Microbiology - Ch. 11 - Genetics Of Bacteria/archea

Front 1

Asexual Reproduction

Back 1

Front 2

Sexual Reproduction

Back 2

Front 3

Natural Selection Flow Chart

Back 3

Front 4

Forces of Evolutionary Change

Back 4

Natural Selection

&

Genetic Drift

Front 5

Natural Selection

Back 5

Front 6

Genetic Drift

Back 6

Front 7

Mutation

Back 7

Heritable change in DNA sequence that can lead to a change in phenotype (observable properties of an organism).

Front 8

Wild-Type Strain

Back 8

Typically refers to strain isolated from nature.

“Wild-type” can also refer to just one gene.

Front 9

Mutant

Back 9

A cell or virus derived from wild type that carries a nucleotide sequence (genotype) change.

Observable properties (phenotype) may also be altered.

Can be obtained from parental strain derived fromwild-type.

Front 10

Genotype

Back 10

Genotype is designated by italicized (three lowercase letters + capital letter) for a gene (e.g., hisC).

Front 11

Mutations

Back 11

Mutations are designated with numbers referring to order of isolation (e.g., hisC1, hisC2).

Front 12

Phenotype

Back 12

Phenotype is designated by capital letter + two lowercase letters and +/– to indicate presence/absence (e.g., His+ or His–).

Front 13

Spontaneous Mutations

Back 13

Those that occur without external intervention.

Most result from occasional errors by DNA polymerase during replication.

Front 14

Induced Mutations

Back 14

Those made environmentally and deliberately.

Can result from exposure to natural radiation or chemicals that chemically modify DNA.

Front 15

Point Mutations

Back 15

Mutations that change only one base pair.

Can lead to single amino acid change in a protein, an incomplete protein, or no change at all.

Front 16

Types of Base-Pair Substitutions

Back 16

• Missense

• Nonsense

• Silent Mutations

Not all mutations change polypeptides due to degeneracy.

Front 17

Silent Mutations

Back 17

Do not affect sequence of encoded polypeptide or phenotype.

Almost always third base of codon.

Front 18

Missense Mutation

Back 18

Changes sequence of amino acids in polypeptide (e.g., UAC to AAC).

If at a critical location, especially active site, could alter activity.

Not all missense mutations lead to dysfunction.

Front 19

Nonsense Mutation

Back 19

Leads to stop codon.

Typically results in truncated (incomplete) protein that lacks normal activity.

Front 20

Base-Pair Substitutions Visual

Back 20

Front 21

Transitions

Back 21

Purines (A/G) substituted for other purines.

Front 22

Transversions

Back 22

Purines substituted for pyrimidines (C/T) or vice versa.

Front 23

Frameshift Mutations

Back 23

Deletions or insertions that result in a shift in the reading frame.

Insertion/deletion of three base pairs adds/deletes an amino acid, which usually is not as bad.

Scrambles entire polypeptide sequence downstream.

Front 24

Insertions/Deletions...

Back 24

... can result in gain/loss of hundreds to thousands of base pairs.

Often result in complete loss of gene function.

May arise from errors during genetic recombination.

Large insertions may be due to transposable elements.

Front 25

Frameshift Visual

Back 25

Front 26

Mutation Rates Pt. 1

Back 26

Mutation rates depend on frequency of DNA changes and efficiency of DNA repair.

For most microorganisms, errors in DNA replication occur at a frequency of 10^-6 to10^-7 per kb.

Since a typical gene is ~1 kb, frequency of mutation in a single gene is in the same range.

Front 27

Mutation Rates Pt. 2

Back 27

Eukaryotes have 10-fold lower error rates.

DNA viruses have error rates 100–1000x greater.

RNA viruses even higher due to less proofreading and lack of RNA repair mechanisms.

Front 28

Mutation Rates Pt. 3

Back 28

Single base errors more likely to lead to missense than nonsense mutations because most substitutions encode amino acids.

Next most frequent single base change leads to silent mutation.

Can increase pool of mutations by treatment with mutagenic agents or under high stress.

Front 29

Mutagens

Back 29

Chemical, Physical, or Biological agents that increase mutation rates.

Front 30

Chemical Mutagens and Radiation Pt. 1

Back 30

Nucleotide Base Analogs:

Resemble nucleotides but have faulty base-pairing.

Replication errors occur at higher frequencies due to incorrect base pairing.

Front 31

Chemical Mutagens and Radiation Pt. 2

Back 31

Induce chemical modifications.

Example: Alkylating agents such as nitrosoguanidine introduce changes in replicating or nonreplicating DNA.

Front 32

Chemical Mutagens and Radiation Pt. 3

Back 32

Chemical mutagens that cause frameshift mutations.

Example: Intercalating agents such as acridines push two base pairs apart, triggering insertions or deletions.

Front 33

Chemical Mutagens and Radiation Pt. 4

Nonionizing Radiation

Back 33

(e.g., Ultraviolet [UV])

Purines and pyrimidines strongly absorb UV.

Pyrimidine dimer (two adjacent Cs or Ts on the same strand become covalently bonded) is primary effect of UV radiation.

Killing cells by UV is primarily due to effect on DNA.

Front 34

Chemical Mutagens and Radiation Pt. 5

Ionizing Radiation

Back 34

(e.g., X-rays, cosmic rays, and gamma rays)

More powerful than UV.

Ionize water, forming free radicals such as hydroxyl radical (OH·) that damage macromolecules, leading to double- or single-stranded breaks and rearrangements or large deletions.

Front 35

Electromagnetic Spectrum Visual

Back 35

Front 36

Homologous Recombination

Back 36

(Their effect of on genotype)

In bacteria, genetic recombination occurs after transformation, transduction, or conjugation.

To detect exchange of DNA, recombinant cells must phenotypically differ from both parents.

Usually use recipient strains lacking a selectable characteristic that recombinants gain.

Front 37

Transformation

Back 37

Genetic transfer process by which free DNA is incorporated into a recipient cell and brings about genetic change.

Front 38

Competence in Transformation

Back 38

Competent: a cell that can take up DNA and be transformed; genetically determined.

Front 39

In Naturally Transformable Bacteria...

Back 39

... competence is regulated, and competence-specific proteins uptake and process DNA.

Quorum sensing in Bacillus subtilis.

Quorum sensing, chitin sensing, catabolite repression in Vibrio cholerae.

High-efficiency natural transformation is rare in Bacteria.

Front 40

In Other Strains...

Back 40

... specific procedures are necessary to make cells competent (e.g., treatment of E. coli with high Ca+2 and chilling).

Electricity can be used to force cells to take up DNA (electroporation).

Front 41

Uptake and Integration of DNA in Transformation Pt. 1

Back 41

Natural transformation starts with reversible DNA binding that becomes irreversible.

Competent cells bind up to 1000x more DNA than noncompetent cells.

Linear DNA first bound by DNA-binding protein similar to pilus.

Front 42

Uptake and Integration of DNA in Transformation Pt. 2

Back 42

Either ds fragment taken in or nuclease degrades one strand and other is taken in.

Competence-specific protein binds and protects DNA.

RecA integrates DNA.

In contrast, plasmid DNA must remain ds and circular for replication.

Front 43

Transformation Visual

Back 43

Front 44

Def: Transduction

Back 44

Transfer of DNA from one cell to another by a bacteriophage.

Front 45

Two Modes of Transduction

Back 45

Generalized Transduction

&

Specialized Transduction

Front 46

Def: Generalized Transduction

Back 46

DNA from any portion of the host genome is packaged inside the virion.

Donor genes cannot replicate independently.will be lost without recombination.

Front 47

Def: Specialized Transduction

Back 47

DNA from a specific region of the host chromosome is integrated directly into the virus genome.

May be integrated during lysogeny, or homologous recombination may occur.

Front 48

Transduction

Back 48

Occurs in many Bacteria and at least one Archaea.

Ex: multiple-antibiotic-resistance genes in Salmonella, Shiga-like toxins in Escherichia coli, virulence factors in Vibrio cholerae, photosynthetic genes in cyanobacteria.

Front 49

Generalized Transduction Pt. 1

Back 49

Virtually any gene can be transferred to recipient (transductant).

Sometimes host DNA accidentally packaged into phage, forming transducing particle that is defective and cannot lead to viral lytic infection.

Front 50

Generalized Transduction Pt. 2

Back 50

Upon lysis, transducing particles and normal virions released.

Recipients of transducing particles may recombine DNA.

Low efficiency: one in 106–108 cells transduced.

Front 51

Lytic Cycle vs. Transduction

Back 51

Front 52

Lysogeny and Specialized Transduction Pt. 1

Back 52

Extremely efficient transfer.

Selective and transfers only small part of bacterial chromosome.

Phage genome is integrated at specific site (e.g., Lambda in E. coli: next to galactose utilization genes).

Front 53

Lysogeny and Specialized Transduction Pt. 2

Back 53

Viral replication is under control of bacterial host chromosome.

Upon induction, viral DNA sometimes excises incorrectly and takes adjacent host genes along with it.

Limit to amount of host DNA that can replace phage DNA, but helper phage can assist.

Front 54

Specialized Transduction Visual

Back 54

Front 55

Phage Conversion Pt. 1

Back 55

Alteration of the phenotype of a host cell by lysogenization.

Prophage from normal, nondefective temperate infection becomes immune to further infection by same phage.

Other phenotypic changes can also occur.

Front 56

Phage Conversion Pt. 2

Back 56

Salmonella enterica serovar Anatum and bacteriophage ε15.

Corynebacterium diphtheriae and bacteriophage β.

Many natural lysogens found, suggesting this is an essential process for survival.

Front 57

Conjugation (Mating) Pt. 1

Back 57

Horizontal gene transfer that requires cell-to-cell contact.

Plasmid-encoded.

Occurs between closely related or distantly related cells.

Front 58

Conjugation (Mating) Pt. 2

Back 58

Donor Cell: contains conjugative plasmid.

Recipient Cell: does not contain plasmid.

Other genetic elements (e.g., other plasmids or chromosome) may be mobilized (transferred during conjugation).

Front 59

F (“fertility”) Plasmid Pt. 1

Back 59

~99 kbp circular DNA molecule.

Contains genes that regulate DNA replication.

Also contains transposable elements that allow the plasmid to integrate into the host chromosome.

Front 60

F (“fertility”) Plasmid Pt. 2

Back 60

Contains tra genes that encode transfer functions (synthesis of sex pilus and type IV secretion system for DNA transfer).

Pili allow specific pairing through receptor contact, pulling cells together, and DNA transferred through junction.

Front 61

F (“fertility”) Plasmid Visual

Back 61

Front 62

Mechanisms of DNA Transfer During Conjugation Pt. 1

Back 62

DNA synthesized by rolling circle replication.

Mechanism also used by some DNA viruses.

Both donor and recipient have complete plasmids afterwards.

Front 63

Mechanisms of DNA Transfer During Conjugation Pt. 2

Back 63

Transfer of plasmids is efficient and rapid; under favorable conditions nearly 100 percent recipients acquire plasmids.

Transfer of F plasmid takes ~ five minutes.

Front 64

Formation of Hfr Strains and Chromosome Mobilization Pt. 1

Back 64

F plasmid is an episome (can integrate into host chromosome).

Cells possessing a nonintegrated F plasmid are called F+.

Front 65

Formation of Hfr Strains and Chromosome Mobilization Pt. 2

Back 65

Cells possessing an integrated F plasmid are called Hfr (high frequency of recombination).

High rates of genetic recombination between genes on the donor (Hfr) and recipient (F–) chromosomes.

Integration provides mechanism for mobilizing a genome.

Front 66

Presence of the F Plasmid Results in Three Distinct Changes

Back 66

1) Ability to synthesize F pilus.

2) Mobilization of DNA for transfer to another cell.

3) Alteration of surface receptors so that cell can no longer be a conjugation recipient

Front 67

Integration of F Plasmid and Chromosome Mobilization Pt. 1

Back 67

Insertion Sequences.

Homologous recombination results in F plasmid integration into chromosome.

After integration, tra functions normally and strain synthesizes pili.

Front 68

Insertion Sequences

Back 68

Present in both the F plasmid and E. coli chromosome providing regions of sequence homology.

(IS; mobile genetic elements)

Front 69

Integration of F plasmid and chromosome mobilization Pt. 2

Back 69

When recipient encountered, part of plasmid and chromosomal genes transferred.

Many Hfr strains possible.

Front 70

CRISPR

Back 70

CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats): A Prokaryotic “immune system” that evades viral destruction and maintains genome stability.

Front 71

CRISPR mechanism Pt. 1

Back 71

Memory bank of incoming nucleic acid sequences for surveillance against foreign DNA.

Consists of segments of foreign DNA (spacers) that previously invaded cell alternating with identical repeated sequences.

Front 72

CRISPR mechanism Pt. 2

Back 72

Key is transcription of long RNA molecule cleaved in the middle of repeated sequences by nuclease activity of CRISPR-associated (Cas) proteins.

Generates CRISPR RNAs (crRNAs) that base-pair with invading nucleic acids, resulting in destruction.

Front 73

Distribution of CRISPR

Back 73

Widely distributed (~90 percent of Archaea and 70 percent of Bacteria).

Bacteriophages can overcome recognition by genome mutation.