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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.
  1. 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.