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 | 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 |