Note_RNAHalfLives – RNAHalfLives

Name
WID Note_RNAHalfLives
Name RNAHalfLives
 
Comments
Comments Half life data for E. coli mRNAs was found in two papers, Selinger et al. [PUB_0601] and Bernstein et al. [PUB_0602]. The data in the two papers varied widely, and so our results may vary widely based on which data set we used. Bernstein et al. provide half lives at two conditions: E. coli grown at 30°C in LB media and M9 media. We have chosen the data in M9 media because this data set contains more calculated half lives for the EC genes we have mapped to MG genes than the Bernstein LB data or the Selinger data. The mean Bernstein M9 half life of these mapped genes is 4.425 min. This is much lower than the mean for the Selinger half life of 15.6 min (not including stable mRNAs). Régnier el al. [PUB_0603] report that the half life of the bulk of E. coli mRNA is 2.4 minutes at 37°C. Selinger et al. report the half life of total mRNA to be 6.8 minutes. So, the average half life of the Bernstein data is closer to the reported half lives of bulk mRNA. This gave us half lives for 274 MG genes (assuming that the half life of an EC mRNA equals that of an MG mRNA). For the remaining MG genes, we used the average half life, 4.425 min. Half lives for tRNA and rRNA are much longer and were estimated. Various papers provide half lives for tRNAs, we used the value in Bailly et al [PUB_0608]. for Asp-tRNA measured at 37°C to be 45min (2006). We estimated the rRNA half life to be 150min using the information regarding the reference strain in Figure 1 of Kaplan and Apirion, 1975 [PUB_0604].
References
  1. Bailly M, Giannouli S, Blaise M, Stathopoulos C, Kern D, Becker HD. A single tRNA base pair mediates bacterial tRNA-dependent biosynthesis of asparagine. Nucleic Acids Res 34, 6083-94 (2006). WholeCell: PUB_0608, PubMed: 17074748

  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. Kaplan R, Apirion D. Decay of ribosomal ribonucleic acid in Escherichia coli cells starved for various nutrients. J Biol Chem 250, 3174-8 (1975). WholeCell: PUB_0604, PubMed: 1091648

  4. Régnier P, Arraiano CM. Degradation of mRNA in bacteria: emergence of ubiquitous features. Bioessays 22, 235-44 (2000). WholeCell: PUB_0603, PubMed: 10684583

  5. Selinger DW, Saxena RM, Cheung KJ, Church GM, Rosenow C. Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res 13, 216-23 (2003). WholeCell: PUB_0601, PubMed: 12566399

 
Metadata
Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:58