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Table 1 Comparisons of translational power

From: Differences in codon bias cannot explain differences in translational power among microbes

Comparison organism

rrn copy#a

Specific growth rateb (culture)c (hr-1)

Actual growth temp.d (cor.)e

Compared byf

E. coli comp. growth rateg (hr-1)

Translational powerh

Ref.

Sphingopyxis alaskensis

1

0.29 (B)

30°C (1.80)

RCi

>1.73j

<17%j

[39]

sulfate reducing strain PT2k

(2)

0.40 (B)

23°C (3.34)

RNA

>1.73j

<17%j

[91]

Streptomyces coelicolor

6

0.54 (B)

30°C (1.80)

RNA

>1.73j

<21%j

[40]

Halobacterium cutirubrum

2

0.10 (B)

37°C

rRNA

0.49

22%

[37]

Rickettsia prowazekii

1

0.09 (B)

34°C (1.28)

RCi

0.37

24%

[38]

Synechococcus sp. 6301

(2)

0.16 (C)

39°C (0.85)

RNA

0.36

42%

[92]

Streptomyces hygroscopicus

(6)

0.58 – 0.90l (B, C)

28°C (2.14)

RNA

0.82 – >1.73j, l

<42%j – 110%l

[93]

Megasphaera elsdenii

-

0.20 (C)

39°C (0.85)

RNA

0.46

44%

[94]

Bacillus cereus

6

0.61 (C)

34°C (1.28)

RNA

1.22

51%

[95]

Selenomonas ruminantium

-

0.30 – 0.43l (C)

39°C (0.85)

RNA

0.35 – 0.88l

50% – 78%l

[96, 97]

Salmonella enterica

7

1.66 (B)

37°C

rRNA

1.63

102%

[1]

Enterobacter aerogenes

(7)

0.94 (C)

35°C (1.18)

RNA

0.80

123% – 154%l

[98]

Lactococcus lactis

6

1.9 (B)

30°C (1.80)

RNA

0.51

391%

[99]

  1. a Number of rrn operons per genome were obtained from the ribosomal RNA operon copy number database [100]. Where rrn copy number is not available for a species, values shown in parentheses are typical for the genus or family, if such estimates are possible.
  2. b Highest growth rates (temperature corrected for 37°C, see text) at which macromolecular data were available, shown as specific growth rate = ln(2)/(generation time).
  3. c Culture type indicated as batch (B) or chemostat (C).
  4. d Temperature at which strains were grown for macromolecular measurements.
  5. e Correction factor applied to actual growth rate to obtain temperature corrected growth rate shown in the third column, based on data from reference [56]
  6. f Similar investment in the translational apparatus between the comparison organism and E. coli assessed as follows: RC, similar ribosome concentration by cell volume; RNA, similar protein:RNA ratio; rRNA, similar protein:rRNA ratio. For all comparisons, E. coli data were taken from reference [3] with interpolation between discrete data points as necessary.
  7. g Growth rate at which E. coli makes a similar investment in the translational apparatus (by the criteria in column 5) as the comparison organism at the growth rate shown in column 3.
  8. h Translational power of the comparison organism expressed as a percentage of the translational power of E. coli.
  9. i For consistency, the comparison of ribosome concentration between this organism and E. coli made in the original reference is not used. Instead, ribosome concentration as a function of growth rate in E. coli was calculated from the data of reference [3] assuming a cell volume of 1.1 fl at a growth rate of 1.03 hr-1 and a constant ratio of cell volume to dry mass across growth rates. The comparison of translational power for this organism assumes that its protein concentration (protein mass per cell volume) is similar to E. coli.
  10. j Comparison organism makes a larger investment in the translational apparatus than E. coli growing at the fastest rate at which data are availabe. The comparison is made conservatively to data from the fastest E. coli growth rate.
  11. k Related to Desulfovibrio vulgaris by 16S rRNA gene sequence analysis.
  12. l Range of values shown corresponds to the maximum growth rates obtained for this organism in different culture conditions
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BMC Bioinformatics

ISSN: 1471-2105

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