Table 1. Protein Stoichiometry of the Syn7942 β-Carboxysome and its Variability in Cells Grown Under Air/ML, CO2/ML, LL, and HL Conditions Determined from Slimfield and Confocal Microscopy.
| Category | Structure | Protein | Air/ML | CO2/ML | LL | HL | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| Peak Value ± HWHM | Number of Functional Units | Peak Value ± HWHM | Number of Functional Units | Peak Value ± HWHM | Number of Functional Units | Peak Value ± HWHM | Number of Functional Units | |||
| Shell proteins | Hexamer | CcmK3 | 92 ± 148 (n = 219) | 15 ± 25 | 172 ± 83 (n = 2,048) | 29 ± 14 | 83 ± 31 (n = 1,516) | 14 ± 5 | 87 ± 52 (n = 2,155) | 14 ± 9 |
| CcmK4 | 314 ± 194 (n = 77) | 52 ± 32 | 562 ± 263 (n = 1,918) | 94 ± 44 | 313 ± 121 (n = 1,766) | 52 ± 20 | 304 ± 95 (n = 3,215) | 51 ± 16 | ||
| Pentamer | CcmL | 37 ± 17 (n = 316) | 7.4 ± 3.4 | 66 ± 24 (n = 311) | 13.2 ± 4.8 | 34 ± 15 (n = 394) | 6.8 ± 3.0 | 69 ± 24 (n = 220) | 13.8 ± 4.8 | |
| Structural proteins | Monomer* | CcmM | 719 ± 1,433 (n = 71) | 719 ± 1,433 | 468 ± 425 (n = 2,313) | 468 ± 425 | 483 ± 366 (n = 3,655) | 483 ± 366 | 1,176 ± 691 (n = 2,318) | 1,176 ± 691 |
| Monomer | CcmN | 74 ± 51 (n = 86) | 74 ± 51 | 52 ± 28 (n = 3,143) | 52 ± 28 | 51 ± 20 (n = 4,022) | 51 ± 20 | 82 ± 34 (n = 5,074) | 82 ± 34 | |
| CA | Hexamer | CcaA | 86 ± 81 (n = 95) | 14 ± 14 | 129 ± 86 (n = 1,354) | 21 ± 14 | 65 ± 21 (n = 217) | 11 ± 4 | 122 ± 59 (n = 2,837) | 20 ± 10 |
| Rubisco enzyme | L8S8 | RbcS | 6,822 ± 9,200 (n = 60) | 853 ± 1,150 | 4,401 ± 6,655 (n = 894) | 550 ± 832 | 2,934 ± 5,492 (n = 752) | 367 ± 687 | 12,057 ± 5,186 (n = 1,974) | 1,507 ± 648 |
| Rubisco chaperone | Dimer | RbcX | 39 ± 32 (n = 211) | 20 ± 16 | 38 ± 10 (n = 1,370) | 19 ± 5 | 40 ± 9 (n = 1,402) | 20 ± 5 | 40 ± 9 (n = 1,861) | 20 ± 5 |
Stoichiometry is presented as peak value ± HWHM, and the sample sizes are indicated as n. Peak values were determined from Slimfield stoichiometry profiles of each carboxysome proteins (Figure 1; Supplemental Figure 3). Quantification of CcmL under the four conditions was acquired from Slimfield for accurate measurement of copies of shell pentamers for capping the carboxysome structure. Copies of other carboxysome proteins were calculated using Slimfield results (bold) with definitive counts of protein copies under Air/ML (see also Supplemental Figure 3) in combination with relative quantification of each protein under the four conditions from confocal imaging (see also Supplemental Figures 7 and 8). Protein structures were derived from previous studies (Kerfeld et al., 2005; Long et al., 2007, 2011; Tanaka et al., 2007, 2008; Kinney et al., 2012; McGurn et al., 2016). *Monomeric unit of CcmM was designated to CcmM35 that is the majority of CcmM; CcmM58 is postulated as a trimer.