Chapter 9 gene transfer mutations and genome evolution
Download
1 / 42

Chapter 9: Gene Transfer, Mutations, and Genome Evolution - PowerPoint PPT Presentation


  • 171 Views
  • Uploaded on

Chapter 9: Gene Transfer, Mutations, and Genome Evolution. Chapter Overview. ● The mosaic nature of genomes ● Gene transfer: Transformation; conjugation; and transduction ● Genetic recombination ● Mutations: Types and causes ● Mechanisms of DNA repair ● Mobile genetic elements

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Chapter 9: Gene Transfer, Mutations, and Genome Evolution' - nina-schwartz


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

Chapter overview
Chapter Overview

  • ● The mosaic nature of genomes

  • ● Gene transfer: Transformation; conjugation; and transduction

  • ● Genetic recombination

  • ● Mutations: Types and causes

  • ● Mechanisms of DNA repair

  • ● Mobile genetic elements

  • - Insertion sequences and transposons

  • ● How genomes evolve


Introduction
Introduction

  • DNA sequences change over generations through various mutations, rearrangements, and inter- and intraspecies gene transfer.

  • But what are the consequences of DNA plasticity?

  • This chapter explores long-standing evolutionary questions and shows how microbial genomes continually change.


Chapter 9 gene transfer mutations and genome evolution

The Mosaic Nature of Genomes

  • A surprise arising from bioinformatic studies is the mosaic nature of all microbial genomes.

  • - For example, E.coli’s genome is rife with genomic islands, inversions, deletions, and paralogs and orthologs

  • - This is the result of heavy horizontal gene transfer, recombinations, and a variety of mutagenic and DNA repair strategies.


Chapter 9 gene transfer mutations and genome evolution

Recombination: Mechanisms of Genetic Transfer

  • In bacteria recombination occurs in a number of ways:

  • Transformation: Free DNA is transferred

  • Transduction: DNA transfer via a virus

  • Conjugation: Cell-to-cell contact and a plasmid is involved.


Gene transfer by transformation
Gene Transfer by Transformation

Transformation is the process of importing free DNA into bacterial cells.

- the cells need to be competent.

Many cells are capable of natural transformation and naturally competent.

-others require artificial manipulations.

- Perturbing the membrane by chemical (CaCl2) or electrical (electroporation) methods


Chapter 9 gene transfer mutations and genome evolution

Gene Transfer by Transformation

  • Not all bacteria can take up free or naked DNA (<1%).

  • Some microbes become competent sometime during their growth cycle


Chapter 9 gene transfer mutations and genome evolution

Gene Transfer by Transformation

Natural Transformation occus Bacillus sp., Haemophilussp., Neisseriasp., Acinetobactersp., Streptococcus sp., Pseudomonas sp.


Chapter 9 gene transfer mutations and genome evolution

Gram-positive bacteria transform DNA using atransformasomecomplex.


Chapter 9 gene transfer mutations and genome evolution

Gram-negative bacteria transform DNA without the use of competence factors (CF).

some Gram negative organisms are always competent or they become competent when starved.

also, they do not use transformasomes.

most Gram-negative species is sequence-specific.

Thus limiting gene exchange between genera


Chapter 9 gene transfer mutations and genome evolution

Conjugation (mating)

  • Conjugation involves a cell-to-cell contact mediated by a special plasmid, conjugative plasmid

  • Gram Negative:The plasmid carries genes that code for a sex-pilus

  • Gram Positive:Sticky molecules help bind two cells together.

  • Gram Negative Bacteria with conjugative plasmids are malesand without it are females


Gene transfer by conjugation
Gene Transfer by Conjugation

Conjugation is the transfer of DNA from one bacterium to another, following cell-to-cell contact by pilus on the donor cell.

- The pilus attaches to the receptor on the recipient cell

- Two cell fuse and single-stranded DNA passes from donor to recipient cell.


Chapter 9 gene transfer mutations and genome evolution

Conjugationrequires the

presence of special

transferable plasmids

(conjugative plasmids).

A well-studied example in E. coli is the fertility factor (F factor). Also called fertility plasmid

Conjugation begins with contact between the donor cell, called the F+ cell, and a recipient F– cell.


Chapter 9 gene transfer mutations and genome evolution

Conjugation

Female cells become male cells and be able to transfer the plasmid


Chapter 9 gene transfer mutations and genome evolution

Relaxosome: many genes necessary for DNA transfer (halicase, endonuclease, etc.


Chapter 9 gene transfer mutations and genome evolution

Conjugation

The F-factor plasmid can integrate into the chromosome.

- The cell is now designated Hfr, or high-frequency recombination strain.


Chapter 9 gene transfer mutations and genome evolution

Conjugation

Hfr + F-  Hfr + F-

Conjugation between

an Hfr and F-, the

recipient gets some

of the Hfr genes

plus some of the donor’s

genes. The recipient

becomes a

recombinant F-,

since not all Hfr

genes are transferes.

The entire chromosome take about 100 min to transfer as opposed only 5 min for free plasmid


Chapter 9 gene transfer mutations and genome evolution

An integrated F-factor can excise from the chromosome.

- Aberrant excision results in an F′ factor or F′ plasmid,which carries chromosomal genes.

Figure 9.5


Chapter 9 gene transfer mutations and genome evolution

Some bacteria can actually transfer genes across biological domains.

Transfer of Genes into Eukaryotes

- Agrobacterium tumefaciens, which causes crown gall disease

- Contains a tumor-inducing plasmid (Ti) that can be transferred via conjugation to plant cells

Figure 9.6


Gene transfer by transduction
Gene Transfer by Transduction domains.

Transduction is the process in which bacteriophages carry host DNA from one cell to another.

There are two basic types:

- Generalized transduction: Can transfer any gene from a donor to a recipient cell

- Specialized transduction: Can transfer only a few closely linked genes between cells


Chapter 9 gene transfer mutations and genome evolution

Generalized Transduction domains.

Salmonella enterica

Any gene from a donor chromosome is packaged into a bacteriophage and transferred to a new cell upon infection.


Chapter 9 gene transfer mutations and genome evolution

Steps of generalized transduction domains.

  • Bacteriophases with a foreign DNA are called transducing particles.

  • The transducing particles transfer any part of the host DNA to a new host (recipient) cells.

  • Recombination occurs at low frequency

    P1 phage of E.Coli. and P22 phage of Samonella are examples of generalized transduction.




Chapter 9 gene transfer mutations and genome evolution

Specialized Transduction domains.

  • The Phage genome is integrated into the host DNA at a specific site.

  • On induction (UV light), the viral DNA separates from the host genome.

  • Under rare events, the phage DNA maybe excised incorrectly.

  • Some of the adjacent bacterial genes are excised along with the viral genome.

  • When the phage infects new crop of cells, it allows transduction to occur at high frequency


Chapter 9 gene transfer mutations and genome evolution

Bacteria have developed a kind of “safe sex” approach to gene exchange.

This protection system, called restriction and modification, involves:

- Enzymatic cleavage (restriction) of alien DNA, by restriction endonucleases

- Protective methylation (modification) of host DNA

DNA Restriction and Modification


Chapter 9 gene transfer mutations and genome evolution

Figure 9.9 gene exchange.


Recombination
Recombination gene exchange.

Two different DNA molecules in a cell can recombine by one of several mechanisms:

- Generalized recombination requires that the two recombining molecules have a considerable stretch of homologous DNA sequences (>50 bp).

- Site-specific recombination requires very little sequence homology between the recombining DNA molecules.

- But it does require a short sequence recognized by the recombination enzyme


Chapter 9 gene transfer mutations and genome evolution

Recombination gene exchange.

Homologus DNA

Crossing

over

Recombinants


Chapter 9 gene transfer mutations and genome evolution

RecA gene exchange. proteins or Synaptases play critical role in recombination

-double stranded DNA becomes single-stranded DNA by creating a nick

-DNA unwinds

-single-stranded binding proteins bind to the ssDNA

-RecA finds homology and mediated strand invasion


Chapter 9 gene transfer mutations and genome evolution

A gene exchange.mutation is a heritable change in the DNA.

Mutations can come in several different forms:

Types of Mutations

- Point mutation: Change in a single base

- Insertion (addition) and deletion (subtraction) of one or more bases

-Inversion: DNA is flipped in orientation

- Reversion: DNA mutates back to original sequence


Chapter 9 gene transfer mutations and genome evolution

Mutations can be categorized into several information classes:

- Silent mutation:Does not change the amino acid sequence

DNA template  TTT point mutation  T TC

DNA coding  AAA  AAG

m-RNA  UUU  UUC

Amino acid  Phenylalanine  Phenylalanine

Though DNA strand has changed, the protein sequence is the same

Mutations


Chapter 9 gene transfer mutations and genome evolution

Missense mutation classes::Changes the amino acid sequence to another


Chapter 9 gene transfer mutations and genome evolution

Nonsense mutation classes::Changes the amino acid sequence to a stop codon


Chapter 9 gene transfer mutations and genome evolution

Frame-shift mutation classes:: Changes the open-reading frame of the gene



Chapter 9 gene transfer mutations and genome evolution

Spontaneous mutations are rare because of the efficiency of DNA proofreading and repair pathways.

However, they can arise for many reasons:

1)Tautomeric shifts in DNA bases that alter base-pairing properties [ GT or A  C]

2) Oxidative deamination of bases

Mutations Arise in Diverse Ways


Chapter 9 gene transfer mutations and genome evolution

3) Formation of apurinic sites DNA proofreading and repair pathways.[loss of purine]


Chapter 9 gene transfer mutations and genome evolution

Mutations can be caused by DNA proofreading and repair pathways.mutagens:

Chemical agents

- Base analogs

- Base modifiers

- Intercalators

Electromagnetic radiation

- X-rays and gamma rays: Break the DNA

- Ultraviolet rays: Form pyrimidine dimers

Mutations Arise in Diverse Ways


Chapter 9 gene transfer mutations and genome evolution

Mutagenic agents and their effects. DNA proofreading and repair pathways.


Chapter 9 gene transfer mutations and genome evolution

UV radiation can induce dimerization DNA proofreading and repair pathways.