Escherichia coli K-12 substr. MG1655 tRNA: tRNAalaV

Gene: alaV Accession Numbers: EG30010 (EcoCyc), b0203, ECK0203

Superclasses: a tRNAala

Regulation Summary Diagram: ?

Regulation summary diagram for alaV

tRNA(alaV) is one of five alanine tRNAs.

tRNA(alaV) interacts with tmRNA[Gillet01].

tRNAs are the adapters that allow synthesis of proteins from mRNAs. Each tRNA carries a specific amino acid to the ribosome for protein synthesis. There, the tRNA recognizes an RNA codon with its own three-nucleotide anticodon, thus allowing synthesis of a specific peptide based on an mRNA template.

tRNAs are processed to their active, mature forms by RNA cleavage and by modification of their bases. RNA cleavage consists of removal of both 5' and 3' extensions in a multistep process involving many RNases [Morl01]. RNases taking part in tRNA processing include ribonuclease E, RNase BN, RNase D, ribonuclease II, and RNase T. tRNAs are also subject to a wide variety of base modifications catalyzed by proteins such as tRNA-dihydrouridine synthase A, tRNA(i6A37) synthase, isopentenyl-adenosine A37 tRNA methylthiolase, tRNA-specific 2-thiouridylase, fused 5-methylaminomethyl-2-thiouridine-forming methyltransferase and FAD-dependent demodification enzyme, tRNA-guanine transglycosylase, tRNA m7G46 methyltransferase, tRNA pseudouridine 13 synthase, tRNA pseudouridine 65 synthase, tRNA pseudouridine 55 synthase, tRNA pseudouridine synthase I, tRNA (Gm18) 2'-O-methyltransferase, and tRNA m5U54 methyltransferase.

Mature tRNAs are linked via a 3' CCA sequence to their cognate amino acid in an ATP-dependent fashion by the appropriate amino-acid-tRNA synthetase, as shown in the tRNA charging. Subsequently, these charged tRNAs interact with the ribosome and template mRNA to generate polypeptides. The discovery of the role of tRNA in protein synthesis is reviewed in detail in [Siekevitz81].

Bases A73 and G20 are key determinants of tRNA(ala) identity, as is the G3-U70 pairing in the acceptor stem [Tamura, Ramos97].

Map Position: [225,500 -> 225,575] (4.86 centisomes, 17°)
Length: 76 bp

Anticodon: UGC

Reactions known to consume the compound:

tRNA charging :
a tRNAala + L-alanine + ATP + H+ → an L-alanyl-[tRNAala] + AMP + diphosphate

Reactions known to produce the compound:

tRNA processing :
a tRNA precursor with a short 3' extension → an uncharged tRNA + n a nucleoside 5'-monophosphate
a tRNA precursor with a short 3' extension + n phosphate → an uncharged tRNA + n a ribonucleoside diphosphate
a tRNA precursor with a 5' extension + H2O → an uncharged tRNA + a single-stranded RNA

Not in pathways:
an N-modified aminoacyl-[tRNA] + H2O → an uncharged tRNA + an N-modified amino acid + 2 H+
a D-aminoacyl-[tRNA] + H2O → a D-amino acid + an uncharged tRNA + 2 H+

Not in pathways:
a tRNA precursor + H2O → a tRNA + a nucleoside 5'-monophosphate

tRNA processing :
a tRNA precursor with a 5' extension and a short 3' extension + H2O → a tRNA precursor with a short 3' extension + a single-stranded RNA
a tRNA precursor with a 5' extension + H2O → an uncharged tRNA + a single-stranded RNA

Not in pathways:
YhaV endonuclease degradation substrate mRNA + H2O → 2 a single-stranded RNA
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
RNase E degradation substrate mRNA + n H2O → n a single-stranded RNA
YhaV endonuclease degradation substrate rRNA + H2O → 2 a single-stranded RNA
RNase III mRNA processing substrate + 2 H2O → RNase III processing product mRNA + 2 a single-stranded RNA
23S rRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
an mRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
RNase G degradation substrate mRNA + H2O → 2 a single-stranded RNA
9S rRNA + 2 H2O → 5S rRNA + 2 a single-stranded RNA
RNase E mRNA processing substrate + n H2O → RNase E processing product mRNA + n a single-stranded RNA

Reactions known to both consume and produce the compound:

Not in pathways:
a single-stranded RNA + phosphate ↔ a single-stranded RNA + a nucleoside diphosphate

In Reactions of unknown directionality:

Not in pathways:
rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for alaV

Unification Links: ASAP:ABE-0000682 , CGSC:1036 , EchoBASE:EB4173 , EcoGene:EG30010 , EcoliWiki:b0203 , OU-Microarray:b0203 , PortEco:alaV , RegulonDB:EG30010

GO Terms:

Molecular Function: GO:0030533 - triplet codon-amino acid adaptor activity
Cellular Component: GO:0005737 - cytoplasm
GO:0005829 - cytosol

MultiFun Terms: information transfer RNA related tRNA

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b0203 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG30010.

Last-Curated ? 26-Apr-2006 by Shearer A , SRI International


Gillet01: Gillet R, Felden B (2001). "Transfer RNA(Ala) recognizes transfer-messenger RNA with specificity; a functional complex prior to entering the ribosome?." EMBO J 20(11);2966-76. PMID: 11387229

Morl01: Morl M, Marchfelder A (2001). "The final cut. The importance of tRNA 3'-processing." EMBO Rep 2(1);17-20. PMID: 11252717

Ramos97: Ramos A, Varani G (1997). "Structure of the acceptor stem of Escherichia coli tRNA Ala: role of the G3.U70 base pair in synthetase recognition." Nucleic Acids Res 25(11);2083-90. PMID: 9153306

Siekevitz81: Siekevitz P, Zamecnik PC (1981). "Ribosomes and protein synthesis." J Cell Biol 91(3 Pt 2);53s-65s. PMID: 7033244

Tamura: Tamura K, Asahara H, Himeno H, Hasegawa T, Shimizu M "Identity elements of Escherichia coli tRNA(Ala)." J Mol Recognit 4(4);129-32. PMID: 1799462

Other References Related to Gene Regulation

Afflerbach98: Afflerbach H, Schroder O, Wagner R (1998). "Effects of the Escherichia coli DNA-binding protein H-NS on rRNA synthesis in vivo." Mol Microbiol 28(3);641-53. PMID: 9632265

Artsimovitch04: Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG (2004). "Structural basis for transcription regulation by alarmone ppGpp." Cell 117(3);299-310. PMID: 15109491

Condon95: Condon C, Squires C, Squires CL (1995). "Control of rRNA transcription in Escherichia coli." Microbiol Rev 59(4);623-45. PMID: 8531889

Dennis04: Dennis PP, Ehrenberg M, Bremer H (2004). "Control of rRNA synthesis in Escherichia coli: a systems biology approach." Microbiol Mol Biol Rev 68(4);639-68. PMID: 15590778

Gralla05: Gralla JD (2005). "Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein." Mol Microbiol 55(4);973-7. PMID: 15686546

Hillebrand05: Hillebrand A, Wurm R, Menzel A, Wagner R (2005). "The seven E. coli ribosomal RNA operon upstream regulatory regions differ in structure and transcription factor binding efficiencies." Biol Chem 386(6);523-34. PMID: 16006239

Hirvonen01: Hirvonen CA, Ross W, Wozniak CE, Marasco E, Anthony JR, Aiyar SE, Newburn VH, Gourse RL (2001). "Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli." J Bacteriol 183(21);6305-14. PMID: 11591675

Lemke11: Lemke JJ, Sanchez-Vazquez P, Burgos HL, Hedberg G, Ross W, Gourse RL (2011). "Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA." Proc Natl Acad Sci U S A 108(14);5712-7. PMID: 21402902

Lindahl86: Lindahl L, Zengel JM (1986). "Ribosomal genes in Escherichia coli." Annu Rev Genet 20;297-326. PMID: 2434021

Maciag11a: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Neidhardt96: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE "Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition." American Society for Microbiology, Washington, D.C., 1996.

Newlands93: Newlands JT, Gaal T, Mecsas J, Gourse RL (1993). "Transcription of the Escherichia coli rrnB P1 promoter by the heat shock RNA polymerase (E sigma 32) in vitro." J Bacteriol 175(3);661-8. PMID: 8423142

Paul04: Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, Foster JW, Gourse RL (2004). "DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP." Cell 118(3);311-22. PMID: 15294157

Paul04a: Paul BJ, Ross W, Gaal T, Gourse RL (2004). "rRNA Transcription in Escherichia coli." Annu Rev Genet 38:749-70. PMID: 15568992

Pul05: Pul U, Wurm R, Lux B, Meltzer M, Menzel A, Wagner R (2005). "LRP and H-NS--cooperative partners for transcription regulation at Escherichia coli rRNA promoters." Mol Microbiol 58(3);864-76. PMID: 16238633

Schneider03b: Schneider DA, Gourse RL (2003). "Changes in Escherichia coli rRNA promoter activity correlate with changes in initiating nucleoside triphosphate and guanosine 5' diphosphate 3'-diphosphate concentrations after induction of feedback control of ribosome synthesis." J Bacteriol 185(20);6185-91. PMID: 14526030

Zengel94: Zengel JM, Lindahl L (1994). "Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli." Prog Nucleic Acid Res Mol Biol 47;331-70. PMID: 7517053

Zhang02d: Zhang X, Dennis P, Ehrenberg M, Bremer H (2002). "Kinetic properties of rrn promoters in Escherichia coli." Biochimie 84(10);981-96. PMID: 12504278

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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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