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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.