Microbiology - Ch. 6

Front 1

Do Microbes Make Unnecessary Proteins?

Back 1

No, the microbe will not waste energy making unneeded proteins.

- It uses elegant mechanisms to

control gene expression at

various levels.

Front 2

Central Dogma Visual

Back 2

Front 3

The two Approaches to Regulation

Back 3

Regulation of gene expression...

- transcription initiation.

- transcription elongation.

- translation.

&

Alter activity of enzymes and proteins...

- posttranslational.

Front 4

The 2 different outcomes from DNA binding...

Back 4

The binding event can block transcription (negative regulation).

The binding event can activate transcription (positive regulation).

Front 5

Def: Negative Control

Back 5

Negative control: a regulatory mechanism that stops transcription.

Front 6

Def: Repression

Back 6

Preventing the synthesis of an enzyme in response to sufficient amounts of a product.

- specific effect.

- widespread control for amino

acid and nucleotide precursors.

- Usually, final product of a

biosynthetic pathway represses

enzymes.

- Usually affects biosynthetic

anabolic enzymes.

Front 7

Repression Visual

Back 7

Front 8

Negative Control: Induction

Back 8

The production of an enzyme in response to presence of substrate.

- Typically affects catabolic

enzymes (e.g., lac operon).

- Ensures enzymes are

synthesized only when needed.

Front 9

Induction Visual

Back 9

Front 10

Oppressions: Repression Visual

Back 10

Front 11

Oppressions: Induction Visual

Back 11

Front 12

Negative Control: Inducer

Back 12

Substance that induces enzyme synthesis.

Front 13

Negative Control: Corepressor

Back 13

A substance that represses enzyme synthesis.

Front 14

Negative Control: Effectors

Back 14

Collective term for inducers and corepressors. (Basically anything that "effects" an enzyme)

- typically small molecules.

- can be structural analogs of

substrates/products, (e.g.,

allolactose).

Front 15

Effectors and Transcription

Back 15

Effectors indirectly affect transcription by binding to specific DNA-binding proteins.

- Corepressors bind to an allosteric

repressor protein.

- Allosteric repressor is activated

and binds to region of DNA near

promoter called the operator.

Front 16

Corepressor and Repressor Visual

Back 16

Front 17

Def: Operon

Back 17

Cluster of consecutive genes whose expression is under control of a single operator.

- All genes transcribed as single

mRNA.

- Transcription physically blocked

when repressor binds to

operator.

Front 18

Enzyme Induction

Back 18

Enzyme induction can also be controlled by a repressor.

- Addition of inducer inactivates

repressor, and transcription can

proceed.

Repressor's role is inhibitory (preventing mRNA synthesis), so it is called negative control.

Front 19

Repressor and Inducer Visual

Back 19

Front 20

Def: Positive Control

Back 20

Regulator protein that activates the binding of RNA polymerase to DNA.

DNA Activator proteins bind specifically to activator-binding site (certain DNA sequence that is not called an operator).

Front 21

Ex of Positive Control: Maltose & E. Coli

Back 21

Maltose catabolism in E. Coli

- Maltose activator protein cannot

bind to DNA unless it first binds

maltose (inducer).

- Subsequent binding.

Front 22

Maltose and Inducer Visual

Back 22

Front 23

Activation of Positive Control

Back 23

Promoters of positively controlled operons only weakly bind RNA polymerase.

Activator protein helps RNA polymerase recognize promoter.

- May bend DNA structure

- May interact directly with RNA

polymerase.

Many operons have multiple types of control.

Front 24

Activator Protein & Positive Control Visual

Back 24

Front 25

Regulons

Back 25

Genes for maltose are spread out over the chromosome in several operons.

- Each operon has an

activator-binding site.

- Multiple operons controlled by the

same regulatory protein are called

a regulon.

Regulons also exist for negatively controlled systems (e.g., arginine regulon).

Front 26

Operon Visual

Back 26

Front 27

Key Components of Operons:

Promoter

Back 27

Site on the DNA bound by the RNA polymerase; directs the initiation of transcription.

Front 28

Key Components of Operons:

Activator

Back 28

Protein that binds to a site on the DNA; assists binding of the RNA polymerase to the promoter, resulting in increased transcription initiation.

Front 29

Key Components of Operons:

Activator Binding Site

Back 29

Site on the DNA bound by the activator.

Front 30

Key Components of Operons:

Repressor

Back 30

Protein that binds to the operator site on the DNA, inhibiting transcription.

Front 31

Key Components of Operons:

Operator

Back 31

Site on the DNA bound by the repressor.

Front 32

Key Components of Operons:

Effector

Back 32

Small molecule thst binds to activator or repressor proteins, modifying their gene regulation activity.

Front 33

Key Components of Operons:

Inducer

Back 33

Effector that increases transcription by either enabling an activator or disabling a repressor.

Front 34

Key Components of Operons:

Corepressor

Back 34

Effector that decreases transcription by enabling a repressor.

Front 35

Def: Global Control Systems

Back 35

Regulate expression of many different genes simultaneously (e.g., lactose operon and maltose regulon).

Front 36

Ex of Global Control System

Back 36

Catabolite repression is an example of global control.

- Controls use of carbon sources if

more than one present.

- Synthesis of unrelated catabolic

enzymes (e.g., lactose operon and

maltose regulon) is repressed if

glucose is present in growth

medium.

- Also called “glucose effect”.

- Ensures that the "best" carbon

and energy source is used first.

Front 37

Diauxic Growth

Back 37

Two exponential growth phases if two energy sources available.

- Better energy source consumed

first, growth stops.

- After lag, growth resumes with

second energy source.

(When controlling the aux cord, sometimes you have a lull inbetween playing two dope songs. The first one was clearly the best though).

Front 38

Diauxic Growth Visual

Back 38

Front 39

CRP

Back 39

CRP = Cyclic AMP Receptor Protein.

In catabolite repression, transcription is controlled by the (CRP), an activator protein, a form of positive control.

CRP binds to DNA only if it has bound cyclic adenosine monophosphate (cyclic AMP or cAMP), a regulatory nucleotide derived from a nucleic acid precursor (ATP)

Front 40

Cyclic AMP

Back 40

Cyclic Adenosine Monophosphate - Cyclic AMP or cAMP.

Regulatory nucleotide derived from a nucleic acid precursor (ATP).

Permits the binding of CRP to DNA. It must be bound first.

Front 41

Cyclic AMP Structure Visual

Back 41

Front 42

For lac genes to be transcribed...

Back 42

Cyclic AMP level must be high enough for CRP protein to bind to CRP-binding site.

Lactose or another inducer must be present to prevent lactose repressor (LacI) binding.

Front 43

Cyclic AMP Pathway Visual

Back 43

Front 44

Prokaryotes and their Environments

Back 44

Prokaryotes regulate cellular metabolism in response to environmental fluctuations.

- External signal may be transmitted

directly to the target.

- External signal may be detected by

sensor and transmitted to

regulatory machinery (signal

transduction).

• Most signal transduction

systems are two-component

regulatory systems.

Front 45

Two-Component Regulatory Systems

Back 45

Made up of two different proteins

- Sensor kinase (in cytoplasmic

membrane): detects environmental

signal and autophosphorylates. - Response regulator (in cytoplasm):

DNA-binding protein that regulates

transcription.

Front 46

Feedback Loop

Back 46

Terminates signal.

Uses phosphatase that removes phosphate from response regulator.

Front 47

Feedback Visual

Back 47

Front 48

Chemotaxis

Back 48

The ability of an organism to sense chemical gradients and modify its motility in response.

- It is a behavior in which motile

bacteria swim toward favorable

environments (chemoattractants)

or away from unfavorable

environments (chemorepellents).

Front 49

Modified Two-Component System

Back 49

Used in chemotaxis to...

- Sense temporal changes in

attractants or repellents.

- Regulate flagellar rotation.

- Thus regulate activity of

preexisting proteins instead of

modifying transcription

of genes.

Front 50

Def: Sensory Proteins

Back 50

Located in the cytoplasmic membrane, they sense attractants and repellents, and interact with cytoplasmic sensor kinases.

Front 51

Def: MCPs

Back 51

Methyl-accepting chemotaxis proteins (MCPs)

- Bind attractant or repellent and

initiate flagellar rotation.

- Interact with CheA (sensor

kinase) and CheW.

Front 52

Def: CheA

Back 52

The cytoplasmic domains of each MCP binds to the protein CheA and controls its activity.

CheA works as the sensor kinase, becoming phosphorylated.

CheA then phosphorylates CheY (the Response Regulator or RR protein).

- Phosphorylated RR proteins

do not bind DNA; they bind to

the flagellar motor, changing

its activity.

Front 53

The direction of Flagellar Motor Rotation...

Back 53

...determines the type of movement:

Controlled by CheY protein.

- CheY = counterclockwise and

smooth swimming).

- CheY-P (phosphorylated) =

clockwise and random. Forms

when no atractants are present

in environment.

- Random movement = drop in

CheY-P, CheY returns along with

CCW and smooth movement.

- CheZ dephosphorylates CheY-P.

Front 54

Chemotaxis w/ Attractant Visual

Back 54

Front 55

Chemotaxis w/out Attractants Visual

Back 55

Front 56

Fx. of Chemotaxis Proteins Visual

Back 56

Front 57

CheR

Back 57

Methylates MCPs.

Front 58

CheA

Back 58

Sensor Kinase.

Front 59

CheY

Back 59

Response regulator: controls direction of flagellar rotation.

Front 60

CheB

Back 60

Response regulators, demethylates MCP.

Front 61

CheZ

Back 61

Dephosphorylates CheY-P

Front 62

CheW

Back 62

Involved in transduction of signal from MCP to CheA.

Front 63

Chemotaxis Adaptation

Back 63

Stop responding and reset.

Front 64

Chemotaxis Feedback Loop

Back 64

Allows the system to reset itself to continue to sense the presence of a signal.

- Relies on response regulator CheB.

- Involves modification of MCPs:

methylation stops response to

attractants and increases

response to repellants.

- Reversible methylation or

demethylation of MCPs

desensitizes or sensitizes MCPs,

respectively.

Front 65

Chemotaxis Visual

Back 65

Front 66

Do Prokaryotes communicate with one another?

Back 66

Prokaryotes can respond to the presence of other cells of the same species.

Front 67

Quorum Sensing

Back 67

Mechanism by which Bacteria and some Archaea assess their population density.

Ensures that a sufficient number of cells are present before initiating a response that, to be effective, requires a certain cell density (e.g., toxin production by pathogenic bacterium).

Front 68

Autoinducer

Back 68

A specific signaling molecule that each species of bacterium produces.

Diffuses freely across the cell envelope.

Reaches high concentrations inside cell only if many cells are nearby and making the same autoinducer.

Binds to specific activator protein or sensor kinase, triggering transcription of specific genes.

Front 69

Quorum Sensing Visual

Back 69

Front 70

Virulence Factors

Back 70

Ex: Escherichia coli O157:H7

- Shiga toxin–producing strain.

- Produces AHL AI-3 that induces

virulence genes.

- Epinephrine plus norepinephrine

plus AI-3 bind to sensor molecules

in plasma membrane.

• Activates motility, toxin

secretion, and production of

lesion-forming proteins.

Front 71

Virulence Factors Visual

Back 71

Front 72

Stringent Response

Back 72

Used to survive nutrient deprivation, environmental stress, and antibiotics.

Shuts down macromolecule synthesis and activates stress survival pathways.

Front 73

Stringent Response - E. Coli

Back 73

AA excess -> limitation = rRNA + tRNA + ribosome synthesis stops.

Protein + DNA synthesis stop, new AAs biosynthesized.

Later, rRNA + ribosome prod. begins but at much lower rate.

Triggered by (p)ppGpp: the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp).

RelA and SpoT proteins also important.

Front 74

Stringent Response Visual

Back 74

Front 75

Stringent Response and Microbial Ecology (Part 1)

Back 75

Environment/habitat determines response.

Ex: voiding E. coli in feces reduces nutrients, initiates ppGpp synthesis, stringent response occurs.

Ex: Caulobacter stringent response triggered by carbon/ammonia starvation instead of amino acid limitation.

- ppGpp increases swarmer (motile)

cell formation, may reach a niche

with more nutrients.

Front 76

Stringent Response and Microbial Ecology (Part 2)

Back 76

Ex: Mycobacterium tuberculosis lungs hypoxic and phosphate-limited, triggering stringent response.

Converts a subpopulation of dormant persister cells resistant to antibiotics that can revert back to infective cells.

Front 77

Limited vs. Stringent Response Visual

Back 77

Front 78

Back 78