TABLE 3.
Genomic evolution within U136B populationsa
| Phage population |
|||||||||
|---|---|---|---|---|---|---|---|---|---|
| Genome position | BP change | Amino acid change (codon) | Impact on amino acid | Gene no. | Putative gene function | Pop+2 | Pop+4 | Pop+6 | Pop+8 |
| 11,048 | T→G | R116R (CGT→CGG) |
Synonymous | 33 | Portal protein | 6.7% | 7.6% | 6.9% | |
| 19,245 | T→G | None, Intergenic |
Not applicable | 046–047 | TMP-TMP protein | 9.5% | |||
| 19,261 | A→T | V3V (GTA→GTT) |
Synonymous | 47 | Tail tape measure protein | 5.6% | 5.7% | 5.4% | |
| 19,272 | C→G | A7G (GCT→GGT) |
Nonpolar to polar | 47 | Tail tape measure protein | 5.0% | |||
| 28,296 | C→A | H1186N (CAT→AAT) |
Positive to neutral, large to small | 52 | Tail fiber protein | 100% | |||
| 28,321 | C→A | T1194K (ACG→AAG) |
Neutral to positive, small to large | 52 | Tail fiber protein | 100% | |||
| *28,380 | C→A | Q1214K (CAA→AAA) |
Neutral to positive, small to large | 52 | Tail fiber protein | 100% | 100% | 100% | |
| 28,381 | A→G | Q1214R (CAA→CGA) | Neutral to positive, small to large | 52 | Tail fiber protein | 100% | |||
| 28,383 | G→A | A1215T (GCT→ACT) |
Nonpolar to polar | 52 | Tail fiber protein | 100% | |||
| 28,446 | C→A | L1236I (CTT→ATT) |
Nonsynonymous conserved | 52 | Tail fiber protein | 100% | |||
| 28,463 | C→G | N1241K (AAC→AAG) |
Neutral to positive, small to large | 52 | Tail fiber protein | 100% | 100% | ||
| 28,469 | C→A | N1243K (AAC→AAA) |
Neutral to positive, small to large | 52 | Tail fiber protein | 100% | |||
| 31,700 | +82 bp | +82 bp (2281/2373 nt) | Frame-shifting insertion | 57 | Tail fiber protein | 77.2% | |||
| 31,718 | +86 bp | +86 bp (2263/2373 nt) | Frame-shifting insertion | 57 | Tail fiber protein | 63.6% | |||
| 31,917 | C→A | K688N (AAG→AAT) |
Positive to neutral, small to large | 57 | Tail fiber protein | 100% | 100% | ||
| 38,211 | Δ1 bp | none, intergenic | Not applicable | 061–062 | Endonuclease, hypothetical protein | 100% | |||
| 39,132 | T→G | F192V (TTT→GTT) |
Large to small | 63 | Methylase | 5.0% | 5.3% | ||
| 39,139 | C→A | S194Y (TCT→TAT) |
Polar to nonpolar, small to large | 63 | Methylase | 6.6% | 6.9% | ||
| 48,412 | G→T | S15* (TCA→TAA) |
Early stop codon | 85 | Hypothetical protein | 5.8% | 5.1% | 5.4% | |
| 48,438 | G→T | F6L (TTC→TTA) |
Large to small | 85 | Hypothetical protein | 8.9% | 8.6% | 8.9% | |
| 48,444 | T→A | L4F (TTA→TTT) |
Small to large | 85 | Hypothetical protein | 6.4% | 5.5% | 5.5% | |
| 48,446 | A→C | L4V (TTA→GTA) |
Nonsynonymous conserved | 85 | Hypothetical protein | 10.6% | 9.9% | ||
Percentages indicate the frequency of DNA sequencing reads supporting each mutation in each population, with “100%” (dark gray shading) indicating that no other alleles at that locus were detected, and other percentages (light gray shading) indicating multiple alleles were detected. For populations with phage extinctions (Pop+1, Pop+3, Pop+5, Pop+7, and Pop+10) or near extinction (Pop+9), no phage DNA was detected. 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). 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 main text.