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Related Concept Videos

DNA-only Transposons02:57

DNA-only Transposons

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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
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Transposons01:24

Transposons

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Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Overview of Transposition and Recombination02:13

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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
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Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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Updated: Sep 30, 2025

Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing
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Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing

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Putative Phenotypically Neutral Genomic Insertion Points in Prokaryotes.

Casey B Bernhards1,2, Alvin T Liem1,3, Kimberly L Berk1

  • 1U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States.

ACS Synthetic Biology
|March 10, 2022
PubMed
Summary
This summary is machine-generated.

Researchers developed a new algorithm to find neutral genome editing sites in bacteria. This tool helps insert new genetic functions without harming the organism, aiding synthetic biology applications.

Keywords:
CRISPRgenetic barcodinggenome editinginsertion sitesneutral sitessynthetic biology

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Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
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Area of Science:

  • Microbiology
  • Genomics
  • Synthetic Biology

Background:

  • Genome editing technologies are advancing rapidly across diverse prokaryotic organisms.
  • Efficiently identifying neutral genomic insertion sites is crucial for introducing new genetic functions without impacting organism fitness, especially for noncoding DNA applications like barcoding.

Purpose of the Study:

  • To describe a novel approach and algorithm for identifying putatively neutral insertion sites in prokaryotes.
  • To provide a computational tool and identified targets for common synthetic biology chassis organisms.

Main Methods:

  • Developed an algorithm (targetFinder) to identify convergently transcribed genes with specific gap sizes.
  • Scanned gaps for annotations and evaluated potential insertion sites.
  • Experimentally validated the neutrality of selected sites in *Escherichia coli* by inserting DNA barcodes.

Main Results:

  • Identified putative neutral editing targets in 10 common synthetic biology chassis organisms.
  • Provided software for applying the algorithm to other prokaryotic genomes.
  • Experimental validation in *Escherichia coli* confirmed the neutrality of six identified targets.

Conclusions:

  • The targetFinder algorithm and identified sites offer a valuable resource for synthetic biologists.
  • This approach facilitates the precise and non-disruptive integration of genetic elements in prokaryotes.