA helicase RhlB in the degradosome [PrudhommeGenere04]. DeaD can stabilize overexpressed mRNAs [Iost94], including cspA mRNA [Brandi99], or may be involved in selective degradation of cold shock protein mRNAs [Yamanaka01a].mRNAs whose abundance is significantly changed by mutation or overexpression of DeaD at 15°C were identified by microarray analysis [Phadtare12]. Crosslinking immunoprecipitation (HITS-CLIP) showed direct in vivo interactions of DeaD with 39 mRNAs [Vakulskas14].

RhlE as well as CspA and RNase R complement the cold-sensitive phenotype of a deaD mutant [Awano07, Jain08]. An rhlE mutation exacerbates the growth defect of a deaD mutant at 20°C [Jain08].

Deletion of the deaD gene causes a growth defect at low temperature [Jones96, Charollais04, Jagessar10]. Expression of DeaD is induced by cold shock [Jones96]. DeaD has been isolated as a multicopy suppressor of the cold-sensitive phenotype of the smbA2 mutation [Yamanaka94]. It also suppresses the effects of a temperature sensitive mutation in ribosomal protein S2 (rpsB(ts)) [Toone91, Moll02] by restoring assembly of both S1 and S2 with the ribosome at the non-permissive temperature [Moll02]. A Tn10 insertion mutant in deaD restores colony-forming ability to an rne mutant [Tamura12]. Carbon source utilization by the rne deaD double mutant differs from both wild type and deaD single mutants [Tamura13]. A deaD mutant accumulates unprocessed 23S rRNA and shows an altered ribosome profile [Jain08, Jagessar10], accumulating ribosome large subunit assembly intermediates [Peil08]. In a deaD mutant strain, DsrA-rpoS duplex formation does not occur [Resch10].

A mutant strain with deletions of all five DEAD-box proteins (ΔdeaD dbpA rhlB rhlE srmB) is viable. Alternative growth conditions such as growth in minimal media or at elevated temperatures can alleviate the growth defects of this strain [Jagessar10].

CsdA: "cold-shock DEAD-box protein A" [Jones96]

RhlD: "RNA helicase-like" [Kalman91]

Reviews: [Inouye04, Iost06, Carpousis07, ElSharoud07, Phadtare10, Phadtare11, Shajani11, Kaberdin13, Iost13, Barria13]

Citations: [LopezRamirez11, Pierce11, Chen13b]

Locations: cytosol

Map Position: [3,303,993 <- 3,305,882] (71.21 centisomes)
Length: 1890 bp / 629 aa

Molecular Weight of Polypeptide: 70.546 kD (from nucleotide sequence), 70.0 kD (experimental) [Jones96 ]

Unification Links: ASAP:ABE-0010392 , CGSC:33472 , DIP:DIP-35752N , EchoBASE:EB0211 , EcoGene:EG10215 , EcoliWiki:b3162 , Mint:MINT-1219396 , OU-Microarray:b3162 , PortEco:deaD , PR:PRO_000022422 , Pride:P0A9P6 , Protein Model Portal:P0A9P6 , RefSeq:NP_417631 , RegulonDB:EG10215 , SMR:P0A9P6 , String:511145.b3162 , Swiss-Model:P0A9P6 , UniProt:P0A9P6

Relationship Links: InterPro:IN-FAMILY:IPR000629 , InterPro:IN-FAMILY:IPR001650 , InterPro:IN-FAMILY:IPR005580 , InterPro:IN-FAMILY:IPR011545 , InterPro:IN-FAMILY:IPR014001 , InterPro:IN-FAMILY:IPR014014 , InterPro:IN-FAMILY:IPR021046 , InterPro:IN-FAMILY:IPR027417 , Pfam:IN-FAMILY:PF00270 , Pfam:IN-FAMILY:PF00271 , Pfam:IN-FAMILY:PF03880 , Pfam:IN-FAMILY:PF12343 , Prosite:IN-FAMILY:PS00039 , Prosite:IN-FAMILY:PS51192 , Prosite:IN-FAMILY:PS51194 , Prosite:IN-FAMILY:PS51195 , Smart:IN-FAMILY:SM00487 , Smart:IN-FAMILY:SM00490

In Paralogous Gene Group: 502 (2 members)

GO Terms:

Biological Process: GO:0000027 - ribosomal large subunit assembly Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Charollais04]
GO:0006200 - ATP catabolic process Inferred by computational analysis Inferred from experiment [Turner07, Bizebard04, GOA06, GOA01]
GO:0006401 - RNA catabolic process Inferred from experiment Inferred by computational analysis [GOA06, PrudhommeGenere04]
GO:0045727 - positive regulation of translation Inferred from experiment [Vakulskas14]
GO:0048255 - mRNA stabilization Inferred from experiment [Iost94]
GO:0070417 - cellular response to cold Inferred from experiment Inferred by computational analysis [GOA01, Jagessar10, Jones96]
GO:0006950 - response to stress Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003724 - RNA helicase activity Inferred from experiment [Jones96]
GO:0004004 - ATP-dependent RNA helicase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Turner07, Bizebard04]
GO:0005515 - protein binding Inferred from experiment [Raynal99, Sato05]
GO:0033592 - RNA strand annealing activity Inferred from experiment [Stampfl13]
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:0004386 - helicase activity Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0008026 - ATP-dependent helicase activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0016817 - hydrolase activity, acting on acid anhydrides Inferred by computational analysis [GOA01]
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: cell structure ribosomes

Activates: mntR Inferred from experiment [Vakulskas14] , sdiA Inferred from experiment [Vakulskas14] , uvrY Inferred from experiment [Vakulskas14]

Regulated Transcription Units (7 total): ?

Notes:

Essentiality data for deaD 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:
Last-Curated ? 21-Apr-2014 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Lu99a, Jones96, Jones96]
 
Chain 2 -> 629
[UniProt09]
UniProt: Cold-shock DEAD box protein A;
Protein-Segment 6 -> 34
[UniProt10]
UniProt: Q motif; Sequence Annotation Type: short sequence motif;
Conserved-Region 37 -> 208
[UniProt09]
UniProt: Helicase ATP-binding;
Nucleotide-Phosphate-Binding-Region 50 -> 57
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Protein-Segment 156 -> 159
[UniProt10]
UniProt: DEAD box; Sequence Annotation Type: short sequence motif;
Mutagenesis-Variant 157
[Turner07, UniProt11]
Alternate sequence: E → Q; UniProt: Abolishes ATPase activity, drastically reduces helicase activity. In vivo acts as a dominant negative mutation in the presence of the wild-type protein at low temperature.
Conserved-Region 232 -> 379
[UniProt09]
UniProt: Helicase C-terminal;
Sequence-Conflict 444
[Toone91, UniProt10]
Alternate sequence: A → G; UniProt: (in Ref. 1; AAA23674);
Protein-Segment 568 -> 629
[UniProt09]
UniProt: Arg/Glu/Gly-rich; Sequence Annotation Type: compositionally biased region;


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 ].
10/20/97 Gene b3162 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10215; confirmed by SwissProt match.


References

Awano07: Awano N, Xu C, Ke H, Inoue K, Inouye M, Phadtare S (2007). "Complementation analysis of the cold-sensitive phenotype of the Escherichia coli csdA deletion strain." J Bacteriol 189(16);5808-15. PMID: 17557820

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

Barria13: Barria C, Malecki M, Arraiano CM (2013). "Bacterial adaptation to cold." Microbiology 159(Pt 12);2437-43. PMID: 24068238

Bizebard04: Bizebard T, Ferlenghi I, Iost I, Dreyfus M (2004). "Studies on Three E. coli DEAD-Box Helicases Point to an Unwinding Mechanism Different from that of Model DNA Helicases." Biochemistry 43(24);7857-66. PMID: 15196029

Brandi99: Brandi A, Spurio R, Gualerzi CO, Pon CL (1999). "Massive presence of the Escherichia coli 'major cold-shock protein' CspA under non-stress conditions." EMBO J 18(6);1653-9. PMID: 10075935

Butland07: Butland G, Krogan NJ, Xu J, Yang WH, Aoki H, Li JS, Krogan N, Menendez J, Cagney G, Kiani GC, Jessulat MG, Datta N, Ivanov I, Abouhaidar MG, Emili A, Greenblatt J, Ganoza MC, Golshani A (2007). "Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs." J Cell Biochem 100(3);642-52. PMID: 16983699

Carpousis07: Carpousis AJ (2007). "The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E." Annu Rev Microbiol 61;71-87. PMID: 17447862

Charollais04: Charollais J, Dreyfus M, Iost I (2004). "CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit." Nucleic Acids Res 32(9);2751-9. PMID: 15148362

Chen13b: Chen SS, Williamson JR (2013). "Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry." J Mol Biol 425(4);767-79. PMID: 23228329

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

ElSharoud07: El-Sharoud WM, Graumann PL (2007). "Cold shock proteins aid coupling of transcription and translation in bacteria." Sci Prog 90(Pt 1);15-27. PMID: 17455763

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

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."

Inouye04: Inouye M, Phadtare S (2004). "Cold shock response and adaptation at near-freezing temperature in microorganisms." Sci STKE 2004(237);pe26. PMID: 15199224

Iost06: Iost I, Dreyfus M (2006). "DEAD-box RNA helicases in Escherichia coli." Nucleic Acids Res 34(15);4189-97. PMID: 16935881

Iost13: Iost I, Bizebard T, Dreyfus M (2013). "Functions of DEAD-box proteins in bacteria: current knowledge and pending questions." Biochim Biophys Acta 1829(8);866-77. PMID: 23415794

Iost94: Iost I, Dreyfus M (1994). "mRNAs can be stabilized by DEAD-box proteins." Nature 372(6502);193-6. PMID: 7526223

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

Jagessar10: Jagessar KL, Jain C (2010). "Functional and molecular analysis of Escherichia coli strains lacking multiple DEAD-box helicases." RNA 16(7);1386-92. PMID: 20484467

Jain08: Jain C (2008). "The E. coli RhlE RNA helicase regulates the function of related RNA helicases during ribosome assembly." RNA 14(2):381-9. PMID: 18083833

Jones96: Jones PG, Mitta M, Kim Y, Jiang W, Inouye M (1996). "Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli." Proc Natl Acad Sci U S A 93(1);76-80. PMID: 8552679

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

Kaberdin13: Kaberdin VR, Blasi U (2013). "Bacterial helicases in post-transcriptional control." Biochim Biophys Acta 1829(8);878-83. PMID: 23291566

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

Kitahara09: Kitahara K, Suzuki T (2009). "The ordered transcription of RNA domains is not essential for ribosome biogenesis in Escherichia coli." Mol Cell 34(6);760-6. PMID: 19560426

LopezRamirez11: Lopez-Ramirez V, Alcaraz LD, Moreno-Hagelsieb G, Olmedo-Álvarez G (2011). "Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins." J Mol Evol 72(4);413-31. PMID: 21437710

Lu99a: Lu J, Aoki H, Ganoza MC (1999). "Molecular characterization of a prokaryotic translation factor homologous to the eukaryotic initiation factor eIF4A." Int J Biochem Cell Biol 31(1);215-29. PMID: 10216955

Moll02: Moll I, Grill S, Grundling A, Blasi U (2002). "Effects of ribosomal proteins S1, S2 and the DeaD/CsdA DEAD-box helicase on translation of leaderless and canonical mRNAs in Escherichia coli." Mol Microbiol 44(5);1387-96. PMID: 12068815

Peil08: Peil L, Virumae K, Remme J (2008). "Ribosome assembly in Escherichia coli strains lacking the RNA helicase DeaD/CsdA or DbpA." FEBS J 275(15);3772-82. PMID: 18565105

Phadtare10: Phadtare S, Severinov K (2010). "RNA remodeling and gene regulation by cold shock proteins." RNA Biol 7(6);788-95. PMID: 21045540

Phadtare11: Phadtare S (2011). "Unwinding activity of cold shock proteins and RNA metabolism." RNA Biol 8(3);394-7. PMID: 21445001

Phadtare12: Phadtare S (2012). "Escherichia coli cold-shock gene profiles in response to over-expression/deletion of CsdA, RNase R and PNPase and relevance to low-temperature RNA metabolism." Genes Cells 17(10);850-74. PMID: 22957931

Pierce11: Pierce A, Gillette D, Jones PG (2011). "Escherichia coli cold shock protein CsdA effects an increase in septation and the resultant formation of coccobacilli at low temperature." Arch Microbiol 193(5);373-84. PMID: 21359956

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

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

Resch10: Resch A, Vecerek B, Palavra K, Blasi U (2010). "Requirement of the CsdA DEAD-box helicase for low temperature riboregulation of rpoS mRNA." RNA Biol 7(6);796-802. PMID: 21045550

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

Sato05: Sato A, Kobayashi G, Hayashi H, Yoshida H, Wada A, Maeda M, Hiraga S, Takeyasu K, Wada C (2005). "The GTP binding protein Obg homolog ObgE is involved in ribosome maturation." Genes Cells 10(5);393-408. PMID: 15836769

Shajani11: Shajani Z, Sykes MT, Williamson JR (2011). "Assembly of bacterial ribosomes." Annu Rev Biochem 80;501-26. PMID: 21529161

Stampfl13: Stampfl S, Doetsch M, Beich-Frandsen M, Schroeder R (2013). "Characterization of the kinetics of RNA annealing and strand displacement activities of the E. coli DEAD-box helicase CsdA." RNA Biol 10(1);149-56. PMID: 23291905

Tamura12: Tamura M, Kers JA, Cohen SN (2012). "Second-site suppression of RNase E essentiality by mutation of the deaD RNA helicase in Escherichia coli." J Bacteriol 194(8);1919-26. PMID: 22328678

Tamura13: Tamura M, Moore CJ, Cohen SN (2013). "Nutrient dependence of RNase E essentiality in Escherichia coli." J Bacteriol 195(6);1133-41. PMID: 23275245

Toone91: Toone WM, Rudd KE, Friesen JD (1991). "deaD, a new Escherichia coli gene encoding a presumed ATP-dependent RNA helicase, can suppress a mutation in rpsB, the gene encoding ribosomal protein S2." J Bacteriol 173(11);3291-302. PMID: 2045359

Turner07: Turner AM, Love CF, Alexander RW, Jones PG (2007). "Mutational analysis of the Escherichia coli DEAD box protein CsdA." J Bacteriol 189(7);2769-76. PMID: 17259309

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."

Vakulskas14: Vakulskas CA, Pannuri A, Cortes-Selva D, Zere TR, Ahmer BM, Babitzke P, Romeo T (2014). "Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures." Mol Microbiol 92(5);945-58. PMID: 24708042

Yamanaka01a: Yamanaka K, Inouye M (2001). "Selective mRNA degradation by polynucleotide phosphorylase in cold shock adaptation in Escherichia coli." J Bacteriol 183(9);2808-16. PMID: 11292800

Yamanaka94: Yamanaka K, Ogura T, Koonin EV, Niki H, Hiraga S (1994). "Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia coli." Mol Gen Genet 243(1);9-16. PMID: 8190075

Zhao11b: Zhao X, Jain C (2011). "DEAD-box proteins from Escherichia coli exhibit multiple ATP-independent activities." J Bacteriol 193(9);2236-41. PMID: 21378185


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Tue Nov 25, 2014, BIOCYC13B.