TABLE 2.
Amino acid(s) | ND prion formation librarya |
ORD prion formation libraryb |
Prion maintenance libraryc |
||||||
---|---|---|---|---|---|---|---|---|---|
Frequency of amino acid in: |
Odds ratiod | Frequency of amino acid in: |
Odds ratiod | Frequency of amino acid in: |
Odds ratioe | ||||
Selected [PSI+] library | Unselected naive library | Selected [PSI+] library | Unselected naive library | White [PSI+] colonies | Red [psi−] colonies | ||||
Individual amino acids | |||||||||
Alanine | 0.053 | 0.055 | 0.96 | 0.095 | 0.068 | 1.40 | 0.089 | 0.069 | 1.32 |
Arginine | 0.024 | 0.095 | 0.26*** | 0.044 | 0.107 | 0.41** | 0.054 | 0.121 | 0.41**** |
Asparagine | 0.061 | 0.031 | 1.95 | 0.047 | 0.021 | 2.24 | 0.038 | 0.032 | 1.20 |
Aspartic acid | 0.028 | 0.046 | 0.60 | 0.033 | 0.058 | 0.57 | 0.054 | 0.064 | 0.83 |
Cysteine | 0.065 | 0.071 | 0.91 | 0.084 | 0.062 | 1.35 | 0.072 | 0.047 | 1.58* |
Glutamic acid | 0.003 | 0.008 | 0.42 | 0.006 | 0.012 | 0.53 | 0.015 | 0.006 | 2.70 |
Glutamine | 0.007 | 0.016 | 0.41 | 0.003 | 0.003 | 0.94 | 0.008 | 0.007 | 1.12 |
Glycine | 0.13 | 0.213 | 0.61* | 0.144 | 0.151 | 0.95 | 0.114 | 0.109 | 1.05 |
Histidine | 0.031 | 0.029 | 1.08 | 0.047 | 0.038 | 1.26 | 0.04 | 0.043 | 0.94 |
Isoleucine | 0.088 | 0.055 | 1.60 | 0.04 | 0.058 | 0.69 | 0.025 | 0.043 | 0.57 |
Leucine | 0.065 | 0.071 | 0.91 | 0.058 | 0.06 | 0.96 | 0.04 | 0.063 | 0.62* |
Lysine | 0 | 0 | N/A | 0.016 | 0.009 | 0.31 | 0 | 0.003 | 0.00 |
Methionine | 0.014 | 0.014 | 0.96 | 0.088 | 0.06 | 1.89 | 0.002 | 0.009 | 0.17 |
Phenylalanine | 0.121 | 0.042 | 2.88*** | 0.037 | 0.053 | 1.45 | 0.068 | 0.049 | 1.40 |
Proline | 0.017 | 0.035 | 0.48 | 0.123 | 0.113 | 0.70 | 0.048 | 0.045 | 1.07 |
Serine | 0.109 | 0.125 | 0.87 | 0.04 | 0.038 | 1.09 | 0.12 | 0.102 | 1.20 |
Threonine | 0.061 | 0.042 | 1.45 | 0.016 | 0.016 | 1.07 | 0.037 | 0.039 | 0.94 |
Tryptophan | 0.014 | 0.021 | 0.67 | 0.076 | 0.055 | 1.04 | 0.018 | 0.005 | 4.07* |
Tyrosine | 0.069 | 0.042 | 1.63 | 0.076 | 0.086 | 1.40 | 0.074 | 0.028 | 2.81**** |
Valine | 0.125 | 0.078 | 1.60 | 0.095 | 0.068 | 0.89 | 0.085 | 0.116 | 0.70* |
Groups of amino acids | |||||||||
Charged (D, E, K, R) | 0.054 | 0.139 | 0.35*** | 0.129 | 0.210 | 0.43*** | 0.123 | 0.194 | 0.58*** |
Nonaromatic hydrophobic (I, L, M, V) | 0.267 | 0.206 | 1.41 | 0.181 | 0.200 | 0.88 | 0.151 | 0.231 | 0.59**** |
Prion-promoting nonaromatic hydrophobic (I, M, V) | 0.206 | 0.139 | 1.61* | 0.126 | 0.143 | 0.86 | 0.111 | 0.168 | 0.62** |
Aromatic (F, W, Y) | 0.186 | 0.101 | 2.04** | 0.168 | 0.124 | 1.42 | 0.160 | 0.082 | 2.14*** |
Polar (N, Q, S, T) | 0.220 | 0.198 | 1.14 | 0.197 | 0.162 | 1.27 | 0.203 | 0.180 | 1.16 |
The ND library consists of 37 selected [PSI+] sequences (296 amino acids) and 62 unselected sequences (496 amino acids).
The ORD prion formation library consists of 31 selected [PSI+] sequences (310 amino acids) and 58 unselected sequences (580 amino acids).
The prion maintenance library consists of 65 white [PSI+] sequences (650 amino acids) and 87 red [psi−] sequences (870 amino acids).
Odds ratios reflect the degree of overrepresentation or underrepresentation of each amino acid among the prion-forming isolates, as calculated according to equation 1. Values above 1 indicate overrepresentation among prion-forming isolates. Statistical significance of the over- or underrepresentation is indicated: *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001.
Odds ratios reflect the degree of overrepresentation or underrepresentation of each amino acid among the white (prion-propagating) isolates, as calculated using equation 3.