Table 1 General characteristics of putative horizontally transferred elements found in the genome of P. profundum SS9 strain.
From: Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains
Element | Absent in strain | Start-end position | Size (kbp) | GC content percent (chr1_42%; chr2_41.2%) | tRNA | Integrase-like genes at the end | Expression level | Relevant resident genes |
|---|---|---|---|---|---|---|---|---|
Plasmid | 3TCK DSJ4 | 1–80,033 | 80 | 44% | NO | NO | moderate (4,458) |  |
Chr1.1-LF | 3TCK | 13,500–51,360 | 38 | 45% | NO | NO | low (1,079) | LF-lateral flagella coding region; there are two genes up-regulated at 0.1 MPa at both ends (PBPRA0013- PBPRA0050). |
Chr1.2 | 3TCK DSJ4 | 479,200–490,850 | 11.6 | 44% | NO | NO | low (2,623) | Xylose transport and metabolism; one gene up-regulated at 4°C (PBPRA0466). |
Chr1.3 | 3TCK | 717,590–751,055 | 33.4 | 41% | NO | NO | moderate (3,879) |  |
Chr1.4 | 3TCK DSJ4 | 957,470–983,750 | 26.3 | 40% | YES | YES (PBPRA0877) | moderate (3,744) |  |
Chr1.5 | 3TCK DSJ4 | 1,081,250–1,093,850 | 12.6 | 41% | NO | NO | low (1,094) |  |
Chr1.6 | DSJ4 | 1,262,100–1,281,040 | 21.7 | 41% | NO | NO | low (1,111) | One up-regulated gene at 0.1 MPa near 5'-end (PBPRA1136). |
Chr1.7 | DSJ4 | 1,436,830–1,453,450 | 16.6 | 42% | NO | NO | low (2,432) | ORFs involved in amino acid metabolism and transport. |
Chr1.8 | 3TCK DSJ4 | 1,482,130–1,528,980 | 46.8 | 40% | NO | YES (PBPRA1336) | moderate (3,453) | 12 phage-related proteins and genes involved in tryptophan transport and metabolism. |
Chr1.9 | 3TCK DSJ4 (smaller) | 1,803,270–1,847,340; 1,803,270–1,837,500 | 44.1 3TCK; 34.2 DSJ4 | 40% 41% | NO | NO | moderate (4,586) | One gene up-regulated at 28 MPa (vs. 0.1 MPa) (PBPRA1598) and numerous transposases. |
Chr1.10 | 3TCK-DSJ4 | 1,887,600–1,921,860 | 34.2 | 42.9% | YES | NO | low (2,509) | Genes involved in fatty acid synthesis and tryptophan biosynthesis. |
Chr1.11 | 3TCK-DSJ4 | 2,063,315–2,097,000 | 33.7 | 40% | YES | NO | moderate (3,276) | One gene (PBPRA1810) up-regulated at 16°C. |
Chr1.12 | DSJ4 | 2,399,560–2,410,040 | 10.5 DSJ4 | 40% | YES | NO | moderate (4,179) | Three genes differentially expressed (PBPRA2084, PBPRA2086, PBPRA2087). |
Chr1.13 | 3TCK (smaller) DSJ4 | 2,640,200–2,650,840 | 10.6 3TCK 17.7 DSJ4; | 41% | YES | NO | moderate (12,480-7,436) | Gene cluster involved in tricarboxylic acid fermentation and transport; some genes were up-regulated at 16°C and/or 0.1 MPa. |
Chr1.14 | DSJ4 | 2,892,510–2,901,270 | 8.8 | 45.9% | NO | NO | high (11,847) | Genes involved in pilus assembly, three genes up-regulated at 28 MPa (vs. 0.1 MPa) and/or down-regulated at 45 MPa (PBPRA2498, PBPRA2499, PBPRA2505). |
Chr1.15 | 3TCK-DSJ4 | 3,104,770–3,110,020; 3,145,100-3,145,095 | 5.2+ 29.3 | 29%–37% | YES | NO | moderate (9,965) | flm genes; two genes down-regulated at 4°C (PBPRA2692, PBPRA2701). |
Chr1.16 | 3TCK-DSJ4 | 3,220,530–3,230,610 | 10 | 43.9% | NO | NO | moderate (4,394) | Genes coding for a phosphotransferase system cellobiose-specific; one gene up-regulated at 4°C (PBPRA2779). |
Chr1.17 | 3TCK-DSJ4 | 3,706,515–3,712,920 | 6.4 | 45.3% | NO | NO | moderate (6,448) |  |
Chr2.1 | 3TCK-DSJ4 | 159,600–184,460 | 24.9 | 43.4% | NO | NO | low (2,659) | Genes involved in pentose and glucuronate interconversions and PTS system. |
Chr2.2 | 3TCK-DSJ4 | 342,190–349,500 | 7.3 | 43.2% | NO | NO | low (1,741) | Very small region, no orthologous in other Vibrio species |
Chr2.3 | 3TCK-DSJ4 | 637,160–679,550 | 42.4 | 41.1% | NO | YES (PBPRB0551) | low (2,485) | 12 phage-related proteins; similarities with Gifsy -1, Gifsy -2 prophages protein. |
Chr2.4 | DSJ4 | 1,179,200–1,191,215 | 12 | 42.8% | NO | NO | low (1,191) | Phosphotransferase system (PTS) N-acetylgalactosamine-specific genes. |
Chr2.5 | 3TCK (smaller) DSJ4 | 1,419,870–1,427,600; 1,419,870–1,439,670 | 19.8 | 46.2% | NO | YES (PBPRB1271) | low (1,737) | 12 phage-related proteins. |
Chr2.6 | 3TCK-DSJ4 | 1,661,040–1,685,300 | 24.3 | 39.2% | YES | NO | moderate (3,201) | Four transposases in the central part; genes involved in pentose and glucuronate interconversions; genes involved in C4-dicarboxylate transport system |
Chr2.7-PI | 3TCK DSJ4 | 1,745,750–1,814,900 | 69.1 | 44.8% | NO | YES (PBPRB1675) | low (2,060) | This region could be derived from a plasmid integration. |
Chr2.8 | 3TCK-DSJ4 | 1,872,240–1,891,940 | 19.7 | 40.4% | NO | NO | moderate (4,347) | Genes involved in C4-dicarboxylate transport system and in pentose and glucuronate interconversion pathway. |
Chr2.9 | DSJ4 | 1,901,330–1,928,060 | 26.7 | 41.9% | YES? | NO | moderate (4,074) | Highly discontinuous region. |
Chr2.10 | 3TCK-DSJ4 | 2,013,000–2,087,900; 1,975,200–2,095,800 | ~108 3TCK; ~145 DSJ4 | 41.2%–42.7% |  |  |  | This region is probably duplicated in the test strains (DSJ4 and 3TCK. |