scholarly journals Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences

PLoS Biology ◽  
2004 ◽  
Vol 2 (8) ◽  
pp. e234 ◽  
Author(s):  
Rick S Mitchell ◽  
Brett F Beitzel ◽  
Astrid R. W Schroder ◽  
Paul Shinn ◽  
Huaming Chen ◽  
...  
Keyword(s):  
Target Site ◽  
Dna Integration ◽  
Site Preferences

scholarly journals DNA Integration by Ty Integrase in yku70Mutant Saccharomyces cerevisiae Cells

2000 ◽  
Vol 20 (23) ◽  
pp. 8836-8844 ◽  
Author(s):  
Markus Kiechle ◽  
Anna A. Friedl ◽  
Palaniyandi Manivasakam ◽  
Friederike Eckardt-Schupp ◽  
Robert H. Schiestl
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Plasmid Dna ◽  
Integration Site ◽  
Cellular Function ◽  
Target Site ◽  
Target Site Duplication ◽  
Wild Type ◽  
Dna Integration ◽  
Site Preferences

ABSTRACT In the present work we examined nonhomologous integration of plasmid DNA in a yku70 mutant. Ten of 14 plasmids integrated as composite elements, including Ty sequences probably originating from erroneous strand-switching and/or priming events. Three additional plasmids integrated via Ty integrase without cointegrating Ty sequences, as inferred from 5-bp target site duplication and integration site preferences. Ty integrase-mediated integration of non-Ty DNA has never been observed in wild-type cells, although purified integrase is capable of using non-Ty DNA as a substrate in vitro. Hence our data implicate yKu70 as the cellular function preventing integrase from accepting non-Ty DNA as a substrate.

scholarly journals Disintegration promotes proto-spacer integration by the Cas1-Cas2 complex

2020 ◽  
Author(s):  
Chien-Hui Ma ◽  
Kamyab Javanmardi ◽  
Ilya J. Finkelstein ◽  
Makkuni Jayaram
Keyword(s):  
Dna Repair ◽  
Streptococcus Pyogenes ◽  
Target Site ◽  
Dna Transposition ◽  
Insertion Event ◽  
Dna Integration ◽  
Biochemical Investigation ◽  
Target Sites ◽  
Repair Pathways ◽  
Integration Event

Abstract‘Disintegration’—the reversal of transposon DNA integration at a target site—is regarded as an abortive off-pathway reaction. Here we challenge this view with a biochemical investigation of the mechanism of protospacer insertion by the Streptococcus pyogenes Cas1-Cas2 complex, which is mechanistically analogous to DNA transposition. In supercoiled target sites, the predominant outcome is the disintegration of one-ended insertions that fail to complete the second integration event. In linear target sites, one-ended insertions far outnumber complete proto-spacer insertions. The second insertion event is most often accompanied by disintegration of the first, mediated either by the 3’-hydroxyl exposed during integration or by water. One-ended integration intermediates may mature into complete spacer insertions via DNA repair pathways that are also involved in transposon mobility. We propose that disintegration-promoted integration is functionally important in the adaptive phase of CRISPR-mediated bacterial immunity, and perhaps in other analogous transposition reactions.

Target-site Preferences of Sleeping Beauty Transposons

2005 ◽  
Vol 346 (1) ◽  
pp. 161-173 ◽  
Author(s):  
Geyi Liu ◽  
Aron M. Geurts ◽  
Kojiro Yae ◽  
A.R. Srinivasan ◽  
Scott C. Fahrenkrug ◽  
...  
Keyword(s):  
Sleeping Beauty ◽  
Target Site ◽  
Site Preferences

scholarly journals Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection

2006 ◽  
Vol 2 (6) ◽  
pp. e60 ◽  
Author(s):  
Mary K Lewinski ◽  
Masahiro Yamashita ◽  
Michael Emerman ◽  
Angela Ciuffi ◽  
Heather Marshall ◽  
...  
Keyword(s):  
Site Selection ◽  
Target Site ◽  
Dna Integration ◽  
Target Site Selection

scholarly journals Use of Patient-Derived Human Immunodeficiency Virus Type 1 Integrases To Identify a Protein Residue That Affects Target Site Selection

2001 ◽  
Vol 75 (16) ◽  
pp. 7756-7762 ◽  
Author(s):  
Amy L. Harper ◽  
Lynn M. Skinner ◽  
Malgorzata Sudol ◽  
Michael Katzman
Keyword(s):  
Human Immunodeficiency Virus ◽  
Amino Acid ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Target Site ◽  
Site Preferences ◽  
Immunodeficiency Virus ◽  
Cellular Dna ◽  
Hiv 1

ABSTRACT To identify parts of retroviral integrase that interact with cellular DNA, we tested patient-derived human immunodeficiency virus type 1 (HIV-1) integrases for alterations in the choice of nonviral target DNA sites. This strategy took advantage of the genetic diversity of HIV-1, which provided 75 integrase variants that differed by a small number of amino acids. Moreover, our hypothesis that biological pressures on the choice of nonviral sites would be minimal was validated when most of the proteins that catalyzed DNA joining exhibited altered target site preferences. Comparison of the sequences of proteins with the same preferences then guided mutagenesis of a laboratory integrase. The results showed that single amino acid substitutions at one particular residue yielded the same target site patterns as naturally occurring integrases that included these substitutions. Similar results were found with DNA joining reactions conducted with Mn2+ or with Mg2+ and were confirmed with a nonspecific alcoholysis assay. Other amino acid changes at this position also affected target site preferences. Thus, this novel approach has identified a residue in the central domain of HIV-1 integrase that interacts with or influences interactions with cellular DNA. The data also support a model in which integrase has distinct sites for viral and cellular DNA.

scholarly journals Disintegration promotes protospacer integration by the Cas1-Cas2 complex

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Chien-Hui Ma ◽  
Kamyab Javanmardi ◽  
Ilya J Finkelstein ◽  
Makkuni Jayaram
Keyword(s):  
Dna Repair ◽  
Streptococcus Pyogenes ◽  
Target Site ◽  
Dna Transposition ◽  
Insertion Event ◽  
Dna Integration ◽  
Biochemical Investigation ◽  
Target Sites ◽  
Repair Pathways ◽  
Integration Event

‘Disintegration’—the reversal of transposon DNA integration at a target site—is regarded as an abortive off-pathway reaction. Here, we challenge this view with a biochemical investigation of the mechanism of protospacer insertion, which is mechanistically analogous to DNA transposition, by the Streptococcus pyogenes Cas1-Cas2 complex. In supercoiled target sites, the predominant outcome is the disintegration of one-ended insertions that fail to complete the second integration event. In linear target sites, one-ended insertions far outnumber complete protospacer insertions. The second insertion event is most often accompanied by the disintegration of the first, mediated either by the 3′-hydroxyl exposed during integration or by water. One-ended integration intermediates may mature into complete spacer insertions via DNA repair pathways that are also involved in transposon mobility. We propose that disintegration-promoted integration is functionally important in the adaptive phase of CRISPR-mediated bacterial immunity, and perhaps in other analogous transposition reactions.

scholarly journals An Amino Acid in the Central Catalytic Domain of Three Retroviral Integrases That Affects Target Site Selection in Nonviral DNA

2003 ◽  
Vol 77 (6) ◽  
pp. 3838-3845 ◽  
Author(s):  
Amy L. Harper ◽  
Malgorzata Sudol ◽  
Michael Katzman
Keyword(s):  
Amino Acid ◽  
Catalytic Domain ◽  
Target Site ◽  
Rous Sarcoma ◽  
Site Preferences ◽  
Target Dna ◽  
Sarcoma Virus ◽  
Cellular Dna

ABSTRACT Integrase can insert retroviral DNA into almost any site in cellular DNA; however, target site preferences are noted in vitro and in vivo. We recently demonstrated that amino acid 119, in the α2 helix of the central domain of the human immunodeficiency virus type 1 integrase, affected the choice of nonviral target DNA sites. We have now extended these findings to the integrases of a nonprimate lentivirus and a more distantly related alpharetrovirus. We found that substitutions at the analogous positions in visna virus integrase and Rous sarcoma virus integrase changed the target site preferences in five assays that monitor insertion into nonviral DNA. Thus, the importance of this protein residue in the selection of nonviral target DNA sites is likely to be a general property of retroviral integrases. Moreover, this amino acid might be part of the cellular DNA binding site on integrase proteins.

scholarly journals Conjugative transposition of the vancomycin resistance carrying Tn1549: enzymatic requirements and target site preferences

2018 ◽  
Vol 107 (5) ◽  
pp. 639-658 ◽  
Author(s):  
Lotte Lambertsen ◽  
Anna Rubio-Cosials ◽  
Kiran Raosaheb Patil ◽  
Orsolya Barabas
Keyword(s):  
Vancomycin Resistance ◽  
Target Site ◽  
Site Preferences ◽  
Conjugative Transposition
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