The Bacterial Genetics

The Bacterial Genome

The Bacterial Genome is the total collection of genes carried by a bacterium both on its chromosome and on its extrachromosomal genetic elements (plasmids)

The Bacterial Genome

A Gene
A gene (unit of heredity) is a nucleotide sequence of DNA which determines the synthesis of polypeptide, or replication of suitable molecule of RNA Genes essential for bacterial growth are carried on a single chromosome - nucleoid All the bacterial cells are therefore haploid

The Bacterial Genome

DNA Structure
a) A schematic, nonhelical model

b) A schematic drawing of the Watson-Crick structure of DNA, showing helical sugar-phosphate backbones of the two strands held together by hydrogen bonding between the basis

c) Space-filling model of DNA

The Bacterial Genome

DNA Forms

a) The DNA double helix of most procaryotes has the shape of a closed circle

b) The circular DNA strands, already coiled in a double helix, are twisted a second time to produce supercoils

The Bacterial Genome

DNA Forms
The total length of E.coli chromosome is about 1 mm The Bacterium itself is only several micrometers in length The DNA is about 1000 times longer than bacterium and must be condensed (supercoiling)

The Bacterial Genome

DNA Replication
Semiconservative Replication of DNA The replication fork of DNA showing the synthesis of two progeny strands. Each copy contain one new and one old strand. Bacterial chromosome is called Replicon Replicon – a part of the genome that contains an origin site and is replicated as a whole unit
The Bacterial Genome

DNA Replication

An autoradiograph of a replicating E.coli chromosome; about one-third of the chromosome has been replicated

The Bacterial Genome

Replication of circular DNA

Vegetative

The Bacterial Genome

Replication of circular DNA
Conjugative

Mechanism used by some bacterial viruses, plasmids and in chromosomal transfer

The Bacterial Genome

Transposable elements
  IS – Insertion sequences Tn - Transposones

IS are small DNA pieces, about 1-2 kilobases long with 2 distinctive traits: - CORE area containing genes for transposition - Specific INVERTED REPEATS at their ends Tn is a genetic element that containing genes for transposition and additional extragenes, which provide resistance against antibiotics or synthesis enzymes of specific metabolic pathways These elements can transfer from chromosomal location to another, and from a chromosome to a plasmid or back
The Bacterial Genome

Transposable elements

The Bacterial Genome

Transposable elements
Main roles: • • • Cause deletion and inversions of DNA sequences (internal or biological mutagenic agents) Insert into genes and inactivate those genes Spread of antibiotic resistance genes

Mobile genetic elements are responsible for the major part of genetic variability in natural bacterial populations Tn-s may enter other genera of bacteria during transfer of plasmids or via transducing phage

The Bacterial Genome

Plasmids
Plasmids is a small genetic elements
capable of independent replication in bacteria. Most plasmids are circular doublestranded DNA molecule, but some are linear. Plasmids made their presence by conferring phenotypes of cell harboring them.

F-Plasmid

F - fertility factor R - antibiotic resistance Col - colicin production
Virulence plasmids:

Ent - enterotoxin production Hly - hemolysin production CFA-I; CFA-II - adhesins production
The Bacterial Genome

Bacteriophages
Litic cycle

Lysogenic cycle

The Bacterial Genome

Bacteriophages
Virulent bacteriophage – a bacteriophage which always causes the lytic cycle, resulting in a death of a cell and production of new phage particles Temperate (or lysogenic) bacteriophage – a bacteriophage whose DNA integrates into bacterial chromosome, but doesn’t cause the lysis of the cell and production new phage particles. The integrative phage’s DNA is called prophage A bacterial cell with prophage is called lysogenic cell

The Bacterial Genome

Bacteriophages
Lysogenic conversion is a state when bacterial cell exhibit new properties, that are coded by the prophage genes Example: - Toxigenic (tox+) and nontoxigenic strains of Corynebacterium diphtheriae - Production of erythrogenic toxin by Streptococcus pyogenes - Production botulinal toxin of Clostridium botulinum

The Bacterial Genome

Genetic Variation

Mutations are stable hereditary changes in the coding sequence of DNA Occur spontaneously or are induced by different mutagens

Various kind of mutations

The Bacterial Genome

Genetic Variation
Genetic recombination at the molecular level is the process by which DNA from a donor cell and DNA from a recipient cell combine to yield a new genome containing information from both sources Molecular Mechanisms of Recombination

Homologous (legitimate)

Nonhomologous (illegitimate)

The Bacterial Genome

Genetic Variation
Homologues recombination occurs between closely related DNA sequences and generally substitutes one sequence to another. The process requires a set of enzymes produced by the group “rec” genes, and homology in 100-200 n.p. Nonhomologues recombination occurs between dissimilar DNA sequences and generally produces insertions or deletions or both. This process usually requires specialized (site-specific) recombination enzymes, such as those produced by many transposons and lysogenic bacteriophages

The Bacterial Genome

Gene Transfer
The transfer of genetic material between procaryotes is called horizontal (or lateral) gene transfer. It takes place in one of 3 ways: 4. Transformation 5. Conjugation 6. Transduction

The Bacterial Genome

Gene Transfer
Transformation Was discovered by Griffits in 1928 during the experiments with Streptococcus pneumoniae. Later Avery, MacLeod and McCarty identified the DNA as the transforming agent and as the genetic material Transformation is the process by which bacteria take up fragment of naked DNA and incorporate this molecule into recipient chromosome in a heritable form

The Bacterial Genome

Gene Transfer
Transformation The requirement for the DNA fragment from the donor bacterium Molecular weight (M) 105 -106 D Double-stranded fragment of DNA The state of recipient cell is called competence Competency is a complex phenomenon which is dependent on several conditions: - Certain stage of bacterial culture’s growth (exponential phase) - Secretion of a small protein, called competence factor, that stimulates the production of 8 to 10 new proteins is required for transformation (DNA-biding protein, endonucleases, autolysins)
The Bacterial Genome

Gene Transfer
Conjugation Was discovered in 1946 by Lederberg and Tatum. In 1952 Hayes demonstrated that the gene transfer was polar. Polarity is mediated by plasmid, known as F-factor. Donor (F+, or fertile) and recipient (F-, or nonfertile) were defined. F plasmid contains tra-operon. Genes of tra-operon encode proteins for building the sex pili and proteins needed to construct the type four secretion system that will transfer DNA from donor to the recipient

The Bacterial Genome

Gene Transfer
Conjugation

IS3

γδ IS3

tra
F-plasmid F

IS2

100 kb

oriT oriV
The Bacterial Genome

Gene Transfer
Conjugation Donor Types: • F+ cells with free F-plasmid F+ x FF+ • Hfr cells with integrated plasmid Hfr x FF- (F+100) • F’ free F-plasmid with a portion of chromosomal genes F’ x FF’

The Bacterial Genome

Gene Transfer
Cell-to-cell transfer of a conjugative plasmid

Integration of conjugative plasmid into the bacterial chromosome an Hfr

The order of genes on the bacterial chromosome can be determined by the time of entry of the genes into a recipient cell
The Bacterial Genome

Gene Transfer
Conjugation is very useful for genetic mapping of bacteria

A circular genetic map of E.coli K12 with the location of selected genes. The map is divided into 100 minutes

The Bacterial Genome

Gene Transfer
Transduction Was discovered by Zinder and Lederberg in 1951-1953. Transduction is a process of transfer of the bacterial DNA with bacteriophages. Transduction can be classified as: - Generalized any gene of the host bacterium can be transferred and doesn’t require lysogeny (Salmonella enterica – P-22) - Specialized only specific genes near the attachment sites of a lysogenic phage in the host chromosome can be transferred (E.coli- λ) - Abortive the transferred DNA is not integrated but often is able to temporary survive and express. The fragment inherits linearly and lost in progeny
The Bacterial Genome

Transduction

The Bacterial Genome

Genetic Engineering
Genetic Engineering – a combination of methods which allows to conduct artificial recombination of DNA and produce chimerical molecules, non-typical for nature

The Bacterial Genome

Genetic Engineering
Main aims of Genetic Engineering: 3. 4. 5. The production of medically useful proteins (somatostotine, insulin, human growth harmone, interferons, interleukin-2, etc.) Recombinant vaccines (hepatitis B vaccine) Gene therapy (involves the insertion of a normal gene into cell to correct a defective gene

The Bacterial Genome

Genetic Engineering
The basic tools of Genetic Engineering: 3. Cloning vectors which can be used to deliver the DNA sequences into receptive bacteria Restriction enzymes which are used to cleave DNA at defined sequences DNA – ligase – the enzyme that links the fragment to the cloning vector

4. 5.

The Bacterial Genome

Genetic Engineering
Types of vector: 3. 4. 5. 6. Plasmid (pUC, pBR322, pGEM) are used for DNA fragments up to 20Kb Bacteriophages (λ, T7) are used for larger fragments up to 25Kb Cosmid (combination of plasmid and phage genes, pJC720) for fragments up to 45Kb Viruses (poxvaccine)

The Bacterial Genome

Genetic Engineering
The specific properties of plasmid cloning vectors: 3. 4. 5. 6. 7. Small size to be easy inserted into bacteria High number of copies to be easily purified in sufficient quantities Ability to replicate within a host cell Selectable traits (resistance to an antibiotic) One or few sites for restriction endonucleases which cut DNA and allow the insertion of foreign DNA

The Bacterial Genome

Genetic Engineering
Steps in Cloning a Gene: • • • • • Isolate a DNA to be cloned Use restriction enzyme to generate fragments of DNA Generate a recombinant molecule by inserting DNA fragments into a cloning vector Introduce recombinant molecule into new host Select bacterial clones carrying specific genes

The Bacterial Genome

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