MOBILE GENETIC ELEMENTS

MOBILE GENETIC ELEMENTS

BIOL 300: PRINCIPLES OF GENETICS DISCUSSION

Big Picture

• Overview of key topics:

  • Transposons

  • Replicative Transposition vs. Non-replicative Transposition

  • Retroviruses and Retrotransposons

Transposons

• Definition:

  • Discrete DNA sequences (DNA elements) that transport to other locations within the genome.

  • Referred to as "jumping genes" due to their ability to integrate almost anywhere in the genome without relying on donor/recipient site sequences.

  • These sequences are distributed throughout the entire genome; they constitute approximately 40% of the human genome.

• Characteristics:

  • A large class of mobile DNA elements found in both prokaryotes and eukaryotes.

  • They can be silenced by mechanisms such as methylation.

• Insertion Sequence (IS):

  • A basic type of transposon found in bacteria that includes the transposase gene and inverted repeats.

Transposase

• Overview:

  • An enzyme that recognizes inverted repeats in transposons, excises the sequence from its original location, and transports it to a new site within the genome.

  • The target sequence at the new location becomes duplicated when the transposon integrates.

  • Excision of the transposon is rarely precise and may include nearby genomic information, potentially interrupting genes or promoters.

Non-replicative Transposition

• Class 2 Transposons (DNA transposons):

  • The process involves a cut and paste mechanism, where the transposon makes a single copy.

• Steps:

  1. Donor DNA: The original location of the transposon

  2. Excision: The transposon is excised to create a DNA intermediate.

  3. Integration: The transposon integrates into a target site, filling in gaps in the target DNA at insertion points.

     • Example of Sequence:

     • Target DNA sequences before and after integration can represent direct repeats.

Types of Transposons

• Insertion Sequences (IS):

  • Composed of inverted terminal repeats; these can be found on the arms of DNA.

• Composite Transposons (Tn Elements):

  • Contain genes for transposase and can carry additional genes, such as those for antibiotic resistance.

Class II. DNA Transposon Features

• Terminal Inverted Repeat:

  • Recognized by transposase; sequences are in opposite direction and palindromic.

• Open Reading Frame (ORF):

  • Autonomous Transposon: Contains ORFs that express the transposase.

  • Nonautonomous Transposon: Lacks functional ORFs necessary for transposase expression.

• Target/Direct Repeat:

  • A sequence in the original genome that is replicated during integration but does not participate in the transposition process itself.

Transposition Mechanisms

• 1. Non-replicative (Cut and Paste):

  • Method where the transposon remains as a single copy after excision; the donor DNA is altered while the recipient gains the transposon.

• 2. Replicative (Copy and Paste):

  • Results in an increase in the number of transposons; requires both transposase and resolvase, which are rare among transposons.

  • The donor has a break at the site of the transposon while the recipient gains a copy.

Replicative Transposition

• Process:

  • Operates using a "copy and paste" mechanism:

  1. Before transposition: Donor DNA remains intact while recipient DNA is unaltered.

  2. After integration, the donor maintains its original position, while the recipient acquires an additional copy of the transposon.

• Crossover Structure:

  • Formed when target sequences attach to transposons through the assistance of resolvase, leading to duplication during transposition.

Non-replicative Transposition Overview

• Cut and Paste:

  • The transposon moves physically from one location to another without duplication; it does not require a resolvase.

  • Transposase nicks create single/ double-stranded breaks allowing for the insertion.

Retroviruses

• Definition:

  • Infectious viruses with an RNA genome (can be single-stranded or double-stranded).

  • Recognizes Long Terminal Repeats (LTRs) and converts RNA to DNA within the host cells through reverse transcription.

  • Key Enzymes:

  • Reverse Transcriptase (RTase): Converts ssRNA to dsDNA.

  • Integrase: Inserts the DNA copy of the viral RNA into the host genome.

Structure of a Retrovirus

• Functionality:

  • Retroviruses are closely related to transposons; they operate through similar mechanisms for replication and integration using a gene cassette.

Retroviral Genes

• Gene Cassette:

  • Groups of genes that serve similar functions and are located near each other, generally organized into three major cassettes:

  1. gag: Requires genes for packaging such as matrix, capsid, and nucleocapsid.

  2. pol: Includes enzymes like reverse transcriptase, integrase, and proteases needed to process the retroviral genome.

  3. env: Contains genes for signaling proteins including surface and transmembrane proteins.

Reverse Transcription Process

• Mechanism Overview:

  • Involves multiple steps facilitated by RT, including:

  1. RNA-dependent DNA polymerase activity

  2. Ribonuclease H activity to degrade RNA

  3. DNA-dependent DNA polymerase activity which completes the synthesis of DNA.

Retrotransposons

• Definition:

  • Genetic elements that amplify themselves using an RNA intermediate; not infectious and do not move between organisms or cells.

• Comparison to Retroviruses:

  • Similar mechanisms but lack a viral envelope for infection and do not transfer between cells.

Retrotransposon Structure and Function

• Characteristics:

  • Contains regions such as LTR, gag, pol, int, env and forms viral-like particles (VLP) which lack components essential for infection.

  • Non-LTR Retrotransposons (LINES):

  • Include ORF1, utilize a different recombination mechanism, do not encode integrase/protease.

  • Short-interspersed Nuclear Elements (SINES):

  • Non-autonomous elements that use machinery from LINES for transposition.

Summary of Retrovirus vs. Retrotransposons

• Retrovirus:

  • Begins with RNA genome;

  • Template for reverse transcription to produce integrated DNA expressed as new RNA for future viruses.

• Retrotransposons:

  • Starts with pre-existing elements within the host chromosomes;

  • Utilizes integrated DNA to produce RNAs for duplication, does not package for cellular transfer.