Cargando…

Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element

Mariner-like elements (MLE) are a super-family of DNA transposons widespread in animal and plant genomes. Based on their transposition characteristics, such as random insertions and high-frequency heterogeneous transpositions, several MLEs have been developed to be used as tools in gene tagging and...

Descripción completa

Detalles Bibliográficos
Autores principales: Ramakrishnan, Muthusamy, Zhou, Mingbing, Pan, Chunfang, Hänninen, Heikki, Yrjälä, Kim, Vinod, Kunnummal Kurungara, Tang, Dingqin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6696609/
https://www.ncbi.nlm.nih.gov/pubmed/31357686
http://dx.doi.org/10.3390/ijms20153692
_version_ 1783444291430907904
author Ramakrishnan, Muthusamy
Zhou, Mingbing
Pan, Chunfang
Hänninen, Heikki
Yrjälä, Kim
Vinod, Kunnummal Kurungara
Tang, Dingqin
author_facet Ramakrishnan, Muthusamy
Zhou, Mingbing
Pan, Chunfang
Hänninen, Heikki
Yrjälä, Kim
Vinod, Kunnummal Kurungara
Tang, Dingqin
author_sort Ramakrishnan, Muthusamy
collection PubMed
description Mariner-like elements (MLE) are a super-family of DNA transposons widespread in animal and plant genomes. Based on their transposition characteristics, such as random insertions and high-frequency heterogeneous transpositions, several MLEs have been developed to be used as tools in gene tagging and gene therapy. Two active MLEs, Ppmar1 and Ppmar2, have previously been identified in moso bamboo (Phyllostachys edulis). Both of these have a preferential insertion affinity to AT-rich region and their insertion sites are close to random in the host genome. In Ppmar2 element, we studied the affinities of terminal inverted repeats (TIRs) to DNA binding domain (DBD) and their influence on the transposition activity. We could identify two putative boxes in the TIRs which play a significant role in defining the TIR’s affinities to the DBD. Seven mutated TIRs were constructed, differing in affinities based on similarities with those of other plant MLEs. Gel mobility shift assays showed that the TIR mutants with mutation sites G669A-C671A had significantly higher affinities than the mutants with mutation sites C657T-A660T. The high-affinity TIRs indicated that their transposition frequency was 1.5–2.0 times higher than that of the wild type TIRs in yeast transposition assays. The MLE mutants with low-affinity TIRs had relatively lower transposition frequency from that of wild types. We conclude that TIR affinity to DBD significantly affects the transposition activity of Ppmar2. The mutant MLEs highly active TIRs constructed in this study can be used as a tool for bamboo genetic studies.
format Online
Article
Text
id pubmed-6696609
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-66966092019-09-05 Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element Ramakrishnan, Muthusamy Zhou, Mingbing Pan, Chunfang Hänninen, Heikki Yrjälä, Kim Vinod, Kunnummal Kurungara Tang, Dingqin Int J Mol Sci Article Mariner-like elements (MLE) are a super-family of DNA transposons widespread in animal and plant genomes. Based on their transposition characteristics, such as random insertions and high-frequency heterogeneous transpositions, several MLEs have been developed to be used as tools in gene tagging and gene therapy. Two active MLEs, Ppmar1 and Ppmar2, have previously been identified in moso bamboo (Phyllostachys edulis). Both of these have a preferential insertion affinity to AT-rich region and their insertion sites are close to random in the host genome. In Ppmar2 element, we studied the affinities of terminal inverted repeats (TIRs) to DNA binding domain (DBD) and their influence on the transposition activity. We could identify two putative boxes in the TIRs which play a significant role in defining the TIR’s affinities to the DBD. Seven mutated TIRs were constructed, differing in affinities based on similarities with those of other plant MLEs. Gel mobility shift assays showed that the TIR mutants with mutation sites G669A-C671A had significantly higher affinities than the mutants with mutation sites C657T-A660T. The high-affinity TIRs indicated that their transposition frequency was 1.5–2.0 times higher than that of the wild type TIRs in yeast transposition assays. The MLE mutants with low-affinity TIRs had relatively lower transposition frequency from that of wild types. We conclude that TIR affinity to DBD significantly affects the transposition activity of Ppmar2. The mutant MLEs highly active TIRs constructed in this study can be used as a tool for bamboo genetic studies. MDPI 2019-07-28 /pmc/articles/PMC6696609/ /pubmed/31357686 http://dx.doi.org/10.3390/ijms20153692 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ramakrishnan, Muthusamy
Zhou, Mingbing
Pan, Chunfang
Hänninen, Heikki
Yrjälä, Kim
Vinod, Kunnummal Kurungara
Tang, Dingqin
Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element
title Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element
title_full Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element
title_fullStr Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element
title_full_unstemmed Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element
title_short Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element
title_sort affinities of terminal inverted repeats to dna binding domain of transposase affect the transposition activity of bamboo ppmar2 mariner-like element
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6696609/
https://www.ncbi.nlm.nih.gov/pubmed/31357686
http://dx.doi.org/10.3390/ijms20153692
work_keys_str_mv AT ramakrishnanmuthusamy affinitiesofterminalinvertedrepeatstodnabindingdomainoftransposaseaffectthetranspositionactivityofbambooppmar2marinerlikeelement
AT zhoumingbing affinitiesofterminalinvertedrepeatstodnabindingdomainoftransposaseaffectthetranspositionactivityofbambooppmar2marinerlikeelement
AT panchunfang affinitiesofterminalinvertedrepeatstodnabindingdomainoftransposaseaffectthetranspositionactivityofbambooppmar2marinerlikeelement
AT hanninenheikki affinitiesofterminalinvertedrepeatstodnabindingdomainoftransposaseaffectthetranspositionactivityofbambooppmar2marinerlikeelement
AT yrjalakim affinitiesofterminalinvertedrepeatstodnabindingdomainoftransposaseaffectthetranspositionactivityofbambooppmar2marinerlikeelement
AT vinodkunnummalkurungara affinitiesofterminalinvertedrepeatstodnabindingdomainoftransposaseaffectthetranspositionactivityofbambooppmar2marinerlikeelement
AT tangdingqin affinitiesofterminalinvertedrepeatstodnabindingdomainoftransposaseaffectthetranspositionactivityofbambooppmar2marinerlikeelement