TRT, a Vertebrate and Protozoan Tc1-Like Transposon: Current Activity and Horizontal Transfer.
We report a Danio rerio transposon named DrTRT, for D. rerio Transposon Related to Tc1 The complete sequence of the DrTRT transposon is 1,563 base pairs (bp) in length, and its transposase putatively encodes a 338-amino acid protein that harbors a DD37E motif in its catalytic domain. We present evidence based on searches of publicly available genomes that TRT elements commonly occur in vertebrates and protozoa. Phylogenetic and functional domain comparisons confirm that TRT constitutes a new subfamily within the Tc1 family. Hallmark features of having no premature termination codons within the transposase, the presence of all expected functional domains, and its occurrence in the bony fish transcriptome suggest that TRT might have current or recent activity in these species. Further analysis showed that the activity of TRT elements in these species might have arisen about between 4 and 19 Ma. Interestingly, our results also implied that the widespread distribution of TRT among fishes, frog, and snakes is the result of multiple independent HT events, probably from bony fishes to snakes or frog. Finally, the mechanisms underlying horizontal transfer of TRT elements are discussed.
State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
Hua-Hao
HH
Zhang
Department of pathology, Hanzhoung Hospital, Hanzhoung city, Shaanxi, China.
Guo-Yin
GY
Li
Clinical Medical College, Jiujiang University, Jiujiang, China.
Xiao-Min
XM
Xiong
State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China.
Min-Jin
MJ
Han
College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
Xiao-Gu
XG
Zhang
State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China fydai@swu.edu.cn.
Fang-Yin
FY
Dai
D020816:Amino Acid Motifs; D000818:Animals; D020134:Catalytic Domain; D018388:Codon, Terminator; D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D022761:Gene Transfer, Horizontal; D010802:Phylogeny; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019895:Transposases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015027:Zebrafish / Q000235:genetics; D029961:Zebrafish Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
D018388:Codon, Terminator; D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins; D015800:Protozoan Proteins; D029961:Zebrafish Proteins; C111652:mariner transposases; D019895:Transposases
DD37E; Tc1/mariner transposons; horizontal transfer
Bioinformatics. 2000 Apr;16(4):404-5
10869041
Mol Biol Evol. 2012 Feb;29(2):503-15
21771716
Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11781-6
16081532
Genome Biol Evol. 2014 May 27;6(6):1375-86
24868016
Bioinformatics. 2006 Dec 1;22(23):2971-2
17021158
Genetics. 2007 Dec;177(4):2553-8
17947403
Nat Commun. 2016 Apr 21;7:11396
27097561
Mol Phylogenet Evol. 2013 Jan;66(1):223-32
23032571
Bioinformatics. 2003 Aug 12;19(12):1572-4
12912839
Genome Biol Evol. 2012;4(9):929-36
22887124
Cytogenet Genome Res. 2005;110(1-4):462-7
16093699
Genetica. 2007 Jun;130(2):105-20
16912840
Genetics. 2010 Dec;186(4):1085-93
21156958
Genome. 2014 Apr;57(4):193-9
24905071
Gene. 2001 Jun 27;271(2):203-14
11418241
Proc Natl Acad Sci U S A. 1986 Nov;83(22):8684-8
3022302
Trends Genet. 1999 Aug;15(8):326-32
10431195
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
15034147
Trends Ecol Evol. 2010 Sep;25(9):537-46
20591532
J Hered. 2001 Jul-Aug;92(4):371-3
11535656
Genetics. 1996 Nov;144(3):1087-95
8913752
Trends Genet. 2000 Jun;16(6):276-7
10827456
Mar Biotechnol (NY). 1999 Jan;1(1):60-67
10373611
Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12046-51
17623783
Methods Mol Biol. 2014;1116:271-302
24395370
J Mol Biol. 1990 Oct 5;215(3):403-10
2231712
Nucleic Acids Res. 2009 Mar;37(4):1239-47
19136468
Mob DNA. 2014 Jun 03;5:17
24926322
Annu Rev Genet. 2007;41:331-68
18076328
Nat Commun. 2016 Mar 30;7:11126
27025571
Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):1012-6
23277587
Genome Biol. 2007;8 Suppl 1:S2
18047694
BMC Genomics. 2013 Feb 27;14:134
23445260
Bioinformatics. 2011 Apr 15;27(8):1164-5
21335321
Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17023-8
18936483
Mol Biol Evol. 2000 Sep;17(9):1313-25
10958848
Genetics. 2001 Nov;159(3):1103-15
11729156
Mol Biol Evol. 2007 Aug;24(8):1596-9
17488738
Dev Genet. 1986;6(4):281-91
2840224
Bioinformatics. 2015 Sep 1;31(17):2915-7
25940562
Nature. 2010 Apr 29;464(7293):1347-50
20428170
Mol Biol Evol. 2006 Jul;23(7):1414-9
16672286
Gene. 2010 Jan 1;449(1-2):85-94
19747963
Mol Gen Genet. 1994 Sep 28;244(6):606-12
7969029