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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