Cloning and characterization of Tc1 family-derived PPTN related transposons from ridged-eye flounder (Pleuronichthys cornutus) and inshore hagfish (Eptatretus burgeri)

다국어 초록 (Multilingual Abstract)

The Tc1 transposable element is the most widespread family among animal transposon and these elements consist of an inverted repeat (IR) sequence flanking a transposase gene that belongs to Class II type transposon, which is highly conserved in the genome of the nematode C. elegans. In order to characterize Tc1-like transposable elements from several fishes, PPTN (Tc1-like transposon was isolated from Pleuronectes platessa, marine flatfish species) IR primer-specific amplified elements were cloned from the genomic DNA of several fishes.
Transposable elements were found in ridged-eye flounder (Pleuronichthys cornutus) and inshore hagfish (Eptatretus burgeri) and named as PCTN and EBTN, respectively.
Amino acid sequence alignment and phylogenetic analysis confirmed that the PPTN-like transposons belonged to the Tc1 superfamily of transposons, but they comprised a unique clade of Tc1-like transposons. The IR-PCR analysis using MMTS-IR and PPTN-IR specific primers from Paralichthys olivaceus (Paralichthyidae), Paraplagusia japonica (Cynoglossidae), P. yokohamae (Pleuronectidae)and Pagurus cornutus (Pleuronectidae) (within the same order, Pleuronectiformes but different families) exhibited mutually exclusive distribution of Tc1 family-derived PPTN and MMTS-like transposons in these fish genomes.
These results indicate that Tc1 family-derived PPTN and MMTS related Tc1-like transposable elements have uniquely evolved in piscine genome, and can be used as phylogenetic markers for the distribution of subfamilies of Tc1-like transposon and the involvement of horizontal and vertical transmission in the evolution of fish genome.

참고문헌 (Reference)

• 1 Radice AD, "Widespread occurrence of the Tc1 transposon family: Tc1-like transposons from teleost fish" 244 : 606-612, 1994
• 2 Schouten GJ, "Transposon Tc1 of the nematode Caenorhabditis elegans jumps in human cells" 26 : 3013-3017, 1998
• 3 Dingwall C, "The nucleoplasmin nuclear location sequence is larger and more complex than that of SV-40 large T antigen" 107 : 841-849, 1988
• 4 Saitou N, "The neighbor-joining method: a new method for reconstructing phylogenetic trees" 4 : 406-425, 1987
• 5 van Luenen HG, "The mechanism of transposition Tc3 of C. elegans" 79 : 293-301, 1994
• 6 Sinzelle L, "The mariner transposons belonging to the irritans subfamily were maintained in chordate genomes by vertical transmission" 62 : 53-65, 2006
• 7 Yuan YW, "The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies" 108 : 7884-7889, 2011
• 8 Thompson JD, "The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools" 25 : 4876-4882, 1997
• 9 Goodier JL, "Tc1 transposon-like sequences are widely distributed in salmonids" 241 : 26-34, 1994
• 10 Vos JC, "Tc1 transposase of Caenorhabditis elegans is an endonuclease with a bipartite DNA binding domain" 13 : 6125-6132, 1994
• 11 Zwaal RR, "Target-selected gene inactivation in Caenorhabditis elegans by using a frozen transposon insertion mutant bank" 90 : 7431-7435, 1993
• 12 Leaver MJ, "Structure and expression of a cluster of glutathione S-transferase genes from a marine fish, the plaice (Pleuronectes platessa)" 321 : 405-412, 1997
• 13 Rosenzweig B, "Sequence of the C. elegans transposable element Tc1" 11 : 4201-4209, 1983
• 14 Harris LJ, "Sequence identity between an inverted repeat family of transposable elements in Drosophila and Caenorhabditis" 16 : 5991-5998, 1988
• 15 Clements KD, "Rapid evolutionary divergences in reef fishes of the family Acanthuridae (Perciformes: Teleostei)" 26 : 190-201, 2003
• 16 Clark KJ, "Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells" 37 : 1239-1247, 2009
• 17 Bao W, "New superfamilies of eukaryotic DNA transposons and their internal divisions" 26 : 983-993, 2009
• 18 Jacobson JW, "Molecular structure of a somatically unstable transposable element in Drosophila" 83 : 8684-8688, 1986
• 19 Ivics Z, "Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells" 91 : 501-510, 1997
• 20 Kapitonov VV, "Molecular paleontology of transposable elements in the Drosophila melanogaster genome" 100 : 6569-6574, 2003
• 21 Feschotte C, "Merlin, a new superfamily of DNA transposons identified in diverse animal genomes and related to bacterial IS1016 insertion sequences" 21 : 1769-1780, 2004
• 22 안상중, "MMTS, a New Subfamily of Tc1-like Transposons" 한국분자세포생물학회 26 (26): 387-395, 2008
• 23 Tamura K, "MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0" 24 : 1596-1599, 2007
• 24 Ivics Z, "Identification of functional domains and evolution of Tc1-like transposable elements" 93 : 5008-5013, 1996
• 25 Pocwierz-Kotus A, "Family of Tc1-like elements from fish genomes and horizontal transfer" 390 : 243-251, 2007
• 26 Prasad SS, "Evolutionarily conserved regions in Caenorhabditis transposable elements deduced by sequence comparison" 34 : 6-12, 1991
• 27 Robertson HM, "Evolution of DNA transposons, In Mobile DNA II" American Society for Microbiology Press 1093-1110, 2002
• 28 Kocher TD, "Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers" 86 : 6196-6200, 1989
• 29 Capy P, "Dynamics and evolution of transposable elements" Springer 1998
• 30 Lam WL, "Discovery of amphibian Tc1-like transposon families" 257 : 359-366, 1996
• 31 Thompson JD, "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice" 22 : 4673-4680, 1994
• 32 Hall TA, "BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT" 41 : 95-98, 1999
• 33 Kalderon D, "A short amino acid sequence able to specify nuclear location" 39 : 499-509, 1984
• 34 Doak TG, "A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common ‘‘D35E’’ motif" 91 : 942-946, 1994
• 35 Leaver MJ, "A family of Tc1-like transposons from the genomes of fishes and frogs: evidence for horizontal transmission" 271 : 203-214, 2001
• 36 김무상, "A LINE Element from the Olive Flounder (Paralichthys olivaceus) Shows Similarity to the Maui non-LTR Retrotransposon" 한국유전학회 28 (28): 229-236, 2006