Week 5 - Prokaryote Transposons Flashcards Preview

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Flashcards in Week 5 - Prokaryote Transposons Deck (17)
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1

What are transposons?

* A primary group of transposable elements.
• More complex than insertion sequences
• Contain transposase genes and genetic markers (e.g. antibiotic resistance genes)
• Flanked by repeats, direct (same orientation) or inverted
(opposite orientation)
• Two types: composite and non‐composite (replicative)

2

What are transposable elements / transposable genetic elements?

• DNA elements capable of transferring from one location in the genome to another by a process OTHER than homologous recombination.
• Normal components of the genomes of prokaryotes and eukaryotes
• Also known as “jumping genes” due to their ability to move around the genome, “junk” DNA (don't code for proteins), “selfish” DNA
• Mobile segments of DNA that can move from one location in the genome to another
• Usually detected by the changes they bring about in the expression and activities of the genes at or near the sites
into which they integrate
• Biological significance?
- Can affect gene expression
- Provide a means for genomic change
and variation

3

Insertion Sequences (IS)

• The simplest form of transposable genetic element. IS contain a transposase gene flanked by Inverted Repeats (IR), which are identical or nearly identical ends running in opposite directions.
• Contain only the genes required to mobilise the element and insert it into a new location in the genome
• Normal constituents of bacterial chromosomes and plasmids
• First identified in E. coli – due to their effects on the expression of the three genes that control the metabolism of the sugar galactose
• Not typical mutations (point or deletions) but instead had an insertion of an 800 bp DNA segment into a gene.
• Normal components of genomes
• 0.3% of genome
• 768 – 5000 bp in length
• E. coli has a number of IS elements – including IS1, IS2 and IS10R (each present up to 30 copies)
• Frequency of transposition – 10‐5 to 10‐7 per generation
• Inverted repeats (IR) – present in IS, range from 9 – 40 bp in length.

4

Transposons (Tn)

Complex forms of transposable elements.

5

Transposition

The mechanism of movement of a transposable element.

6

What is transposition (movement of transposable elements) also called?

Non‐homologous recombination. Transposable elements insert into locations in the genome where they have no sequence homology.

7

Why are transposable elements important?

• Produce mutations (insert into genes)
• Alter gene expression (insert into gene regulatory
sequences)
• Produce chromosomal mutations
• Major influence in reshaping genomes in evolution

8

Where can transposable elements move to in bacteria and in eukaryotes?

• Bacteria – transposable elements can move to:
- New locations on the same chromosome (only one
chromsome)
- New locations on plasmids
- New locations on bacteriophage chromosomes
• Eukaryotes – transposable elements can move to:
- New positions on the same chromosome
- New positions on a different chromosome

9

Classification of Transposable Elements

• Classified based on how they move from location to location in the genome.
• Transposable elements can move as a DNA segment
- Found in both prokaryotes and eukaryotes
- Class I: cut and paste (conservative) transposition
- Class II: replicative transposition
• Transposable elements move via an RNA
- Found only in eukaryotes
- Related to retroviruses
- Class III: Retrotransposons
- RNA copy
- Reverse transcription

10

How does a class I transposable element move around in DNA?

Class I – cut and paste (conservative) transposition:
- The element itself moves from the donor site into the target site.
- Start with conservative transposon and a target site
- Excision and re‐integration (DNA intermediate)
- Inserts directly into target site.

11

How does a class II transposable element move around in DNA?

Class II – Replicative transposition:
- The element moves a copy of itself to a new site via a DNA intermediate.
- Start with a replicative transposon and a target site.
- Makes a copy (DNA intermediate)
- Donor site (copy) produced.
- Copy inserts into target site.

12

How does a class III transposable element move around in RNA?

Class III – Retrotransposition:
- The element makes an RNA copy of itself which is reversed‐transcribed into a DNA copy which is then inserted.
- Start with a retrotransposon and a target site.
- Transcription into RNA (RNA intermediate).
- Reverse transcription using specialised enzymes produces cDNA.
- cDNA inserts into target site.

13

The two ways in which prokaryotic transposable elements move to a new position on the same chromosome?

1. Insertion Sequences (IS)
2. Transposons –
• Composite
• Non‐composite

14

What is transposase?

* Enzyme required for transposition (recognises IRs).
* Able to make a staggered cut in the target site on the chromosome.
* The insertion sequence (IS) slots in, leaving single-sided gaps at the ends (i.e. where the sitcky ends were), which are filled in by DNA polymerase and DNA ligase.
* This creates a duplication of that segment of DNA that wouldn't have otherwise been in the host's DNA, with the IS sitting between the duplicated sequence. They are direct repeats, i.e. are going in the same direction, whereas the IRs are travelling in opposite directions.

15

What are inverted repeats (IR)?

• IR – short identical/nearly identical sequences at its ends
• Always in inverted orientation with respect to each other
• Range from 9 – 40 bp
• They are characteristic to most but not all types of transposons
• Mutations within IR – transposons lose their ability to move
• Therefore, IR plays an important part in the transposition process.

16

Structure of composite transposons? What is the mechanism of transposition?

• Two identical IS elements (L and R) each containing a transposase gene, placed in the same or inverted orientation.
• A central region containing genes not involved in transposition (e.g. antibiotic resistance genes).
• Tn10 – moves via “cut and paste transposition” (similar to IS10)
• Acts as a large IS element in transposition
• Transposition is initiated by the IS transposase
• Transposition results in target site duplication
Mechanism:
Direct transposition:
• Insertion sequences
• Composite transposons
• Conservative (non‐replicative) or “cut‐and‐paste” transposition
• The mobile element is lost from the original position

17

Structure of non-composite transposons? What is the mechanism of transposition?

• No flanking IS elements
• Inverted Repeats instead – required for transposition
• Genes contained in central region encode transposase, resolvase and antibiotic resistance enzymes
• Resolvase – involved in recombinational events associated with transposition.
• Non‐composite Tn also cause target site duplication.
Mechanism:
Replicative (copy and paste):
* The donor and recipient cointegrate
* Undergo resolution via resolvase
* Recombination between two transposon elements via resolvase.