Table 1.
General characteristics of putative horizontally transferred elements found in the genome of P. profundum SS9 strain.
| 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. |
Low, moderate and high expression values are calculated on the basis of the microarray clones fluorescence intensity and correspond respectively to values lower than 3,000, comprise between 3,000 and 10,000 and higher than 10,000 arbitrary fluorescence units. Negative controls clones have a mean fluorescence value of 377 arbitrary fluorescence units. As an example, clones localized in the ATP synthase operon have a mean fluorescence value of 36,100 arbitrary fluorescence units and clones localized in polar flagellum cluster have a mean fluorescence value of 10,200. For region Chr2.10 mean fluorescence value are not reported because it is very large and a mean fluorescence value has little significance.