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What are the two mechanisms by which bacteria regulate gene expression in order to adapt to new environments?

1) Regulation of transcription
2) Control of transcription by DNA rearrangement


Describe how bacteria regulate transcription when adapting to new environments

- Bacteria can increase/decrease transcription based on the new environments
- Done by DNA-binding proteins (interact with promoter regions)

Takes me back to the M2M days... but it makes sense, right?


Describe how control transcription by DNA rearrangement when adapting to new environments

This is best illustrated with an example

- Salmonella contain 2 genes for making flagella (H1 and H2) --- but they can only make 1
- The environment controls which one is expressed b/c the promoter can be *inverted*
- If the bacteria wants H2 expressed, it will produce an H1 repressor that minds to the operator portion of gene --->> prevents transcription of H1


What are the different mechanisms that generate genetic diversity within a bacterial species?

1) Spontaneous mutation
2) Recombination
3) Acquisition of *new* DNA segments


Describe spontaneous mutation.

- Errors b/c of base pair changes, deletions, duplications --- often don't affect anything
- RARE: a mutation can do something positive
- Occur 1 in a billion but b/c bacteria grow in great density, it happens more often than you'd think

OVERALL: mostly not noticeable, but if it is, mostly bad, rarely good


What are the two types of recombination seen in bacterial genetic variation?

1) Antigenic variation
2) Genetic exchange between related organisms


Describe antigenic variation

Similar concept to the H1/H2 Salmonella gene inversion

- Some bacterial genes have multiple silent- non-expressed copies of variant genes for the same structure expression


Describe genetic exchange between related organisms.

- Produce recombinants that have new phenotypic traits
- Relates to plasmid exchange or transposons
- More on this later


What are the different ways to acquire new DNA segments?

1) Acquisition of transposable elements
2) Bacteriophage conversion
3) Acquisition of plasmids
4) Acquisition of pathogenicity islands


What is a transposon? Discuss its replication. For what type of protein does it encode?

AKA: transposable element

- DNA segment that can move itself (or a copy of itself) from one chromosome to another
- Not capable of self-replication except as part of a plasmid, bacterial chromosome, or virus
- Typically encodes for one/more proteins that mediate transposition (TRANSPOSASE)


Describe the process of transposition

- A transposon is introduced into a cell --- as a component of plasmid/bacteriophage
- Distinct nucleotides will be recognized by enzyme and moved
- It may transpose and become stable and permanently integrated into the new chromosome


What is an insertion sequence?


- Transposons that encode transposase
- Play role in genome evolution
- Inactivates genes into which they transpose
- OR turn on gene expression adjacent to the genes they've transposed


What are complex transposons?

- Carry add'l genes
- Encode antibiotic resistance, toxins, adhesions, and other virulence factors


Describe bacteriophage conversion

- Certain virulence genes are on bacteriophages --- not a normal part of bacterial genome
- THEREFORE a virulence factor is only carried/expression by bacterial strains that have been lysogenized and bacteriophage is maintained by bacterium


What are bacterial plasmids?

- Self-replicating, extrachromosomal DNA elements
- Usually circular
- Range from a few genes to a few % of chromosome
- Non-essential


What are the functions of bacterial plasmids?

Can be any of the following:

1) Resistance to antibiotics, heavy metals
2) Virulence factors
3) Metabolic functions
4) Self-transmission (can promote their own transfer from one cell to another!) WOWOW


What are pathogenicity islands?

- large segments of DNA present in some bacterial species

- Encode genes that contribute to virulence --- bacteria w/o PI not virulent or have different disease causing potential
- Molecular appearance suggests they were acquired by an unrelated organism


Describe transformation as a mechanism of gene transfer. Identify the "salient" features.

- Occur in G(+) and G(-) bacteria
- Active component: naked DNA (chromosome fragments from lysing cells or plasmids!)
- Only able to be transformed into new cell at certain points of the growth cycle (competency)
- Occurs most frequently between the same species


Describe transduction generally speaking

- Gene xfer mediated by a bacteriophage
- Closely related with lift cycles of bacteriophages


What are the stages of bacteriophage reproduction?

1) Growth of virulent bacteriophage
2) Temperate phages and lysogenic bacteria
3) Mechanism of transduction
4) Bacteriophage conversion


Describe the growth of virulent bacteriophage

- Virus adsorbs to bacterial cell surface
- Injects its nucleic acid into cell
- Viral genome is replicated, transcribed, and translated


What is a lytic response?

Leads to:
1) Phage multiplication
2) Host cell lysis


What is a lysogenic response?

- Host cell stays alive (unlike lytic response)
- The infecting phage DNA maintained by host cell in a non-infectious stage (PROPHAGE)


Describe the life of a prophage

- Can be induced to enter lytic state --->> viral replication/production, cell lysis
- *Repressor protein* maintains lysogenic stage, which blocks gene expression necessary for viral DNA replications/lytic development

Under stress --->> lytic state


What is a temperate phage?

- Do not invariably kill their host cells
- May elicit a lytic or lysogenic response


Describe bacteriophage/lysogenic conversion

- Temp bacteriophages can encode genes that express during lysogenic phase --->> appearance of a new phenotypic trait
- Genes controlling the new phenotype trait are found ONLY as a component of the phage genome


Describe bacterial conjugation

- Form of genetic transfer dependent on physical contact between donor and recipient cells
- Mediated by bacterial plasmids


Describe the plasmid F paradigm. What is the mechanism of conjugation?

- Plasmid F: prototype self-transmissible plasmid
- Contains genes that encode for:
1) Autonomous replication of plasmid DNA
2) Sex pili synthesis
3) Conjugative xfer of F DNA to recipient cells
4) Ability to integrate into bacterial chromosome



What are conjugate transposons?

- Mobile elements
- Mediate conjugation between pairs of cells
- The transferred DNA is the conjugative transposon!
- The thingy transposes to recipient chromosome

May encode for antibiotic resistance!!