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Table 1 Estimated coefficients and P- values of the growth rate-dependent mRNA half-life models

From: Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates

Parameter Dependent variable: half-life
  μ= 0.10 h −1 μ= 0.20 h −1 μ= 0.40 h −1 μ= 0.63 h −1
  Est. Coeff. P-value Est. Coeff. P-value Est. Coeff. P-value Est. Coeff. P-value
[mRNA] −0.91 <10 −226 −0.80 1.4E10 −223 −0.80 2.9E10 −225 −0.79 4.3E10 −205
CAI 0.13 2.6E10 −15 0.18 1.7E10 −15 0.18 5.5E10 −17 0.25 7.9E10 −28
ORF length −0.14 2.8E10 −5 −0.16 2.2E10 −4 −0.19 1.1E10 −5 −0.12 7.7E10 −3
5UTR + ORF length 0.05 9.4E10 −2 0.06 1.3E10 −1 0.14 9.1E10 −4 0.09 5.2E10 −2
5’UTR + ORF GC% −0.05 4.4E10 −4 −0.07 3.1E10 −4 −0.10 1.3E10 −7 −0.09 8.0E10 −6
Essential genes 0.06 8.1E10 −3 0.12 4.4E10 −5 0.10 2.7E10 −4 0.06 4.5E10 −2
No. of genes in operon         
1 0.29 2.3E10 −1 0.55 8.1E10 −2 0.46 1.4E10 −1 0.43 2.0E10 −1
2 −0.15 2.4E10 −3 −0.16 1.1E10 −2 −0.29 3.8E10 −6 −0.09 1.7E10 −1
3 −0.16 1.3E10 −3 −0.21 2.0E10 −3 −0.31 2.3E10 −6 −0.16 2.1E10 −2
4 −0.10 8.2E10 −2 −0.10 1.9E10 −1 −0.19 9.0E10 −3 −0.11 1.5E10 −1
5 −0.02 7.8E10 −1 −0.06 4.3E10 −1 −0.14 8.1E10 −2 −0.06 4.6E10 −1
6 −0.14 3.2E10 −2 −0.09 3.1E10 −1 −0.12 1.6E10 −1 −0.11 2.2E10 −1
7 0.03 7.1E10 −1 0.08 4.0E10 −1 0.06 5.4E10 −1 0.08 4.3E10 −1
8 −0.07 6.3E10 −1 −0.07 6.9E10 −1 −0.04 8.3E10 −1 −0.01 9.4E10 −1
9 −0.08 3.9E10 −1 0.04 7.2E10 −1 0.04 7.4E10 −1 −0.03 8.3E10 −1
10 −0.13 3.1E10 −1 −0.11 5.2E10 −1 −0.10 5.1E10 −1 0.05 7.5E10 −1
11 −0.29 4.1E10 −1 −0.52 2.4E10 −1 −0.43 3.3E10 −1 −0.65 1.7E10 −1
12 0.45 3.3E10 −4 0.50 2.2E10 −3 0.74 4.0E10 −6 0.84 1.3E10 −6
13 0.48 1.8E10 −4 0.49 3.3E10 −3 0.59 2.9E10 −4 0.31 8.1E10 −2
16 −0.12 6.2E10 −1 −0.36 2.6E10 −1 −0.28 3.7E10 −1 −0.48 1.6E10 −1
COG annotation         
[C] −0.00 1.0E10 −0 0.02 8.8E10 −1 0.05 7.5E10 −1 −0.01 9.3E10 −1
[D] 0.39 8.2E10 −13 0.53 5.8E10 −14 0.59 6.2E10 −18 0.54 1.3E10 −13
[E] −0.21 6.5E10 −2 −0.23 1.3E10 −1 −0.23 1.2E10 −1 −0.41 1.0E10 −2
[F] 0.01 8.4E10 −1 0.05 3.1E10 −1 0.06 2.7E10 −1 0.23 1.8E10 −5
[G] −0.13 6.6E10 −2 −0.16 7.5E10 −2 −0.16 8.4E10 −2 0.24 1.4E10 −2
[H] 0.12 2.0E10 −2 0.20 4.7E10 −3 0.20 3.6E10 −3 0.14 6.3E10 −2
[I] −0.12 4.4E10 −2 −0.18 1.7E10 −2 −0.24 1.4E10 −3 −0.22 6.1E10 −3
[J] 0.20 6.2E10 −3 0.21 2.6E10 −2 0.23 1.3E10 −2 0.31 2.4E10 −3
[K] 0.10 7.2E10 −2 0.04 5.5E10 −1 0.06 3.8E10 −1 −0.03 6.8E10 −1
[L] −0.01 8.4E10 −1 −0.05 4.4E10 −1 −0.07 2.7E10 −1 −0.12 6.6E10 −2
[M] 0.13 2.4E10 −2 0.11 1.6E10 −1 0.02 7.5E10 −1 −0.02 8.3E10 −1
[N] −0.12 3.3E10 −2 −0.15 4.3E10 −2 −0.14 3.6E10 −2 −0.11 1.3E10 −1
[O] 0.16 3.0E10 −1 0.25 2.0E10 −1 0.25 1.9E10 −1 0.28 1.7E10 −1
[P] −0.10 8.7E10 −1 −0.12 1.1E10 −1 −0.11 1.5E10 −1 −0.13 1.2E10 −1
[Q] −0.19 2.4E10 −3 −0.25 2.2E10 −3 −0.19 1.5E10 −2 −0.12 1.5E10 −1
[R] −0.08 5.4E10 −1 −0.12 4.6E10 −1 −0.20 2.2E10 −1 −0.16 3.5E10 −1
[S] 0.01 8.8E10 −1 −0.01 8.0E10 −1 −0.04 4.9E10 −1 −0.03 6.1E10 −1
[T] −0.10 2.7E10 −2 −0.12 5.4E10 −2 −0.10 1.1E10 −1 −0.12 5.5E10 −2
[U] 0.15 4.2E10 −2 0.21 2.6E10 −2 0.30 1.3E10 −3 0.05 5.9E10 −1
[V] −0.19 9.8E10 −2 −0.22 1.4E10 −1 −0.29 4.8E10 −2 −0.31 5.0E10 −2
Cell location         
Cytoplasmic −0.07 4.0E10 −1 −0.08 4.3E10 −1 N.S N.S
Inn. Mb. Lipo. −0.12 1.1E10 −1 −0.11 2.6E10 −1 N.S N.S
Int. Mb. Pr. −0.20 3.9E10 −1 −0.27 3.8E10 −1 N.S N.S
Mb. Anchored 0.04 6.3E10 −1 0.02 8.6E10 −1 N.S N.S
Mb. Lipo. −0.04 6.6E10 −1 −0.11 3.4E10 −1 N.S N.S
Out. Mb. B-Bar Pr. 0.48 1.4E10 −1 0.55 1.9E10 −1 N.S N.S
Out. Mb. Lipo. 0.34 3.7E10 −2 0.48 2.4E10 −2 N.S N.S
Periplasmic −0.20 7.4E10 −1 −0.21 1.5E10 −1 N.S N.S
Unknown −0.23 3.8E10 −2 −0.27 1.0E10 −2 N.S N.S
Peptide signal −0.09 5.4E10 −2 −0.12 5.8E10 −2 N.S N.S
Adjusted R 2 0.74 0.56 0.57 0.51
  1. The coefficients were estimated by the minimization of least squares.
  2. [mRNA]: mRNA concentration. CAI: codon adaptation index. 5’UTR + ORF GC%: percentage of G and C bases in combined 5’UTR and ORF sequences. No. of genes in the operon: Number of genes in the operon in which the gene is located. COG annotation – [C]: Energy production and conversion, [D]: Cell cycle control, cell division, chromosome partitioning, [E] Amino acid transport and metabolism, [F]: Nucleotide transport and metabolism, [G]: Carbohydrate transport and metabolism, [H]: Coenzyme transport and metabolism, [I]: Lipid transport and metabolism, [J]: Translation, ribosomal structure and biogenesis, [K]: Transcription, [L]: Replication, recombination and repair, [M]: Cell wall/membrane/envelope biogenesis, [N]: Cell motility, [O]: Posttranslational modification, protein turnover, chaperones, [P]: Inorganic ion transport and metabolism, [Q]: Secondary metabolite biosynthesis, transport and catabolism, [R]: General function prediction only, [S]: Function unknown, [T]: Signal transduction mechanisms, [U]: Intracellular trafficking, secretion, and vesicular transport, [V]: Defense mechanisms. Cell location: Location of the gene product within the cell – Inn. Mb. Lipo.: inner membrane lipoprotein, Int. Mb. Pr.: integral membrane protein, Mb. Anchored: anchored in the membrane, Mb. Lipo.: membrane lipoprotein, Out. Mb. B-Bar Pr.: outer membrane B-barrel protein, Out. Mb. Lipo.: outer membrane lipoprotein. N.S indicates that the parameter was not selected by the AIC algorithm. Only parameters selected at least once by the AIC algorithm are shown. Model determinants (P-value ≤ 0.05) are displayed in bold.