SEA-PHAGES | tnpA transposase and tnpR resolvavse

Link to this post \| posted 28 Jul, 2017 02:48
washj	TnpA and TnpR encode the transposase and resolvase of the ISL3 family of type II transposons. These two genes are flanked inverted repeats - found in LouisV14 gp34/35. This transposon is distinct from others found in the database such as Omega_21. Shound it be distinguished by calling it TnpA transposase or maybe Tn3 transposase? Likewise for the resolvase - TpnR resolvase or Tn3 resolvase? Thanks!

Link to this post | posted 28 Jul, 2017 02:48

TnpA and TnpR encode the transposase and resolvase of the ISL3 family of type II transposons. These two genes are flanked inverted repeats - found in LouisV14 gp34/35. This transposon is distinct from others found in the database such as Omega_21. Shound it be distinguished by calling it TnpA transposase or maybe Tn3 transposase? Likewise for the resolvase - TpnR resolvase or Tn3 resolvase?

Thanks!

Link to this post \| posted 31 Jul, 2017 15:11
welkin	Hi Jackie, I am not familiar enough with transposase classifications to know if LouisV14 meets all the criteria for the specific assignments you propose. Are there specific catalytic residues we have to look for? Or is the classification based solely on the architecture of the transposon?

Link to this post \| posted 14 Aug, 2017 14:13
washj	HI Welkin, The insertion element is identical to IS1096 which is present in smegmatis~ 16 copies (2278 bp in LouisV14 vs 2275bp in smeg - identical blast alignment e0.0; 3 bp diff may be due to sequencing error). The identification of IS10096 is detailed in the following paper from the Jacobs lab http://jb.asm.org/content/173/24/7772.full.pdf I propose the following designations: tnpA transposase tnpR resolvase Jackie

Link to this post | posted 14 Aug, 2017 14:13

washj

HI Welkin,

The insertion element is identical to IS1096 which is present in smegmatis~ 16 copies (2278 bp in LouisV14 vs 2275bp in smeg - identical blast alignment e0.0; 3 bp diff may be due to sequencing error). The identification of IS10096 is detailed in the following paper from the Jacobs lab http://jb.asm.org/content/173/24/7772.full.pdf
I propose the following designations:
tnpA transposase
tnpR resolvase

Jackie

Link to this post \| posted 10 Mar, 2021 19:31
GregFrederick@letu.edu	washj HI Welkin, The insertion element is identical to IS1096 which is present in smegmatis~ 16 copies (2278 bp in LouisV14 vs 2275bp in smeg - identical blast alignment e0.0; 3 bp diff may be due to sequencing error). The identification of IS10096 is detailed in the following paper from the Jacobs lab http://jb.asm.org/content/173/24/7772.full.pdf I propose the following designations: tnpA transposase tnpR resolvase Jackie Jackie- How did you locate the inverted repeats? We have a transposase hit stronger than that with Omega_21. I really want to call the gene. But identifying the actual presence of the transposon is something I am not 100% certain how to proceed at. Thanks for any insight you or others can provide. Greg

Link to this post | posted 10 Mar, 2021 19:31

GregFrederick@letu.edu

washj
HI Welkin,

The insertion element is identical to IS1096 which is present in smegmatis~ 16 copies (2278 bp in LouisV14 vs 2275bp in smeg - identical blast alignment e0.0; 3 bp diff may be due to sequencing error). The identification of IS10096 is detailed in the following paper from the Jacobs lab http://jb.asm.org/content/173/24/7772.full.pdf
I propose the following designations:
tnpA transposase
tnpR resolvase

Jackie

Jackie- How did you locate the inverted repeats? We have a transposase hit stronger than that with Omega_21. I really want to call the gene. But identifying the actual presence of the transposon is something I am not 100% certain how to proceed at.

Thanks for any insight you or others can provide.

Greg

Link to this post \| posted 10 Mar, 2021 20:37
washj	Hi Greg, You can use the online program einverted (http://bio.biomedicine.gu.se/cgi-bin/emboss/einverted) to find inverted repeats by uploading a fasta file or DNA sequence of interest. Jackie

Link to this post \| posted 11 Mar, 2021 18:07
GregFrederick@letu.edu	Awesome. Thanks for that Jackie. One more Q: How close do inverted repeats need to be in order to consider the sequence a "functional transposon"?

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tnpA transposase and tnpR resolvavse