TABLE 2.
Parallel evolution of tail fiber proteins reveals adaptation associated with host recognition in phage U136Ba
| Phage isolate (source population) |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Genome position | BP change | Amino acid change (codon) | Impact on amino acid | Gene no. | Putative gene function | RB-020 (Pop+2) | RB-022 (Pop+4) | RB-024 (Pop+6) | RB-028 (Pop+8) | ET013 (Pop+9) |
| 28,296 | C→A | H1186N(CAT→AAT) | Positive to neutral, large to small | 52 | Tail fiber protein | x | ||||
| 28,321 | C→A | T1194K (ACG→AAG) |
Neutral to positive, small to large | 52 | Tail fiber protein | x | ||||
| *28,380 | C→A | Q1214K (CAA→AAA) |
Neutral to positive and small to large | 52 | Tail fiber protein | x | x | x | ||
| 28,381 | A→G | Q1214R (CAA→CGA) |
Neutral to positive and small to large | 52 | Tail fiber protein | x | ||||
| 28,383 | G→A | A1215T (GCT→ACT) |
Nonpolar to polar | 52 | Tail fiber protein | x | ||||
| 28,411 | G→T | G1224V (GGA→GTA) |
Polar to nonpolar | 52 | Tail fiber protein | x | ||||
| 28,463 | C→G | N1241K (AAC→AAG) |
Neutral to positive, small to large | 52 | Tail fiber protein | x | x | |||
| 28,469 | C→A | N1243K(AAC→AAA) | Neutral to positive, small to large | 52 | Tail fiber protein | x | X | |||
| 31,917 | C→A | K688N (AAG→AAT) |
Positive to neutral, small to large | 57 | Tail fiber protein | x | x | X | ||
| 35,091 | (A)8→7 | None, intergenic | Not applicable | 58–59 | DNA primase, transcrip. regulator | x | ||||
| 38,215 | (T)5→4 | None, intergenic | Not applicable | 61–62 | Endonuclease, hyp. protein | x | ||||
Mutations were identified by whole-genome sequencing and comparison to the U136B reference genome (GenBank no. MW598258.1). Genome position column indicates location in the genome in bp. BP change column indicates the nucleotide mutation. Amino acid change (codon) column indicates amino acid change and codon change using standard genetic code abbreviations (e.g., H1186N indicates a change from histidine to asparagine at amino acid position 1186, corresponding to a change from cytosine to adenine in the first position of the codon). Impact on amino acid column indicates changes to the amino acid properties. Gene no. column indicates the gene product number within the U136B genome. Putative gene function column indicates the bioinformatic-based manual gene annotation as previously reported (11). Asterisk indicates mutation was detected in original phage stock; see description in the main text. Light gray shading and an “X” indicates the mutation was present in the indicated population.