A New DNA Inversion Mechanism: Recombination of the DNA Foldback Intercoil Structure

Abstract The Hin recombinase catalyzes a site-specific recombination reaction that results in the reversible inversion of a 1-kbp segment of the Salmonella chromosome. The DNA inversion reaction catalyzed by the Salmonella Hin recombinase is a dynamic process proceeding through many intermediate stages, requiring multiple DNA sites and the Fis accessory protein. Biochemical analysis of this reaction has identified intermediate steps in the inversion reaction but has not yet revealed the process by which transition from one step to another occurs. Because transition from one reaction step to another proceeds through interactions between specific amino acids, and between amino acids and DNA bases, it is possible to study these transitions through mutational analysis of the proteins involved. We isolated a large number of mutants in the Hin recombinase that failed to carry out the DNA exchange reaction. We generated genetic tools that allowed the assignment of these mutants to specific transition steps in the recombination reaction. This genetic analysis, combined with further biochemical analysis, allowed us to define contributions by specific amino acids to individual steps in the DNA inversion reaction. Evidence is also presented in support of a model that Fis protein enhances the binding of Hin to the hixR recombination site. These studies identified regions within the Hin recombinase involved in specific transition steps of the reaction and provided new insights into the molecular details of the reaction mechanism.

Download Full-text

The recombinational enhancer for DNA inversion functions independent of its orientation as a consequence of dyad symmetry in the Fis-DNA complex

Nucleic Acids Research ◽

10.1093/nar/17.15.6043 ◽

1989 ◽

Vol 17 (15) ◽

pp. 6043-6054 ◽

Cited By ~ 7

Author(s):

Ronald Kanaar ◽

Jochem P. van Hal ◽

Pieter van de Putte

Keyword(s):

Dna Inversion ◽

Dyad Symmetry ◽

Dna Complex

Download Full-text

A and T homopolymeric stretches mediate a DNA inversion in Plasmodium falciparum which results in loss of gene expression

Molecular and Cellular Biology ◽

10.1128/mcb.10.6.3243-3246.1990 ◽

1990 ◽

Vol 10 (6) ◽

pp. 3243-3246

Author(s):

L G Pologe ◽

D de Bruin ◽

J V Ravetch

Keyword(s):

Gene Expression ◽

Plasmodium Falciparum ◽

Gene Structure ◽

Infected Erythrocyte ◽

Dna Rearrangement ◽

Coding Sequences ◽

Dna Inversion ◽

Erythrocyte Surface ◽

Stable Substrate ◽

Flanking Sequences

Ring-infected erythrocyte surface antigen-negative isolates of Plasmodium falciparum demonstrate a complex DNA rearrangement with inversion of 5' coding sequences, deletion of upstream and flanking sequences, and healing of the truncated chromosome by telomere addition. An inversion intermediate that results in the telomeric gene structure for RESA has been identified in the pathway. This inversion creates a mitotically stable substrate for the sequence-specific addition of telomere repeats at the deletion breakpoint.

Download Full-text

A and T homopolymeric stretches mediate a DNA inversion in Plasmodium falciparum which results in loss of gene expression.

Molecular and Cellular Biology ◽

10.1128/mcb.10.6.3243 ◽

1990 ◽

Vol 10 (6) ◽

pp. 3243-3246 ◽

Cited By ~ 15

Author(s):

L G Pologe ◽

D de Bruin ◽

J V Ravetch

Keyword(s):

Gene Expression ◽

Plasmodium Falciparum ◽

Gene Structure ◽

Infected Erythrocyte ◽

Dna Rearrangement ◽

Coding Sequences ◽

Dna Inversion ◽

Erythrocyte Surface ◽

Stable Substrate ◽

Flanking Sequences

Ring-infected erythrocyte surface antigen-negative isolates of Plasmodium falciparum demonstrate a complex DNA rearrangement with inversion of 5' coding sequences, deletion of upstream and flanking sequences, and healing of the truncated chromosome by telomere addition. An inversion intermediate that results in the telomeric gene structure for RESA has been identified in the pathway. This inversion creates a mitotically stable substrate for the sequence-specific addition of telomere repeats at the deletion breakpoint.

Download Full-text

Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion

eLife ◽

10.7554/elife.01211 ◽

2013 ◽

Vol 2 ◽

Cited By ~ 12

Author(s):

Meghan M McLean ◽

Yong Chang ◽

Gautam Dhar ◽

John K Heiss ◽

Reid C Johnson

Keyword(s):

Catalytic Domain ◽

Control Site ◽

Dna Looping ◽

Enhancer Element ◽

Dna Inversion ◽

Serine Recombinases ◽

Multiple Interfaces ◽

Nucleoprotein Complexes ◽

Beta Hairpin ◽

Basic Region

Serine recombinases are often tightly controlled by elaborate, topologically-defined, nucleoprotein complexes. Hin is a member of the DNA invertase subclass of serine recombinases that are regulated by a remote recombinational enhancer element containing two binding sites for the protein Fis. Two Hin dimers bound to specific recombination sites associate with the Fis-bound enhancer by DNA looping where they are remodeled into a synaptic tetramer competent for DNA chemistry and exchange. Here we show that the flexible beta-hairpin arms of the Fis dimers contact the DNA binding domain of one subunit of each Hin dimer. These contacts sandwich the Hin dimers to promote remodeling into the tetramer. A basic region on the Hin catalytic domain then contacts enhancer DNA to complete assembly of the active Hin tetramer. Our results reveal how the enhancer generates the recombination complex that specifies DNA inversion and regulates DNA exchange by the subunit rotation mechanism.

Download Full-text

Economic analysis inversion mechanism taking into account argument interrelation

Proceedings of the 1st International Scientific Conference "Modern Management Trends and the Digital Economy: from Regional Development to Global Economic Growth" (MTDE 2019) ◽

10.2991/mtde-19.2019.16 ◽

2019 ◽

Author(s):

E.B. Gribanova ◽

I.N. Logvin

Keyword(s):

Economic Analysis ◽

Inversion Mechanism

Download Full-text

Flp Recombinase-Mediated DNA Inversion

Encyclopedia of Genetics ◽

10.1006/rwgn.2001.0466 ◽

2001 ◽

pp. 717-721

Author(s):

M. Jayaram

Keyword(s):

Dna Inversion ◽

Flp Recombinase

Download Full-text

The Genome and Transcriptome Analysis of the Vigna mungo Chloroplast

Plants ◽

10.3390/plants9091247 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1247

Author(s):

Wanapinun Nawae ◽

Chutintorn Yundaeng ◽

Chaiwat Naktang ◽

Wasitthee Kongkachana ◽

Thippawan Yoocha ◽

...

Keyword(s):

Chloroplast Genome ◽

Rna Editing ◽

Genome Engineering ◽

Vigna Mungo ◽

Legume Species ◽

Dna Inversion ◽

Phylogenetic Studies ◽

Dna Base ◽

Chloroplast Genome Sequence ◽

Root Tissues

Vigna mungo is cultivated in approximately 5 million hectares worldwide. The chloroplast genome of this species has not been previously reported. In this study, we sequenced the genome and transcriptome of the V. mungo chloroplast. We identified many positively selected genes in the photosynthetic pathway (e.g., rbcL, ndhF, and atpF) and RNA polymerase genes (e.g., rpoC2) from the comparison of the chloroplast genome of V. mungo, temperate legume species, and tropical legume species. Our transcriptome data from PacBio isoform sequencing showed that the 51-kb DNA inversion could affect the transcriptional regulation of accD polycistronic. Using Illumina deep RNA sequencing, we found RNA editing of clpP in the leaf, shoot, flower, fruit, and root tissues of V. mungo. We also found three G-to-A RNA editing events that change guanine to adenine in the transcripts transcribed from the adenine-rich regions of the ycf4 gene. The edited guanine bases were found particularly in the chloroplast genome of the Vigna species. These G-to-A RNA editing events were likely to provide a mechanism for correcting DNA base mutations. The V. mungo chloroplast genome sequence and the analysis results obtained in this study can apply to phylogenetic studies and chloroplast genome engineering.

Download Full-text