TABLE 1.
All loci in LVS for which a nonsynonymous mutation has been detected by comparison to other sequenced Francisella strains
| ORF locus taga | Predicted product encoded by the locus | Type of mutation | Effect of mutation on protein translationb | Predicted impact on protein functionc | Status of gene in the other four sequenced genomesd | Candidate class |
|---|---|---|---|---|---|---|
| FTL_0039 | Hypothetical membrane protein | SNP | G68R | Deleterious (SIFT) | Functional in all strains | A |
| FTL_0101-FTL_0102 | Cl−:H+ antiporter | 1-bp deletion | 107-aa chimeric protein resulting from a frameshift mutation | Deleterious | Functional in all strains | A |
| FTL_0168 | Hypothetical membrane protein | 1-bp insertion | 15-aa chimeric protein resulting from a frameshift mutation | Deleterious | Functional in all strains | A |
| FTL_0180 | Acyltransferase | SNP | I164S | Deleterious (SIFT) | Functional in all strains | A |
| FTL_0391-FTL-0392 | Pilus assembly protein pilA | 0.5-kb deletion | 55-aa chimeric protein resulting in the fusion of two ORFs | Deleterious | Functional in all strains | A |
| FTL_0439 | Hypothetical protein | 1.5-kb deletion | 551-aa chimeric protein resulting from a gene fusion | Deleterious | Functional in all strains | A |
| FTL_0806 | Amino acid transporter family protein | SNP | F219V | Deleterious (SIFT) | Functional in all strains | A |
| FTL_1066 | Fumaryl acetoacetate hydrolase family protein | SNP | R82I | Deleterious (SIFT) | Functional in all strains | A |
| FTL_1141 | 3-Oxoacyl-(acyl carrier protein) synthase III | SNP | N297H | Deleterious (SIFT) | Functional in all strains | A |
| FTL_1246 | Conserved hypothetical protein | SNP | V144F | Deleterious (SIFT) | Functional in all strains | A |
| FTL_1517 | Hypothetical protein | SNP | A79V | Deleterious (BLOSUM90) | Functional in all strains | A |
| FTL_1521 | Chitinase family 18 protein | 12-bp insertion | Additional NNDQ repeat at position 658 | Deleterious (SIFT) | Functional in all strains | A |
| FTL_1611 | Glycosyltransferase, group 2 family protein | SNP | Q80L | Deleterious (SIFT) | Functional in all strains | A |
| FTL_1773 | Conserved hypothetical protein | 90-bp deletion | 30-aa truncation, positions 132 to 262 | Deleterious (SIFT) | Functional in all strains | A |
| FTL_1860 | Phosphoribosylformylglycinamidine synthase | SNP | T1038I | Deleterious (SIFT) | Functional in all strains | A |
| FTL_0062 | Transcriptional regulator | SNP | E68* (position in predicted FSC200 ORF), protein truncated by 163 aa | Deleterious | Pseudogene in F. tularensis subsp. holarctica | B |
| FTL_0108 | Major facilitator superfamily transport protein | SNP | V248I | Tolerated (SIFT) | Pseudogene in F. tularensis subsp. holarctica | B |
| FTL_0171 | Tetrapyrrole methyltransferase family protein | SNP | L220I | Tolerated (SIFT) | Functional in all strains | B |
| FTL_0212 | Hypothetical protein | 1-bp insertion | 308-aa chimeric protein resulting from a frameshift mutation at position 305 in a variable region | Tolerated (SIFT) | Missing in U112 | B |
| FTL_0341-FTL_0342 | Deoxyribodipyrimidine photolyase | SNP | G143V | Deleterious (SIFT) | Pseudogene in F. tularensis subsp. holarctica | B |
| FTL_0381 | Conserved hypothetical transmembrane protein | SNP | L14F | Tolerated (SIFT) | Pseudogene in Schu S4 | B |
| FTL 0524ae | Hypothetical protein | SNP | V65F | Tolerated (SIFT) | Functional in all strains | B |
| FTL_0847 | Preprotein translocase family protein | SNP | A26S | Tolerated (SIFT) | Functional in all strains | B |
| FTL_0864 | Predicted sugar isomerase | SNP | T2K | Tolerated (SIFT) | Functional in all strains | B |
| FTL_0997ae | Hypothetical protein | SNP | T36* (position in predicted FSC200 ORF), protein truncated by 232 aa | Deleterious | Pseudogene in F. tularensis subsp. holarctica | B |
| FTL_1242 | ThiJ/Pfpl family protein | SNP | D46N | Tolerated (BLOSUM90) | Pseudogene in F. tularensis subsp. holarctica | B |
| FTL_1265 | 2-Amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/ dihydropteroate synthase | SNP | D232N | Tolerated (SIFT) | Functional in all strains | B |
| FTL_1291-FTL_1292 | Conserved hypothetical protein | SNP | Q106*, protein truncated by 222 aa | Deleterious | Pseudogene in Schu S4 | B |
| FTL_1325 | Hypothetical protein | SNP | T786N | Tolerated (SIFT) | Pseudogene in F. tularensis subsp. holarctica | B |
| FTL_1408 | Chitin binding protein | SNP | S192I | Tolerated (SIFT) | Pseudogene in Schu S4 and potentially in F. tularensis subsp. holarctica | B |
| FTL_1552 | Hypothetical membrane protein | SNP | A233T | Tolerated (BLOSUM90) | Functional in all strains | B |
| FTL_1619 | Conserved hypothetical membrane protein | SNP | T141K | Deleterious (BLOSUM90) | Pseudogene in F. tularensis subsp. holarctica | B |
| FTL_1697-FTL_1698 | Metal ion transporter | 2-bp deletion | 25-aa chimeric protein resulting from a frameshift mutation | Deleterious | Pseudogene in F. tularensis subsp. holarctica | B |
| FTL_1731 | licB-like transmembrane protein | SNP | S12F | Tolerated (SIFT) | Functional in all strains | B |
| FTL_1959 | Conserved hypothetical protein | SNP | H7Q | Tolerated (BLOSUM90) | Pseudogene in F. tularensis subsp. holarctica | B |
a
Locus tags from the published sequence NC_007880; when two ORFs resulted from the mutation, the locus tags for both are cited.
b
SNPs are represented by the amino acid and its position in the protein sequence of the virulent F. tularensis subsp. holarctica strains, followed by the substituted amino acid in LVS.; stop codon; aa, amino acids.
c
The method used to assess the impact of the mutation is indicated in parentheses. When no method is mentioned, the mutation was predicted to be deleterious because it truncated the protein by more than 20% of its length.
d
F. tularensis subsp. tularensis Schu S4, F. tularensis subsp. holarctica FSC200, F. tularensis subsp. holarctica OSU18, and F. novicida U112.
e
The ORF in which the mutation took place has no locus tag assigned and is downstream of the locus mentioned.