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Table 2 Analysis of ribosome numbers and respective cited literature provided in Lynch and Marinov [1]

From: Elusive data underlying debate at the prokaryote-eukaryote divide

Species

Ribosome number

Reference(s) cited

Location in cited reference1,2

Comments

Bacillus subtilis

6000

Barrera and Pan [14]

p. 485, col. 1, l. 30

 

9124

Maass et al. [15]

incorrect

L&M take the average of the quantification for the four ribosomal proteins for which there is data in this study, in all three time points. However, rplL should be scaled down as it is present in 4 copies per ribosome3.

Escherichia coli

72000

Bremer and Dennis [16]

p. 9, Table 3, col. 8, row 24

 

45100

Fegatella et al. [17]

p. 4437, Table 3, col. 4, row 9

 

26300

Fegatella et al. [17]

p. 4437, Table 3, col. 4, row 8

 

13500

Fegatella et al. [17]

p. 4437, Table 3, col. 4, row 7

 

6800

Fegatella et al. [17]

p. 4437, Table 3, col. 4, row 6

 

55000

Bakshi et al. [18]

p. 26, col. 2, l. 13

 

20100

no reference provided

  

12000

Arfvidsson and Wahlund [19]

not present

L&M seem to have extrapolated the value from Figure 5, p. 82, however the figure shows a range of ca. 2500-13000.

6514

Wiśniewski et al. [20]

not present

The citation seems to be incorrect. No reference to E. coli in the citation.

17979

Lu et al. [21]

incorrect

L&M take the average of the quantification of all rpl and rps proteins but exclude rpm proteins. Also, rpl should be scaled down as it is present in 4 copies per ribosome3.

Legionella pneumophila

7400

Leskelä et al. [22]

p. 174, col. 2, l. 24

 

Leptospira interrogans

4500

Beck et al. [23]

p. 820, Table 1, col. 2, l. 3

L&M use 4500, which is one number in the range reported: 3400, 3500, 4500. Considering standard deviations, the range reported is 2800-5000.

 

1039

Schmidt et al. [24]

incorrect

L&M take the average of the quantification of all ribosomal proteins for the first time-point of the serum treatment (same value for the doxycycline treatment). The range of averages for all time points and all treatments is 537-2170. The range for the serum treatment is 537-1039.

Mycoplasma pneumoniae

140

Yus et al. [25]

p. S14, col. 1, l. 23

Yus et al. cite their value from “Kuhner et al. accompanying manuscript”.

300

Seybert et al. [26]

p. 351, col. 1, l. 39

 

422

Kühner et al. [27]

p. S38, Figure S9B, l. 9

L&M use the values of the Western Blot estimation. The electron tomography results of the same citation indicate 140

225

Maier et al. [28]

incorrect

L&M take the mean of all values in Table S7 column “direct quantified (copies per cell)”. However, RPL7 needs to be scaled down as it is present more than once per ribosome3.

Mycobacterium tuberculosis

1672

Yamada et al. [30]

p. 9, Table 4, col. 4, row 7

 

Rickettsia prowazekii

1500

Pang and Winkler [31]

p. 117, Table 2, col. 2, row 6

 

Sphingopyxis alaskensis

1850

Fegatella et al. [17]

not present

 
 

200

Fegatella et al. [17]

p. 4435, col. 1, l. 27

The value reported is 2000 (p. 4435, col. 1, l. 24).

Spiroplasma melliferum

275

Ortiz et al. [32]

incorrect

L&M take the number of ribosomes for a portion of the cell. The number reported for the whole cell is 1000 (p.339, col. 2, l. 20).

Staphylococcus aureus

54400

Martin and Iandolo [33]

p. 1139, Table 1, col. 2-3, l. 9

L&M take the mean of estimated ribosomes per cell in rich and poor medium: 83200 (col. 2, row 11); 25600 (col. 3, row 11).

Vibrio angustum

27500

Flärdh et al. [34]

p. 6783, col. 1, l. 13

L&M take the mean of two counts: 20000 and 35,000.

8000

Flärdh et al. [34]

p. 6783, col. 1, l. 14

The reported value is after 4 days of starvation. Value for 24h of starvation (16000) not included.

ARMAN*

92

Comolli et al. [35]

p. 162, col. 2, l. 41

 

Exophiala dermatitidis*

195000

Biswas et al. [36]

p. 137, Table 1, col. 7, row 6

 

Saccharomyces cerevisiae

200000

Warner [37]

p. 437, col. 1, l. 34

 

220000

Yamaguchi et al. [38]

incorrect

L&M take the value from the abstract, which is an approximation. The reported value is 217000 (mean for G1 cells - p.325, Table 1, col. 5, row 11).

153456

Kulak et al. [39]

not reproducible

Not clear how the value was calculated.

72284

Ghaemmaghami et al. [40]

not reproducible

Not clear how the value was calculated.

Schizosaccharomyces pombe

150000

Marguerat et al. [41]

p. 677, col. 1, l. 35

 

500000

Maclean [42]

p. 323, col. 1, l. 66

 

505260

Kulak [39]

not reproducible

Not clear how the value was calculated.

100568

Marguerat et al. [41]

not reproducible

Not clear how the value was calculated.

Tetrahymena pyriformis

7490000

Hallberg and Bruns [5]

incorrect

L&M take the reported number from p. 385, table 1, col. 2, row 1, which is 7.49 OD259 per 106 cells.

Tetrahymena thermophila

74000000

Calzone et al.

p. 6892, Table 3,

L&M take the mean of ribosomes per cell of log phase (10.8 x107) and starved cells (4.0 x107).

[43]

col. 2-3, row 4

Chlamydomonas reinhardtii (chloroplast)

120500

Bourque et al [44]

p. 157, Table 2, col. 9 row 3-4

L&M take the mean of values of cytoplasmic ribosomes per hypothetical cell for the two growth conditions for wildtype cells (0.98x105 and 1.43x105).

Chlamydomonas reinhardtii (chloroplast)

55,000

Bourque et al. [44]

p. 157, Table 2, col. 10, row 3–4

L&M take the mean of the values of chloroplast ribosomes per hypothetical cell for the two growth conditions for wildtype cells (0.53 × 105 and 0.57 × 105).

Ostreococcus tauri *

1250

Henderson et al. [45]

p. 10, col. 2, l. 43

 

Adonis aestivalis (vegetative)

47700000

Lin and Gifford [46]

p. 2481, Table 3, col. 4, row 2-4

L&M take the mean of the total number of ribosomes per cell (in millions) for the vegetative apex: central zone (40.2), peripheral zone (25.7) and rib meristem (77.2).

Adonis aestivalis (transitional)

39066666

Lin and Gifford [46]

p. 2481, Table 3, col. 4, row 5-7

L&M take the mean of the total number of ribosomes per cell (in millions) for the transitional apex: central zone (34.2), peripheral zone (31.1) and rib meristem (51,9).

Adonis aestivalis (floral)

23666666

Lin and Gifford [46]

not present

The mean of the total number of ribosomes per cell (in millions) for the floral apex is 23.9; central zone (30.9), peripheral zone (18.8), rib meristem (22.1).

Glycine max SB-1 cell

9373333

Jackson and Lark [47]

p. 236, Table 1, col. 4, row 3-5

L&M take the mean of ribosomes per cell for SB-1 cells in sucrose (9530000), M-24 cells in maltose (7190000) and M- 200 cells in sucrose (11400000); L&M exclude M-200 cells in maltose.

Rhus toxicodendron*

2400000

Vassilyev [48]

p. 620, Table 4, col. 2–4, row 6

L&M take the mean of the added numbers for cytoplasmic ribosomes per whole epithelial cell from the procambium stage (free 3260000 and bound 480000) and the SER stage (free 810000 and bound 250000).

Zea mays root cell

25500000

Hsiao [49]

not present

The value appears in the literature but not in Hsiao (1970a), but rather in Hsiao (1970b) p.105, Table 1, col. 4, row 4-5.

Hamster, intestinal enterocyte*

1500000

Buschmann and Manke [51, 52]

p. 23, Figure 5

In Buschmann and Manke (1981b). L&M take the mean of total ribosomes per average enterocyte for fasted and lipid-fed cells.

HeLa Cell

3300000

Duncan and Hershey [53]

p. 7229, col. 1, l. 73

Not clear how the value was calculated.

5748830

Kulak et al. [39]

not reproducible

no value

Zhao [54]

Mouse pancreas*

1340000

Dean [55]

117, Table 2, col. 6, row 12

Rat liver cell*

12700000

Weibel et al. [56]

p. 80, Table 2, col. 10, row 12

  1. 1‘ S’ refers to Supplemental Material
  2. 2not present - value cannot be found in the cited paper; incorrect - a wrong value was taken from the cited paper; not reproducible – calculations derived from proteomics study cannot be reproduced
  3. 3(Ilag et al. [57]; Gordiyenko et al. [58]; Garcia et al. [59])
  4. *Species with both volume and ribosome count values verified