MG_0004 – transfer-messenger RNA, tmRNA, MCS6, 10Sa RNA

Name
WID MG_0004 View in model
Name transfer-messenger RNA, tmRNA, MCS6, 10Sa RNA View in model
Symbol ssrA
Cross references CMR: MG_0004
 
Classification
Type sRNA View in model
 
Structure
Structure 404042409430 MG_0003 MG_0004 MG_322 MG_323 MG_324 MG_326 MG_515 View in model
Sequence Chromosome: Mgenitalium_Chr_1, Coordinate: 406542 (nt), Length: 388 (nt), Direction: Reverse, G/C content: 37.1%, Sequence:
1
51
101
151
201
251
301
351
TGGTGGAGATGACGGGAATCGAACCCGTTTCCATAAAGGACACAACAAAC
AGCTTCTACATTTTAGTTTTGTGGATTTTTGTCTTGTTTCCAATTGATCA
CAAAACAATCATGGAAACAACAAGTTCTATTTTTAAAGGTTAAATTGAAC
GATTTAACCTCGAGTCATAAACTATGACAGCTAGCAAACTATGACTATTC
ACCAGCTGTAGCTTTAGTATCTACTTATGCAAAAGCAAAGTTAACACTTG
CTTGTTGGTTAATGATCAAATTTGGATCTACCAACACTTCGTTATTTTCT
TTGTCGGTTATTGAACCTAGCGCTGTAAGGGGCATACCCCAATGCTACTG
TTTGTCTATCAGCATTATGTCAAACCCAAAACATCCCC
50
100
150
200
250
300
350
388
View in model
Transcription unit TU_227 View in model
Empirical formula (pH 7.5) H4145C3756N1568O2721P388
Molecular weight (pH 7.5; Da) 126804.64 View in model
 
Functional genomics
Is essential
Yes (Show evidence)
View in model
Relative expression
147.374 (dimensionless) (Show evidence)
View in model
Half life
89.0 (min) (Show evidence)
View in model
Amino acid ALA View in model
Extinction coefficient 
(260 nm, 25C, pH 7.0)
3893500
pI 4.03
 
Comments
Comments Has tRNA-like structure with an mRNA-like domain. The tRNA-like domain is charged by alanyl tRNA synthetase and with the help of SmpB (MG_059_MONOMER) replaces the tRNA of stalled ribosomes (ribosomes stalled for example due to mRNA damage, mRNA lacking a stop codon, rare codons, or natural stall sequences), adding an alanine to the stalled peptide. Next the mRNA-like domain is translated by the ribosome add the C-terminal amino acid sequence DKENNEVLVEPNLIINQQASVNFAFA to the stalled peptide [PUB_0020]. The added C-terminal tag marks the peptide for degradation [PUB_0014]. MG_0004 has a half-life of 89 min [PUB_0396]. The expression of MG_0004 is 5% that of 5S RNA [PUB_0400].
References
  1. Eds Lund P. Molecular Chaperones in the Cell. Oxford University Press, New York (2001). WholeCell: PUB_0014, ISBN: 9780199638673

  2. Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99, 9697-702 (2002). WholeCell: PUB_0602, PubMed: 12119387

  3. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA 3rd, Smith HO, Venter JC. Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A 103, 425-30 (2006). WholeCell: PUB_0193, PubMed: 16407165

  4. Karzai AW, Roche ED, Sauer RT. The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat Struct Biol 7, 449-55 (2000). WholeCell: PUB_0020, PubMed: 10881189

  5. Keiler KC, Shapiro L. tmRNA in Caulobacter crescentus is cell cycle regulated by temporally controlled transcription and RNA degradation. J Bacteriol 185, 1825-30 (2003). WholeCell: PUB_0396, PubMed: 12618446

  6. ... 2 more

  7. Moore SD, Sauer RT. Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli. Mol Microbiol 58, 456-66 (2005). WholeCell: PUB_0400, PubMed: 16194232

  8. Weiner J 3rd, Zimmerman CU, Göhlmann HW, Herrmann R. Transcription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures. Nucleic Acids Res 31, 6306-20 (2003). WholeCell: PUB_0569, PubMed: 14576319

 
Metadata
Created 2012-10-01 15:07:09
Last updated 2012-10-01 15:12:37